Characterization of microsatellite markers in a threatened species,the White Sands pupfish (Cyprinodon tularosa)

We report the characterization of nine new microsatellite markers for a threatened species, the White Sands pupfish (Cyprinodon tularosa), using an enriched library method. These markers show moderate levels of variation (two to five alleles per locus) in the two native populations of this species and reveal substantial divergence between these two populations as indicated by a high percentage of private alleles. These markers will prove very useful in the conservation management of this rare species.     

PHOSPHOGLUCONATE DEHYDROGENASE POLYMORPHISM AND SALINITY IN THE WHITE SANDS PUPFISH

The phosphogluconate dehydrogenase (Pgdh) locus is the only polymorphic allozyme locus observed among 37 loci examined in all four populations of a New Mexico state Endangered species, the White Sands pupfish (Cyprinodon tularosa). We report evidence suggesting that this polymorphism may be associated with salinity. Salinity levels vary widely within and between habitats occupied by White Sands pupfish. The frequency of the Pgdh¹⁰⁰ allozyme was correlated with salinity but not with temperature. Frequency of Pgdh¹⁰⁰ differed between low (3.76 parts per thousand (ppt)) and high (9.23 ppt) salinity sites at Malpais Spring despite no obvious barriers to fish movement. Frequencies of Pgdh¹⁰⁰ in two introduced populations differed from that of the presumptive founding stock and correlated with salinity in the current habitats.     

Microsatellite DNA analysis of success in conserving genetic diversity after 33 years of refuge management for the desert pupfish complex

Refuge populations of Cyprinodon macularius and Cyprinodon eremus , the extant members of the endangered desert pupfish complex, have been maintained for up to 33 years in semi-natural refuges. We examined the success of the refuge program in maintaining diversity at four microsatellite DNA loci in 24 refuge populations of C. macularius and six of C. eremus that include, respectively, seven and four lineages representing original translocations from the wild. These lineages have been maintained with essentially no inoculations of genetic material from the wild and, except for one refuge, no intermixing of lineages. Comparison with wild-source populations showed marked declines in diversity within local refuges and within lineages, but relatively minor declines for the composite of all refuge populations for each species. In genetic makeup, the refuge populations generally clustered by lineage, indicating significant genetic drift early in lineage history. The results indicate that, with relatively minor adjustments in management, the refuge program can successfully preserve a large portion of the wild genetic diversity in the desert pupfish complex.     

Distribution,habitat and conservation status of desert pupfish (Cyprinodon macularius) in the Lower Colorado River Basin,Mexico

In order to better determine the currentstatus of desert pupfish populations (Cyprinodon macularius macularius) in the LowerColorado River Basin of Mexico, bimonthly fishsampling and habitat evaluations were carriedout from September 1996 to August 1997 in sixlocalities of Baja California and Sonora.Desert pupfish were collected using minnowseines and traps. Four sampling sites are inSonora, in shallow marginal habitats of theCiénega Santa Clara (Hunters' Camp, Outletof the Welton-Mohawk channel, El Doctor andFlor del Desierto) and two are in BajaCalifornia (Cerro Prieto and streams south ofCerro Prieto). The most abundant fish speciessampled was native desert pupfish (C.macularius, 59%) followed by sailfin molly(Poecilia latipinna, 19%), redbellytilapia (Tilapia cf. zilli, 10%) and western mosquito fish (Gambusiaaffinis, 7%). Significant temporalfluctuations in distribution and abundance ofdesert pupfish populations, as previouslyreported for these populations, was againdocumented. The main anthropogenic factorsaffecting distribution and abundance of desertpupfish populations in the Mexican portion ofthe Lower Colorado River Basin are progressivealteration of aquatic and riparian habitats, aswell as presence of exotic fishes that havecaused the displacement or elimination ofnative fish populations. Both habitat andpresence of the desert pupfish populations inthe study area are controlled by theperiodicity, quality and volume of dischargesinto the Mexican portion of the basin from theUnited States.     

