Development of new microsatellite loci and multiplex reactions for muskellunge (Esox masquinongy)

The muskellunge (Esox masquinongy) is a valued fisheries species throughout its native range. Numerous studies have documented performance and phenotypic differences among muskellunge populations, but genetic markers for assessment have been lacking. We characterized 14 microsatellite loci and developed five multiplex polymerase chain reactions. Successful amplification of northern pike (Esox lucius) was observed for seven loci. These microsatellites will be useful for analysing population structure, performance characteristics of propagated strains, and helping to develop and monitor hatchery management guidelines for muskellunge.     

Genetic characterization of 18 novel microsatellite loci in northern pike (Esox lucius L.)

The northern pike (Esox lucius L.), an important predatory freshwater species, is undergoing significant population decline. In this study, 18 novel polymorphic microsatellite loci were isolated and used for assessing genetic variation in the Chinese Ulungur and Hungarian Balaton populations of the species. The number of alleles ranged from 2 to 13, observed heterozygosity from 0.154 to 0.920 and expected heterozygosity from 0.145 to 0.921, thereby indicating the specific usefulness of these suites of markers for investigating genetic variability.     

Influence of cisco (Coregonus artedi,Lesueur) on muskellunge (Esox masquinongy,Mitchill) mean length,population size structure,and maximum size in northern Wisconsin lakes

Population size structure and maximum size of managed sportfish populations are dictated by abiotic, biotic, ecosystem, and anthropogenic influences. In their native ranges of northern Wisconsin, muskellunge (Esox masquinongy) and cisco (Coregonus artedi) are co-adapted cool- and cold-water species where cisco presence may influence population size structure and maximum size of muskellunge. We tested whether muskellunge size structure indices (length-frequency distributions, proportional size distribution), mean length, and mean maximum length of muskellunge differed when cisco were present or absent in Ceded Territory of Wisconsin (CTWI) lakes during 2015–2018. Cisco presence had a positive influence on size structure and mean length of individual muskellunge within populations. In contrast, cisco presence had no influence on the mean maximum length of muskellunge observed in CTWI populations suggesting that other factors may be better predictors of this metric than cisco presence. In cisco lakes, mean muskellunge length was negatively correlated with mean cisco length suggesting that gape limitation may be a factor influencing population size structure and individual growth rates. Therefore, cisco populations with primarily large individuals may be unavailable to muskellunge as forage. Our results suggest that cisco are an important forage species for some aspects of muskellunge population ecology; however, other factors may also contribute to muskellunge population size structure and maximum size outcomes. As such, conservation of remaining cisco populations in Wisconsin is critical because they influence muskellunge population ecology in lakes where the species coexist. Future research is needed to better understand the interactions of cisco, abiotic and biotic factors, and anthropogenic influences on muskellunge growth dynamics.     

Characteristics of Ontario muskellunge (Esox masquinongy) fisheries based on volunteer angler diary information

This paper consolidates and summarizes information on Ontario muskellunge, Esox masquinongy, sport fisheries derived from angler diary programs sponsored by the Ontario Ministry of Natural Resources (OMNR) and Muskies Canada Incorporated (MCI) from 1979 to 2004. Interest in muskellunge as a sport fish has increased substantially over the past 10–15 years. Muskellunge catches were found to be highly correlated with angling effort. Catch rates, expressed in terms of catch-per-unit-of-effort (CUE), have improved over the past decade to the point where, in 2001, the provincial CUE was 0.119. The long term catch rate is 0.069. This improvement in angling quality is attributed to new minimum size limit regulations and increased catch-and-release angling practices. Over the period from 1979–2004, release rates by muskellunge anglers have averaged 94%. Based on a sample size of 9,499 fish, the mean size of angled muskellunge over the past 26 years was 37.0 inches (94 cm). Numerous fish exceeding 50 inches (127 cm) are angled from Ontario waters each year. The incidence of lymphosarcoma, a highly contagious, malignant blood cancer, has averaged only 2% since 1979. Based on an analysis of this information, Ontario’s muskellunge fisheries appear to be stable and sustainable. Volunteer angler diary programs provide an accurate and cost-effective means to monitor the status of muskellunge fisheries in Ontario.     

