Characterization of tetranucleotide microsatellites for Rio Grande cutthroat trout and rainbow trout,and their cross‐amplification in other cutthroat trout subspecies

We describe the isolation and characterization of 12 tetranucleotide microsatellites for Rio Grande cutthroat trout (Oncorhynchus clarkii virginalis) and rainbow trout (Oncorhynchus mykiss), and subsequently investigate their performance in Colorado River cutthroat trout (Oncorhynchus clarkii pleuriticus), greenback cutthroat trout (Oncorhynchus clarkii stomias) and Yellowstone cutthroat trout (Oncorhynchus clarki bouvieri). All 12 loci are polymorphic in all subspecies of O. clarkii examined.     

Summer and fall microhabitat utilization of juvenile bull trout and cutthroat trout in a wilderness stream, Idaho

Microhabitat use and availability were evaluated and compared between different size classes of juvenile resident bull trout (Salvelinus confluentus) and cutthroat trout (Oncorhynchus clarki) in a small wilderness stream within the South Fork Clearwater River basin, Idaho. The objective was to determine if utilization of measured habitat characteristics changed from summer to late fall. Sampling of fish was conducted with night snorkeling. During the summer, smaller juvenile bull trout (<66 mm) total length (TL) were associated with shallow stream margins over coarse substrates. In the fall, they moved to significantly deeper, lower velocity water, and closer to cover (p<0.05), but maintained their association with coarse substrates. During the summer, larger juvenile bull trout and larger juvenile cutthroat trout (66–130 mm TL) occupied significantly deeper water than smaller juvenile bull trout (p<0.05). Generally, larger juvenile bull trout were found closer to the bottom and in lower velocity water than larger juvenile cutthroat trout (p<0.05). In the fall, larger juvenile bull trout and larger juvenile cutthroat trout were associated with significantly deeper, lower velocity water located closer to cover than in summer (p<0.05). However, cutthroat trout occupied slightly deeper water over finer substrates than bull trout. Deep water with low velocities evidently provide important rearing areas for large bull trout and large cutthroat trout in the fall. Land management practices that maintain such environments will benefit these species.     

Isolation and characterization of twelve novel microsatellites in yellow catfish, Pelteobagrus fulvidraco

The yellow catfish Pelteobagrus fulvidraco is a freshwater fish species. Due to overfishing and pollution of freshwater ecosystems, the wild stocks of this fish reduced substantially. We isolated and characterized 12 polymorphic microsatellites of this species. The number of alleles at the 12 microsatellite loci ranged from four to eight, with an average of 6.6/locus. The average observed heterozygosity was 0.72, whereas the expected heterozygosity ranged from 0.60 to 0.86 (average: 0.80). All 12 microsatellites conformed to Hardy–Weinberg Equilibrium and were in linkage equilibrium. These 12 novel microsatellites could facilitate studies of genetic diversity and population structure of the yellow catfish to supply necessary information of conservation of the yellow catfish.     

Allozymes,mtDNA and microsatellites study introgression in a stocked trout population in France

A comparative study of disturbed (downstream) and undisturbed (upstream) populations in a French Mediterranean river (the Sorgue) was conducted to assess the fate of introgressing hatchery-genes in the aboriginal gene pool. Variation was assessed at 27 protein-coding loci, three microsatellite loci and two mtDNA restriction sites. The results were compared to those from another Mediterranean drainage basin (that of the river Orb). The genetic pattern observed among markers and drainage basins was found to be noticeably different. A reduction in population size is hypothesized to explain the lower variability observed in the upper part of the river Sorgue. Estimations of hatchery gene flow were different between loci but in the same range of values between markers.     

Alien invasions in aquatic ecosystems: Toward an understanding of brook trout invasions and potential impacts on inland cutthroat trout in western North America

Experience from case studies of biologicalinvasions in aquatic ecosystems has motivated aset of proposed empirical rules forunderstanding patterns of invasion and impactson native species. Further evidence is neededto better understand these patterns, andperhaps contribute to a useful predictivetheory of invasions. We reviewed the case ofbrook trout (Salvelinus fontinalis)invasions in the western United States andtheir impacts on native cutthroat trout (Oncorhynchus clarki). Unlike many biologicalinvasions, a considerable body of empiricalresearch on brook trout and cutthroat trout isavailable. We reviewed life histories of eachspecies, brook trout invasions, their impactson cutthroat trout, and patterns and causes ofsegregation between brook trout and cutthroattrout. We considered four stages of theinvasion process: transport, establishment,spread, and impacts to native species. Most ofthe research we found focused on impacts. Interspecific interactions, especiallycompetition, were commonly investigated andcited as impacts of brook trout. In many casesit is not clear if brook trout invasions have ameasurable impact. Studies of speciesdistributions in the field and a variety ofexperiments suggest invasion success of brooktrout is associated with environmental factors,including temperature, landscape structure,habitat size, stream flow, and humaninfluences. Research on earlier stages ofbrook trout invasions (transport,establishment, and spread) is relativelylimited, but has provided promising insights. Management alternatives for controllingbrook trout invasions are limited, and actions tocontrol brook trout focus on direct removal,which is variably successful and can haveadverse effects on native species. Themanagement applicability of research has beenconfounded by the complexity of the problem andby a focus on understanding processes atsmaller scales, but not on predicting patternsat larger scales. In the short-term, animproved predictive understanding of brooktrout invasions could prove to be most useful,even if processes are incompletely understood. A stronger connection between research andmanagement is needed to identify more effectivealternatives for controlling brook troutinvasions and for identifying managementpriorities.     

The genetic structure of endangered indigenous populations of the amago salmon, <Emphasis Type="Italic">Oncorhynchus</Emphasis><Emphasis Type="Italic">masou</Emphasis><Emphasis Type="Italic">ishikawae</Emphasis>, in Japan

The amago salmon, Oncorhynchus masou ishikawae, is an endemic subspecies of O. masou in Japan. Owing to the extensive stocking of hatchery fish throughout Japan, indigenous populations of O. m. ishikawae are now on the verge of extinction. We examined the genetic effects of stocking hatchery fish on wild populations in the River Koza, Japan, using microsatellite and mitochondrial DNA (mtDNA) markers. For mtDNA, haplotype mt1, which is common in wild populations, was present exclusively in isolated wild populations assumed to be unaffected by previous stocking, while it was never observed in hatchery fish. Genetic diversity was much higher in wild populations in the stocked area, which shared many mtDNA haplotypes with hatchery fish, than in isolated wild populations with haplotype mt1. Pairwise F _ST estimates based on microsatellites showed significant differentiation among the isolated populations with many microsatellite loci monomorphic. Significant deviation from Hardy–Weinberg equilibrium was observed in wild populations in the area subject to stocking, where a Bayesian-based assignment test showed a high level of introgression with hatchery fish. These results suggest that wild populations with haplotype mt1, which became isolated through anthropogenic environmental change in the 1950–1960s, represent indigenous populations of O. m. ishikawae in the River Koza. They have low genetic diversity, most likely caused by genetic bottlenecks following damming and environmental deterioration, while stocking of hatchery fish over the past 30 years apparently had a large impact on the genetic structure of wild populations in the main channel of the River Koza.     

Development of microsatellite markers for Quercus miyagii Koidz. (Fagaceae), an endemic species in the Ryukyu Islands, Japan

Quercus miyagii is an endemic tree species in the Ryukyu Islands, Japan. We isolated and characterized 15 microsatellite loci in this species. The number of alleles ranged from 2 to 16 and expected heterozygosities from 0.07 to 0.92. This set of markers is potentially useful to investigate the genetic structure, gene flow, and the biogeographic history of Q. miyagii in the Ryukyu Islands, Japan.     

Development of microsatellite markers for <Emphasis Type=Italic>Echinops setifer</Emphasis> (Asteraceae), an endangered grassland plant species in Japan

Echinops setifer is an endangered grassland plant species in Japan. We isolated and characterized nine microsatellite loci in this species. The number of alleles ranged from 3 to 7 and expected heterozygosities from 0.108 to 0.761. These markers described here will be useful for investigating the genetic diversity, genetic structure and gene flow, and planning for conservation of E. setifer.     

A suite of twelve single nucleotide polymorphism markers for detecting introgression between cutthroat and rainbow trout

A suite of 12 subspecies and species-specific single nucleotide polymorphism (species-specific SNP) markers was developed to distinguish rainbow trout (RT) Oncorhynchus mykiss from the four major subspecies of cutthroat trout: westslope cutthroat trout (WCT) Oncorhynchus clarki lewisi, Yellowstone cutthroat trout (YCT) Oncorhynchus clarki bouvieri, coastal cutthroat trout (CCT) Oncorhynchus clarki clarki, Lahontan cutthroat trout (LCT) Oncorhynchus clarki henshawi, and their hybrids. Several of the markers were linked to help strengthen hybrid determinations, and sex-specific species-specific SNP assays were also developed.     