Habitat Restoration as a Means of Controlling Non-Native Fish in a Mojave Desert Oasis

Non‐native fish generally cause native fish decline, and once non‐natives are established, control or elimination is usually problematic. Because non‐native fish colonization has been greatest in anthropogenically altered habitats, restoring habitat similar to predisturbance conditions may offer a viable means of non‐native fish control. In this investigation we identified habitats favoring native over non‐native fish in a Mojave Desert oasis (Ash Meadows) and used this information to restore one of its major warm water spring systems (Kings Pool Spring). Prior to restoration, native fishes predominated in warm water (25–32°C) stream and spring‐pool habitat, whereas non‐natives predominated in cool water (≤23°C) spring‐pool and marsh/slack water habitat. Native Amargosa pupfish (Cyprinodon nevadensis) and Ash Meadows speckled dace (Rhinichthys osculus nevadensis) inhabited significantly faster mean water column velocities (MWCV) and greater total depth (TD) than non‐native Sailfin molly (Poecilia latipinna) and Mosquitofish (Gambusia affinis) in warm water stream habitat, and Ash Meadows speckled dace inhabited significantly faster water than non‐natives in cool water stream habitat. Modification of the outflow of Kings Pool Spring from marsh to warm water stream, with MWCV, TD, and temperature favoring native fish, changed the fish composition from predominantly non‐native Sailfin molly and Mosquitofish to predominantly Ash Meadows pupfish. This result supports the hypothesis that restoring spring systems to a semblance of predisturbance conditions would promote recolonization of native fishes and deter non‐native fish invasion and proliferation.     

Fish habitat preferences in large streams of southern France

1. Relationships between fish and their habitat over whole geographic regions, which are evident from studies of many streams and species, can improve understanding of lotic communities and provide reliable management tools. Nevertheless, most habitat preference studies have been based on single sites, and confined to small streams and to game species.
2. Regional habitat preference models, based on local velocity, depth and roughness, were developed for twenty-four species and their size classes commonly found in large European streams. Fish surveys were conducted in six large streams in southern France over an 8-year period. To limit the influences of habitat variables other than those studied, we estimated fish preferences within each survey and averaged this information across surveys. Preferences were fitted with confidence intervals and their sensitivity to field uncertainty was evaluated.
3. Most species and size classes had significant preferences for local habitat conditions which were consistent across the region. Habitat preferences predominant in the region overall were not always observed at any one site, but habitat conditions preferred on average in the region were never actually avoided locally. These results support the use of regional preference models for fish and the development of similar models for other lotic groups whose sensitivity to local habitat conditions has been reported elsewhere.     

Population size,habitat fragmentation,and the nature of adaptive variation in a stream fish

Whether and how habitat fragmentation and population size jointly affect adaptive genetic variation and adaptive population differentiation are largely unexplored. Owing to pronounced genetic drift, small, fragmented populations are thought to exhibit reduced adaptive genetic variation relative to large populations. Yet fragmentation is known to increase variability within and among habitats as population size decreases. Such variability might instead favour the maintenance of adaptive polymorphisms and/or generate more variability in adaptive differentiation at smaller population size. We investigated these alternative hypotheses by analysing coding-gene, single-nucleotide polymorphisms associated with different biological functions in fragmented brook trout populations of variable sizes. Putative adaptive differentiation was greater between small and large populations or among small populations than among large populations. These trends were stronger for genetic population size measures than demographic ones and were present despite pronounced drift in small populations. Our results suggest that fragmentation affects natural selection and that the changes elicited in the adaptive genetic composition and differentiation of fragmented populations vary with population size. By generating more variable evolutionary responses, the alteration of selective pressures during habitat fragmentation may affect future population persistence independently of, and perhaps long before, the effects of demographic and genetic stochasticity are manifest.     

Effects of habitat size and isolation on species immigration–extinction dynamics and community nestedness in a desert river system

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Effects of longitudinal variations in stream habitat structure on fish abundance: an analysis based on subunit-scale habitat classification

SUMMARY 1. Stream reaches contain assortments of various habitat types that can be defined at different spatial scales, such as channel unit (e.g. pools, riffles) and subunit (patches within channel units). We described longitudinal (upstream–downstream) patterns of stream habitat structure by considering subunits as structural elements, and examined their effects on the abundance of masu salmon ( Oncorhynchus masou ) and rosyface dace ( Leuciscus ezoe ) in a third-order tributary of the Teshio River in northern Hokkaido, Japan.
2. Nine subunit types were determined on the basis of water depth, current velocity and substrate, using 0.5 × 0.5 m grids. Although both masu salmon and rosyface dace used pools as a major habitat, the former preferred a subunit type occurring at pool heads (PH subunit) while the latter preferred a slow-current edge type (SE-2 subunit).
3. Along the course of the stream, slow-edge subunits (SE-1, 2 and 3) increased in frequency downstream while fast-edge subunits (FE-1 and 2) decreased, suggesting a downstream development of slow-current edges. Regression analyses indicated that longitudinal variation in masu salmon abundance was explained by the area of PH, rather than pools. Masu salmon density increased with the area of PH. Rosyface dace abundance was explained by a combination of water depth and the area of SE-2, both effects being positive.
4. Longitudinal variations in the abundance of both species were related to the abundance of their preferred habitat at the subunit scale, rather than channel-unit scale. The results emphasise the importance of fine-scale patchiness when examining stream fish habitats.     