Isolation and characterization of microsatellite markers in the gecko Gekko swinhonis and cross‐species amplification in other gekkonid species

Gekko swinhonis is a gekkonid lizard endemic to China, inhabiting Loess Plateau, Huabei Plain, Huanghuai Plain and areas north of the Yangtze River. We characterized 21 dinucleotide microsatellite loci from an AC/AG‐enriched genomic library of G. swinhonis. The number of alleles per locus ranged from eight to 24 and the observed and expected heterozygosities ranged from 0.160 to 0.834 and from 0.584 to 0.917, respectively. We also tested the utility of these loci in other Gekko and Hemidactylus species; many of these loci can be cross‐amplified.     

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 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.     

Development and characterization of 10 novel microsatellite markers from Chital deer (Cervus axis) and their cross–amplification in other related species

Ten polymorphic microsatellite loci were isolated and characterized from Chital deer (Cervus axis). These loci show high levels of allelic diversity with four to eight alleles per locus in the 22 individuals of the free‐ranging population of Chital deer in Nehru Zoological Park, Hyderabad. In addition, we found that all the loci show cross–amplification in closely related as well as distantly related deer species. The amplification of these markers in different genera further indicates that these can be applied to a wide range of endangered deer species for their population genetics studies and conservation management.     

Development of novel polymerase chain reaction (PCR) based microsatellite markers in Armillaria gallica by cross‐species amplification and species‐specific cloning

Cross‐species PCR amplification of Armillaria mellea group taxa with previously reported A. ostoyae microsatellite markers, indicative of flanking sequence conservation, was exploited for the species‐specific isolation of simple sequence repeat (SSR) motifs from A. gallica. Six SSR motifs were sequence characterized from cloned PCR fragments generated with primers previously developed from A. ostoyae. Five novel primer pairs, designed from motif flanking regions, allowed for improved, efficient amplification in this species. One original A. ostoyae primer pair was used directly. Polymorphims were observed at wide geographical levels only. Relative cross‐species amplification intensities generally supported the currently accepted molecular phylogeny of this group.     

Characterization of microsatellite markers in the endangered Sinojackia xylocarpa (Styracaceae) and cross‐species amplification in closely related taxa

Twenty‐four polymorphic microsatellite loci were isolated and characterized from an AAG‐enriched genomic library of Sinojackia xylocarpa. The average allele number of these microsatellites was 3.3 per locus, ranging from two to seven. The observed and expected heterozygosities at population level were 0.10–0.83 and 0.10–1.00, respectively. In addition, successful cross‐species amplification of this set of microsatellites in three other species of Sinojackia and a closely related taxon, Changiostyrax dolichocarpa, suggested that this set of microsatellite markers should provide a useful tool for genetic and conservation studies of Sinojackia species and other closely related taxa in the Styracaceae.     

Isolation and characterization of microsatellite loci in Lesquerella fendleri (Brassicaceae) and cross‐species amplification

Fifteen novel microsatellite primer pairs are presented for Lesquerella fendleri, which were developed from seven dinucleotide, five trinucleotide and three tetranucleotide microsatellite DNA loci. These loci were characterized for 40 individuals from 24 localities throughout the species range. The number of alleles observed per locus ranged from three to 16, the observed heterozygosity ranged from 0.175 to 0.750, and the polymorphic information content ranged from 0.218 to 0.889. Cross‐species transferability tested on nine species of Lesquerella and one species of the related genus Physaria indicates that these primer pairs may be useful for population genetic studies of other species in Lesquerella and possibly other closely related genera.     

Characterization of microsatellite loci in White‐chinned Petrel (Procellaria aequinoctialis) and cross‐amplification in six other procellariiform species

Six polymorphic dinucleotide microsatellite loci were isolated and characterized from the White‐chinned Petrel Procellaria aequinoctialis, using a degenerate primer and PCR‐based technique to construct and screen an enriched genomic library. Preliminary data on three populations show heterozygosity levels ranging from 0.22 to 0.67 and allele numbers from three to nine. Preliminary data also suggest genetic distance between these three populations (F_ST 0.088). Cross‐species amplification of these six microsatellite loci and one further locus were tested in six other procellariiform species of the genus Procellaria, Macronectes, Thalassarche and Diomedea.     