Hybridization and genetic variation in Danish populations of European crab apple (Malus sylvestris)

The aim of the present study was to investigate the genetic variation in Danish populations of the endangered European crab apple (Malus sylvestris). Special emphasis was given to hybridization between the wild species and its cultivated relative Malus ×domestica. A total of 178 wild individuals from four Danish populations were studied along with a reference sample of 29 old cultivars. The genetic variation within and among samples was studied at ten microsatellite marker loci. Additionally, a morphological analysis was carried out to identify hybrids and test for correspondence between phenotypic and genotypic indices of hybridization. From application of ordination and a model-based cluster analysis to the molecular data, two clusters were identified consisting of wild and cultivated individuals, respectively. This indicates that pronounced admixture between the two species is not present. At the population level, a high correspondence was found between geographic isolation from M. ×domestica and genotypic and morphological indices of hybridization. As expected, isolated populations appeared less affected by hybridization than poorly isolated populations. Isolated “pure” M. sylvestris populations could thus be identified. However, morphological and molecular evidences of hybridization were found to be divergent at the individual level. This is suggestive of some historical introgression into the M. sylvestris gene pool and indicates that relying exclusively on either morphological or molecular characters as diagnostic markers in studies of hybridization between M. ×domestica and M. sylvestris might lead to fallible results. Combined application of genetic and morphological markers is therefore recommended.     

Development of microsatellite markers for <Emphasis Type="Italic">Metrosideros boninensis</Emphasis> (Myrtaceae), an endangered endemic plant species from the Bonin Islands,Japan

Metrosideros boninensis is an endangered endemic plant species from the Bonin Islands. We isolated and characterized nine microsatellite loci in this species. The expected heterozygosities of these nine markers ranged from 0.127 to 0.768. These markers described here will be useful for investigating the genetic diversity, genetic structure and gene flow, and planning for conservation of M. boninensis.     

Mitochondrial haplotype variability of brown trout populations from Northwestern Iberian Peninsula,a secondary contact area between lineages

Previous studies using mitochondrial markers and microsatellites revealed a new highly differentiated Atlantic lineage of brown trout in the Iberian Peninsula mainly confined to the Upper Duero Basin. Data suggest that Duero lineage (DU) hybridizes with previously described Atlantic (AT) lineages in that basin. However, nuclear and cytogenetic data suggest another hybrid zone between divergent lineages might be present in the Miño Basin, another Atlantic drainage located to the north. Here, we extend those studies by analyzing the mitochondrial haplotype variability of brown trout populations from northwestern Spain, a poorly studied area, to obtain an accurate picture of the distribution of DU. Results show that the DU haplotype is fixed in several isolated populations from the upper course of the Miño River and its main tributary the Sil River. DU haplotype co-occurs with two related AT haplotypes in the Miño Basin revealing a new secondary contact zone. The identification of both longtime stable populations of DU and several other populations showing introgression with widespread AT lineages will be useful for the management and conservation of such an endemic lineage.     

Isolation and characterization of microsatellite loci in endangered Cycas changjiangensis (Cycadaceae)

Eight microsatellite loci were isolated from repetitive DNA enriched libraries for Cycas changjiangensis, an endangered endemic species in Hainan Island, China. The number of allele ranged from three to seven. The observed (H _O) and expected (H _E) heterozygosities ranged from 0.0000 to 0.8750 and from 0.2359 to 0.7582, respectively. These microsatellite loci will enrich our scientific understanding for C. changjiangensis conservation.     

Characterization of 13 microsatellites for Lahontan cutthroat trout (Oncorhynchus clarki henshawi) and cross-amplification in six other salmonids

Thirteen newly developed tri- and tetranucleotide repeat microsatellite markers were developed for Lahontan cutthroat trout (Oncorhynchus clarki henshawi), a threatened subspecies endemic to the Lahontan hydrographic basin in the western USA. These loci are highly polymorphic with five to 30 alleles per locus and observed heterozygosities ranging from 0.4 to 0.7. Cross-species amplification of these markers was most successful in the closely related rainbow trout, Oncorhynchus mykiss, with only three loci amplifying in brown trout, Salmo trutta. Nonoverlapping allelic distributions for many of these loci among the six salmonid species screened suggest these markers may be useful for hybrid determination.     