Fish habitat association in an Ozark stream

Synopsis Associations of fishes in physically distinct habitats (riffles, inlets and pools) of Flint Creek were studied to evaluate critically the habitat-guild concept — the notion that fishes associate with patches of stream habitat in discrete groups. There was little evidence of significant interspecific association at the habitat level. Most fishes were very generalized in their habitat-use patterns. Faunal similarity between habitats was unrelated to physical-habitat similarity. Assemblages from physically distinct habitats were little different from those from physically similar habitats. The structure of the associations (constancy within groups of commonly occurring species) varied seasonally and from site to site. There were constant associations in pools from summer through fall and this coincided with conditions of high fish density and low food availability, suggesting that the pattern resulted from past or present interaction between species. However, the timing also coincided with recruitment of young. Pools were the favored habitats of young-of-year fishes which dominated assemblages in these areas during summer and fall months. This apparently adaptive pattern of habitat association, operating in tandem with local reproductive success could have been responsible for the constancy observed in pools. Most of the species considered here made use of a variety of habitat conditions over the course of their life histories. Individual patches of habitat satisfied the needs of few fish, and thus, seemed too small a scale for the study of community-assembly mechanisms. There was better evidence of interspecies association at the scale of two or more of these habitat areas combined.     

Stream fish communities and their associations to habitat variables in a rain forest reserve in southeastern Brazil

This paper describes the spatial variability of fish communities and identifies patterns of association between fish communities and habitat variables, including anthropogenic factors. We sampled streams inside and in the surroundings of a rain forest reserve in the southeast of Brazil in the rainy season. We could distinguish three main groups of streams: upland streams (draining the upland, flat portions of the mountain ridge of Serra de Paranapiacaba), adventitious streams of clearwater mountain torrents (small streams draining confined valleys in the slopes of this sierra), and large streams of clearwater mountain torrents (relatively unconstrained large streams close to the foots of the mountains). Despite the high variability of fish communities associated with these streams we identified some patterns using exploratory statistical analyses. These patterns were corroborated by additional field observations and information from the scientific literature. The main differences in fish community composition and diversity among the three groups of streams are probably related to large-scale factors such as elevation and position of the stream in the watershed. However, differences within these three groups seem to be mostly due to site-specific factors. Differences of instream characteristics are likely to be caused by natural variability of the ecosystems but also, in some cases, by human disturbances like pollution from human settlements, agriculture and mining.     

Beaver dams maintain fish biodiversity by increasing habitat heterogeneity throughout a low‐gradient stream network

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Spatiotemporal patterns and habitat associations of smallmouth bass (Micropterus dolomieu) invading salmon‐rearing habitat

1. Smallmouth bass (Micropterus dolomieu) have been widely introduced to fresh waters throughout the world to promote recreational fishing opportunities. In the Pacific Northwest (U.S.A.), upstream range expansions of predatory bass, especially into subyearling salmon‐rearing grounds, are of increasing conservation concern, yet have received little scientific inquiry. Understanding the habitat characteristics that influence bass distribution and the timing and extent of bass and salmon overlap will facilitate the development of management strategies that mitigate potential ecological impacts of bass. 2. We employed a spatially continuous sampling design to determine the extent of bass and subyearling Chinook salmon (Oncorhynchus tshawytscha) sympatry in the North Fork John Day River (NFJDR), a free‐flowing river system in the Columbia River Basin that contains an upstream expanding population of non‐native bass. Extensive (i.e. 53 km) surveys were conducted over 2 years and during an early and late summer period of each year, because these seasons provide a strong contrast in the river’s water temperature and flow condition. Classification and regression trees were applied to determine the primary habitat correlates of bass abundance at reach and channel‐unit scales. 3. Our study revealed that bass seasonally occupy up to 22% of the length of the mainstem NFJDR where subyearling Chinook salmon occur, and the primary period of sympatry between these species was in the early summer and not during peak water temperatures in late summer. Where these species co‐occurred, bass occupied 60–76% of channel units used by subyearling Chinook salmon in the early summer and 28–46% of the channel units they occupied in the late summer. Because these rearing salmon were well below the gape limitation of bass, this overlap could result in either direct predation or sublethal effects of bass on subyearling Chinook salmon. The upstream extent of bass increased 10–23 km (2009 and 2010, respectively) as stream temperatures seasonally warmed, but subyearling Chinook salmon were also found farther upstream during this time. 4. Our multiscale analysis suggests that bass were selecting habitat based on antecedent thermal history at a broad scale, and if satisfactory temperature conditions were met, mesoscale habitat features (i.e. channel‐unit type and depth) played an additional role in determining bass abundance. The upstream extent of bass in the late summer corresponded to a high‐gradient geomorphic discontinuity in the NFJDR, which probably hindered further upstream movements of bass. The habitat determinants and upstream extent of bass were largely consistent across years, despite marked differences in the magnitude and timing of spring peak flows prior to bass spawning. 5. The overriding influence of water temperature on smallmouth bass distribution suggests that managers may be able limit future upstream range expansions of bass into salmon‐rearing habitat by concentrating on restoration activities that mitigate climate‐ or land‐use‐related stream warming. These management activities could be prioritised to capitalise on survival bottlenecks in the life history of bass and spatially focused on landscape knick points such as high‐gradient discontinuities to discourage further upstream movements of bass.     