Development of microsatellite markers for the European white elm (Ulmus laevis Pall.) and cross‐species amplification within the genus Ulmus

Ulmus laevis Pall. is a broad‐leaved deciduous tree with a central and eastern European distribution. We describe the development of six polymorphic microsatellite markers for this species. These markers were also tested for utility in U. americana, U. glabra, U. minor and U. pumila. One additional marker gave ambiguous results in U. laevis but amplified clearly in three other species. In U. laevis, the number of alleles observed per locus ranged from two to nine. Five loci showed polymorphism in at least one of the nontarget species tested.     

Isolation and characterization of microsatellite loci in Penstemon rostriflorus (Plantaginaceae) and cross‐species amplification

Eight novel microsatellite primer pairs are presented for Penstemon rostriflorus, representing the first microsatellite markers available for this genus. Loci were characterized for 20 individuals from two populations in the Great Basin, USA. All loci are polymorphic within P. rostriflorus (seven to 13 alleles per locus; observed heterozygosity between 0.40 and 0.95), and therefore useful for population genetic studies within the species. Cross‐species transferability was tested on 40 additional species of Penstemon, and results indicate that these primers pairs will likely be useful for population genetic studies on many Penstemon species.     

Five new microsatellite markers for Northern pike (Esox lucius)

Five new microsatellite markers were isolated from Northern pike (Esox lucius), a freshwater fish widely distributed in both Northern Europe and Northern America. Characterization in 30 individuals from a population from France revealed four to seven alleles and an expected heterozygosity of 0.243–0.642. No departure from Hardy–Weinberg equilibrium nor linkage disequilibrium were found. The level of polymorphism was higher than previously reported in the literature for pike populations from Northern America and Northern Europe, but with different microsatellite loci.     

Characterization of microsatellite loci in silver carp (Hypophthalmichthys molitrix), and cross‐amplification in other cyprinid species

Captive populations of silver carp (Hypophthalmichthys molitrix), a major aquaculture species in Asia, would undoubtedly benefit from genetic monitoring and improvement programs. We report the isolation and preliminary characterization of 16 microsatellite loci derived from both conventional and microsatellite‐enriched libraries. Inheritance studies confirmed the allelic nature of observed polymorphisms at all loci, while identifying null alleles at two loci. These loci, having varying degrees of polymorphism, should provide useful markers for applied genetic studies. A high degree of cross‐amplification among 10 other cyprinid species suggests that these loci may have more widespread utility.     

Identification of polymorphic microsatellite markers from RAPD product in turbot (Scophthalmus maximus) and a test of cross‐species amplification

Five polymorphic microsatellite loci have been isolated and characterized from random amplified polymorphic DNA product in turbot, Scophthalmus maximus. Twelve microsatellites were selected for designing microsatellite primers, of which five gave working primer pairs. They had between four and nine alleles. Observed and expected heterozygosities varied from 0.76 to 0.90 and from 0.63 to 0.83, respectively. Five additional fish species assessed for cross‐species amplification revealed between one and three positive amplifications and between zero and two polymorphic loci per species.     

Development and characterization of microsatellite markers for a monoecious Ficus species,Ficus insipida,and cross‐species amplification among different sections of Ficus

The animal‐mediated pollination and seed‐dispersal mutualisms of Ficus species give them key roles in tropical ecosystems, but may make them vulnerable to habitat fragmentation. The development of highly polymorphic markers is needed to analyse their genetic diversity and investigate the effects of fragmentation on gene flow. Of thirteen microsatellite loci isolated from Ficus insipida, a monoecious species in French Guiana, eleven were polymorphic (two to six alleles each). High levels of variation were found among loci; expected heterozygosities ranged from 0.151 to 0.715. All markers revealed a broad cross‐species affinity when tested in 23 other Ficus species.     

Identification of microsatellite loci from Epimedium koreanum and cross‐species amplification in four species of Epimedium (Berberidaceae)

Nineteen polymorphic microsatellite markers were isolated and characterized from a trinucleotide enriched partial genomic library of Epimedium koreanum. The average allele number of these microsatellites was 5.9 per locus, ranging from two to 11. The observed heterozygosity (H_O) and expected heterozygosity (H_E) at the population level were 0.00–0.90 and 0.12–0.90, respectively. In addition, the results of cross‐species amplification of this set of microsatellite markers in four closely related Epimedium species, E. brevicornum, E. sagittatum, E. pubescens and E. wushanense, revealed that these microsatellite markers were useful for population genetic structure evaluation and genotype analysis of major Epimedium species that have been used as traditional Chinese medicines.