Classifying seedlots of Picea sitchensis and P. glauca in zones of introgression using restriction analysis of chloroplast DNA

Summary Chloroplast DNA (cpDNA) restriction analysis was used to classify five reforestation seedlots as to species. The material included two Sitka spruce (Picea sitchensis (Bong.) Carr.), one white spruce (P. glauca (Moench) Voss) from interior British Columbia, and two putative hybrid seedlots from the coast-interior introgression zone in British Columbia. The cpDNA patterns generated by Bam-HI and Bc1-I from individual trees of Sitka spruce, white spruce, western white spruce (P. glauca var. albertiana (S. Brown)), and Engelmann spruce (P. engelmanni (Parry)) were species-specific. They were used as reference patterns for comparisons. In addition, two controlled crosses between white and Sitka spruce were analyzed to demonstrate the paternal inheritance of cpDNA in spruces. The cpDNA restriction patterns for the five seedlots were obtained from composite samples of seedlings from each lot and compared to the typical cpDNA patterns of each species. Restriction patterns for the two Sitka spruce seedlots agreed with those from the Sitka spruce tree, while patterns for the white spruce seedlots from British Columbia agreed with those from the white spruce tree, lacking evidence of any Engelmann spruce component in the sample. On the other hand, one putative hybrid seedlot showed cpDNA patterns similar to white spruce while the other showed fragments unique to both Sitka and white spruce, indicating that this was a hybrid seedlot. The analysis of cpDNA restriction polymorphism has proven to be an effective tool for classifying seedlots in regions of introgression. To our knowledge, these results provide the first demonstration of the use of cpDNA analysis for solving practical forestry problems.     

Genetic distinction of pallid, shovelnose, and Alabama sturgeon: emerging species and the US Endangered Species Act

The sturgeon genus Scaphirhynchus consists of threerecognized species. Pallid and shovelnose sturgeon (S. albusand S. platorynchus, respectively) are sympatric in theMissouri and lower Mississippi Rivers of the central United States. TheAlabama sturgeon (S. suttkusi) is endemic to the nearby MobileRiver drainage and is isolated geographically from the other twospecies. Pallid sturgeon and the extremely rare Alabama sturgeon arelisted as endangered under the US Endangered Species Act (ESA).In contrast, shovelnose sturgeon are relatively common and are notlisted. Despite these taxonomies and morphological evidence, somebiologists have questioned the genetic and taxonomic distinctions of thethree species, thus raising doubts concerning the validity of protectingpallid and Alabama sturgeon under the ESA. To investigate thesequestions, we compared a 436 base-pair sequence of the mitochondrial DNA(mtDNA) control region among the three species. We observed 16 mtDNAhaplotypes defined by 27 single base-pair substitutions (transitions)and one single base-pair insertion/deletion (indel) among 78individuals examined. The maximum sequence divergence among thosehaplotypes (2.06%) was less than values usually observed betweenfish species. However, Alabama sturgeon (n = 3) weredistinguished from the other two taxa (n = 75) by aunique base-pair substitution and haplotype, and pallid and shovelnosesturgeon at their northern range of natural sympatry (upper MissouriRiver) did not share any haplotypes. On the other hand, only frequencydifferences among shared haplotypes distinguished (P < 0.01)pallid and shovelnose sturgeon at their southern range of naturalsympatry (Atchafalaya River), and genetic distances between northern andsouthern localities for each species were nearly as large as thedistances between species. These latter results are consistent withseveral hypotheses, including reports (based on morphology) of putativenatural hybrids in the Atchafalaya River but not in the upper MissouriRiver. Overall, these mtDNA results indicate significant reproductiveisolation between pallid and shovelnose sturgeon in areas of naturalsympatry, and recent evolutionary divergence of Alabama sturgeon. ThesemtDNA results provide the first molecular genetic evidence fordistinguishing the three Scaphirhynchus species and, coupledwith morphological and biogeographic data, indicate that pallid andAlabama sturgeon should be evaluated as distinct species under theESA.     

Isolation and characterization of ten polymorphic microsatellite in the endangered tree Erythrophleum fordii oliv

Erythrophleum fordii oliv is a famous hardwood tree distributed in South China and Vietnam. It is now endangered due to heavy exploitation and deforestation. Ten polymorphic microsatellite loci were isolated and characterized from it. The number of alleles per locus varied from two to six. The expected and observed heterozygosities ranged from 0.3802 to 0.6903, and 0.2083 to 0.7719, respectively. These microsatellite markers will provide genetic information upon which strategies for effective conservation and management could be based.