挠力河流域河流生境质量评价

选择挠力河流域6个河段21个样点进行河流生境质量调查和评价。采用包括河水、河道和人类干扰等3大项目共11项评价指标,涵盖河流水量、水质和速度与深度组合,河道形状、结构、侵蚀程度和植被状况,河岸人类活动、周围土地利用以及水工设施等河流生境质量评价指标系统,进行河流生境质量评价。结果显示,全流域47.6%的样点河流生境质量处于优等或良好等级,33.3%的样点为一般等级,约19.1%的样点为较差等级,没有最差等级的样点。研究表明,挠力河流域河流生境质量整体状况良好,个别样点生境质量较差;河流生境质量受到周围土地利用的重要影响;河流生境质量与河流水质及河流生物完整性密切相关。有关河流生境评价的指标与标准以及参照系等研究有待深入。     

Ontogenetic shift in nocturnal microhabitat selection by giant kokopu in a New Zealand stream

Nocturnal microhabitat selection in relation to size was examined for a New Zealand drift-feeding freshwater fish, the giant kokopu Galaxias argenteus in three coastal Otago streams. Evidence for ontogenetic shifts in microhabitat selection were observed, particularly with respect to water velocity and depth. Small (<80 mm) giant kokopu tended to occur in shallow backwaters adjacent to fast flowing water. In contrast, larger individuals (≥80 mm) were most commonly observed in deeper, slower flowing pools. These patterns of habitat selection are most likely associated with the trade-offs involved with the selection of optimal habitats for drift feeding combined with avoidance of intra-specific competition and the threat of predation from larger conspecifies.     

The effects of riparian restoration following saltcedar (Tamarix spp.) biocontrol on habitat and herpetofauna along a desert stream

Amphibians and reptiles (herpetofauna) have been linked to specific microhabitat characteristics, microclimates, and water resources in riparian forests. Our objective was to relate variation in herpetofauna abundance to changes in habitat caused by a beetle used for Tamarix biocontrol (Diorhabda carinulata; Coleoptera: Chrysomelidae) and riparian restoration. During 2013 and 2014, we measured vegetation and monitored herpetofauna via trapping and visual encounter surveys (VES) at locations affected by biocontrol along the Virgin River in the Mojave Desert of the southwestern United States. Twenty‐one sites were divided into four riparian stand types based on density and percent cover of dominant trees (Tamarix, Prosopis, Populus, and Salix) and presence or absence of restoration. Restoration activities consisted of mechanically removing non‐native trees, transplanting native trees, and restoring hydrologic flows. Restored sites had three times more total lizard and eight times more yellow‐backed spiny lizard (Sceloporus uniformis) captures than other stand types. Woodhouse's toad (Anaxyrus woodhousii) captures were greatest in unrestored and restored Tam‐Pop/Sal sites. Results from VES indicated that herpetofauna abundance was greatest in the restored Tam‐Pop/Sal site compared with the adjacent unrestored Tam‐Pop/Sal site. Tam sites were characterized by having high Tamarix cover, percent canopy cover, and shade. Restored Tam‐Pop/Sal sites were most similar in habitat to Tam‐Pop/Sal sites. