Multi‐scale effects of impoundments on genetic structure of creek chub (Semotilus atromaculatus) in the Kansas River basin

1. Habitat fragmentation has been implicated as a primary cause for the ongoing erosion of global biodiversity, yet our understanding of the consequences in lotic systems is limited for many species and regions. Because of harsh environmental conditions that select for high colonisation rates, prairie stream fishes may be particularly vulnerable to the effects of fragmentation. Hence, there is urgent need for broader understanding of fragmentation in prairie streams such that meaningful conservation strategies can be developed. Further, examination at large spatial scales, including multiple impoundments and un‐impounded catchments, will help identify the spatial extent of species movement through the landscape. 2. Our study used data from 10 microsatellite loci to describe the genetic structure of creek chub (Semotilus atromaculatus) populations across four catchments (three impounded and one un‐impounded) in the Kansas River basin. We investigated whether genetic diversity was eroded in response to habitat fragmentation imposed by reservoirs and whether intervening lentic habitat increased resistance to dispersal among sites within a catchment. 3. Our analyses revealed that genetic diversity estimates were consistent with large populations regardless of the location of the sampled tributaries, and there was little evidence of recent population reductions. Nevertheless, we found a high degree of spatial genetic structure, suggesting that catchments comprise a set of isolated genetic units and that sample sites within catchments are subdivided into groups largely defined by intervening habitat type. Our data therefore suggest that lentic habitat is a barrier to dispersal among tributaries, thus reducing the opportunity for genetic rescue of populations in tributaries draining into reservoirs. Isolation by a reservoir, however, may not be immediately deleterious if the isolated tributary basin supports a large population.     

Characterization of 16 highly variable tetranucleotide microsatellite loci for Oregon chub (Oregonichthys crameri) and cross amplification in Umpqua chub (O. kalawatseti)

We describe the isolation and development of 16 polymorphic tetranucleotide microsatellite loci for the endangered Oregon chub (Oregonichthys crameri). Two loci appear to be duplicated. For the remaining 14 loci, we observed between three and 19 alleles per locus in a sample of 42 fish. Thirteen of these loci were also polymorphic in the closely related Umpqua chub (O. kalawatseti). These loci will aid in our understanding of the molecular ecology and conservation of these two species.     

Spatial heterogeneity in the parasite communities of creek chub (Semotilus atromaculatus) in southeastern Nebraska

The intestinal helminth communities of creek chub (Semotilus atromaculatus) were studied in the streams of southeastern Nebraska to characterize spatial variation, to determine whether drainages act as regional species pools, and to examine the spatial patterning of individual parasite species within and among drainages. Creek chub were sampled in the summer of 2003 and the spring of 2004 at each of 12 sites distributed evenly among 3 drainages in the Big Nemaha River watershed. Four intestinal helminths were recovered: Allocreadium lobatum, Proteocephalus sp., Rhabdochona canadensis, and Paulisentis missouriensis. Host size had little or no effect on the composition of the parasite communities of creek chub, either among individual fish or among samples. In contrast, drainage and sample date explained 82% of the variation in mean infracommunity species richness among samples, and 62% of the variation in mean infracommunity abundance among samples. Drainage differences were determined by the distributions of P. missouriensis and R. canadensis; whereas, A. lobatum and Proteocephalus sp. were more uniformly distributed among drainages. Each drainage was characterized by a unique pattern of species diversity at infracommunity, component community, and drainage levels of organization.     

Effects of dynamic landscape elements on fish dispersal: the example of creek chub (Semotilus atromaculatus)

Barriers along a watercourse and interconnections between drainage systems are dynamic landscape elements that are expected to play major roles in the dispersal and genetic structure of fish species. The objective of this study was to assess the role of these elements using creek chub ( Semotilus atromaculatus ) in the Mastigouche Wildlife Reserve (Québec, Canada) as model. Numerous impassable waterfalls and interconnections among drainage systems were inferred with geographic information systems and confirmed de visu . The analysis of 32 populations using seven nuclear microsatellites revealed the presence of three genetically distinct groups. Some groups were found upstream of impassable barriers and in adjacent portions of distinct drainage systems. Admixture among groups was also detected in some populations. Constraining phylogenetic procedures as well as Mantel correlation tests confirmed that the genetic structure is more likely to result from interconnections between the drainage systems than from the permanent network. This study indicates that landscape elements such as interconnections are of major importance for circumventing impassable barriers and colonizing lakes that are otherwise inaccessible. Such an approach could be relevant for determining the origins of fish species (i.e. native vs. introduced) in the context of conservation.     

Characterization of 32 novel microsatellite loci for population and mating system studies using Campostoma anomalum (central stoneroller)

The central stoneroller (Campostoma anomalum) is an abundant, widespread and sexually dimorphic stream minnow that is a useful model for mating system studies as well as a sentinel species for understanding population-level processes for fishes in headwater communities. We developed one genomic library enriched for dinucleotide repeats and isolated 48 putative, novel microsatellite loci. Of those, we present 32 polymorphic and independent microsatellite markers with 3 to 16 alleles per locus and heterozygosity ranging from 0.23 to 0.95. Hence, these markers will be useful for future behavioural, ecological and evolutionary studies using C. anomalum.     

Characterization of 35 novel microsatellite loci for ecological and evolutionary studies of the bluntnose minnow (Pimephales notatus)

The bluntnose minnow (Pimephales notatus) is abundant and widespread with a broad ecological niche. This species is also sexually dimorphic with strong competition between males during the mating season. We developed two genomic libraries enriched for microsatellite repeats - one dinucleotide and one tetranucleotide - and isolated 48 putative, novel microsatellite loci. Of those, we present 35 polymorphic and statistically independent microsatellite markers with two to 18 alleles per locus and heterozygosities ranging from 0.04 to 1. These markers will be useful for future behavioural, ecological, evolutionary and mating system studies using P. notatus.     

Ontogenetic changes in diel activity,food habits and spatial distribution of juvenile and adult creek chub,Semotilus atromaculatus

Synopsis Juvenile creek chub, Semotilus atromaculatus, differed ecologically from adults. They were essentially diurnal, fed on small prey (adult diptera and aquatic adult coleoptera) and were found mainly in shallow littoral water (0.8 m depth) of a Québec oligotrophic lake. In contrast, adults were principally nocturnal, fed on larger prey (Gammaridae, diptera larvae, diptera pupae and ephemeroptera larvae) and were found in deeper water (1.2, 2.0 and 2.9 m depth). The overlap in diet between juvenile and adult fish was 10 percent. We found that predation by brook charr, Salvelinus fontinalis, upon creek chub was low, as only 5 chart stomachs of the 302 examined contained a total of 16 juvenile chub and none contained adult chub. Laboratory observations revealed that under low light intensity (0.17 lux) adult creek chub fed as efficiently as under high light intensity (22 lux). Several possible hypotheses to explain the evolution of the two different strategies exhibed by adult and juvenile creek chub are discussed.     

The photic environment and scotopic visual pigments of the creek chub,Semotilus atromaculatus and white sucker,Catostomus commersoni

Summary Scotopic visual pigments measured in the creek chub and the white sucker are porphyropsins with mean _max values located at 538.3 and 536.5 nm, respectively. There is a shift of the _max towards shorter wavelengths during the winter in both of these species coinciding with similar changes in the quality of downwelling light. _max is significantly correlated to the P₅₀ and spectrum width of the downwelling light and dissolved oxygen. An analysis of variance shows that there are significant differences between the _max values of: fish in the two lakes, fish at different times, the two species at different times and fish in different lakes at different seasons. The offset visual pigments of both species appear to be well adapted to their photic environment in terms of the contrast hypothesis. This improvement of contrast detection is discussed in relation to their feeding habits.Abbreviations _max wavelength at which absorbance is maximum - P₅₀ wavelength which halves the total number of photons between 400 and 700 nm, a measure of spectral quality - PAR photosynthetically active radiation - MSP microspectrophotometric - SE standard error     

Characterization of nine microsatellite loci in impala (Aepyceros melampus)

Nine microsatellite loci were isolated from a genomic DNA library created from impala (Aepyceros melampus). Observed and expected levels of heterozygosity were computed utilizing 25 individuals from a population in central Kenya. Tests for Hardy–Weinberg equilibria were conducted and found that three of the nine loci deviated from equilibrium in this population. These markers were developed to analyse the genetic effects of culling and isolation on a game preserve in Kenya.     

Characterization of microsatellite loci in the lesser dawn bat (Eonycteris spelaea)

We constructed a genomic DNA library enriched for CA repeat motifs in Eonycteris spelaea. Nine microsatellite loci were isolated and tested on a population of 39 samples from Yunnan Province, China. These nine loci had three to 22 alleles per locus. Observed and expected heterozygosity values ranged from 0.079 to 0.963 and from 0.078 to 0.959. Two loci revealed significant departure from Hardy-Weinberg equilibrium and no linkage disequilibrium was found between loci pairs. These microsatellites can be a powerful molecular tool for population-level studies of E. spelaea.     

Characterization of microsatellite loci isolated in Mountain Plover (Charadrius montanus)

Primers for 15 microsatellite loci were developed for Mountain Plover, a species whose distribution and abundance have been reduced drastically in the past 30 years. In a screen of 126 individuals collected from four breeding locales across the species’ range, levels of polymorphism ranged from two to 13 alleles per locus. No two loci were found to be linked, although one locus revealed significant departures from Hardy–Weinberg equilibrium. These microsatellite loci can be used in population genetic studies, ultimately aiding in management efforts for Mountain Plover. Additionally, these markers can potentially be used in studies investigating the mating system of Mountain Plover.     

Characterization of 11 new microsatellite loci in taro (Colocasia esculenta)

Eleven new microsatellite markers were isolated from taro, Colocasia esculenta (L.) Schott, a root crop widely distributed all over the world. Forty-eight primer pairs were designed from a microsatellite-enriched genomic library, of which 11 primer pairs have polymorphisms in 30 individuals tested from a population in China, which revealed two to six alleles per locus with the observed and expected heterozygosity levels ranging from 0 to 0.733 and from 0.381 to 0.731, respectively. These new genetic markers will be useful for the study of taro germplasm management and population evolution in the future.     

Characterization of porcine polymorphic microsatellite loci

Twenty-seven (CA)_n and two (GA)_n microsatellite clones were isolated out of a size-selected genomic pig library. These were sequenced and the number of uninterrupted dinucleotides was found to range from 12 to 26. Flanking primers were chosen for 11 dinucleotide repeats and optimal conditions for polymerase chain reaction (PCR) amplifications were established. Different microsatellite loci were amplified simultaneously by combining primer sets. Related and unrelated pigs were screened for length polymorphisms of the different microsatellite loci. The polymorphic information content (PIC) of these loci ranged between 0.62 and 0.83. Segregation studies in pig reference families established Mendelian inheritance. Locus S0022 was found to be X-linked.     

Characterization of eight microsatellite loci in Grant's gazelle (Gazella granti)

Eight microsatellite loci were isolated from a genomic DNA library created from Grant's gazelle (Gazella granti). Observed and expected levels of heterozygosity were computed utilizing 20 individuals from a population in Central Kenya. Tests for Hardy–Weinberg equilibria were conducted and found that two of the eight loci deviated from equilibrium in this population. These markers were developed to analyse the genetic effects of culling and isolation on a game preserve in Kenya.     

Characterization of polymorphic tetranucleotide microsatellite loci from the Siberian weasel (Mustela sibirica)

Nine tetrarepeat microsatellite loci for Siberian weasel (Mustela sibirica) were characterized. By using 35 individuals of unknown relationship collected from Taiwan, we evaluated the polymorphism of these loci. The number of alleles for each locus ranged from five to 12 (mean = 8.78 alleles) and the observed heterozygosity from 0.429 to 0.962 (mean = 0.688) and all loci conformed to Hardy–Weinberg expectation.     

Population biology of Allocreadium lobatum Wallin, 1909 (Digenea: Allocreadiidae) in the creek chub, Semotilus atromaculatus, mitchill (Osteichthyes: Cyprinadae), in a Nebraska Creek, USA

Allocreadium lobatum Wallin, 1909 has been reported in cyprinid species of freshwater fish in Canada and in the United States. The population biology of A. lobatum in the host Semotilus atromaculatus Mitchill was studied from May through December 1991, in a USA creek. Overall prevalence (64%) and mean intensity (4.4 +/- 0.4) were greater than previously reported while abundance, reported for the first time, was 2.8 +/- 0.3. Several trends in A. lobatum population biology as a function of S. atromaculatus length were identified. Mean intensity and abundance of A. lobatum increased with host size and significant differences in prevalence and A. lobatum lengths were found to correlate with host lengths.     

Characterization of 26 new microsatellite loci in the dugong (Dugong dugon)

Twenty‐six microsatellite loci have been isolated from a dugong (Dugong dugon). The average heterozygosity was 0.52 with two to 10 alleles per locus surveyed from 50 individuals. The markers are suitable for genetic mark–recapture (P_ID = 5 × 10^?16) in dugongs and they could also be used to quantify physical tag loss, estimate relatedness, assign paternity, elucidate population structure and identify migrants. The loci also amplified in Florida manatees (22/26) and Asian elephants (6/26).     

Characterization of microsatellite loci isolated from the wasp, Microstigmus nigrophthalmus (Hymenoptera)

Fifty‐two microsatellite loci were characterized in 22–31 unrelated females of the wasp (Microstigmus nigrophthalmus) collected from the Mata do Paraiso, Viçosa, M.G., Brazil. Fifty‐one of these loci were developed from a microsatellite‐enriched genomic library derived from M. nigrophthalmus and one was derived from the wasp, Ormyrus nitidulus. The genus Microstigmus represents an independent origin of social behaviour in the Hymenoptera and is thus of great potential in the study of social evolution.     

Characterization of 12 polymorphic microsatellite loci for eastern chipmunks (Tamias striatus)

Eastern chipmunks are small forest rodents for which ecological data at multiple spatial scales exist, but no molecular markers have been developed that provide adequate resolution to examine genetic structure at fine scales in this species. Thus, we developed 12 variable microsatellite loci, which amplified in three multiplexed reactions, and screened them in 27 individuals from northern Indiana, USA. Observed heterozygosities across loci ranged from 0.26 to 0.91 and number of alleles per locus ranged from three to 10. We will use these markers along with ecological data to understand population dynamics of eastern chipmunks at small spatial scales.     

Characterization of polymorphic microsatellite loci in Yucca filamentosa

Yuccas and their pollinator moths are a textbook example of mutualism, yet we lack sufficiently variable markers to properly study the population genetics of the plants. We characterized 13 polymorphic microsatellite loci for Yucca filamentosa by screening primers derived from an expressed sequence tag database. We found four to 13 alleles per locus and the observed heterozygosity ranged from 0.31 to 1. These markers will be useful in future ecological studies of Y. filamentosa.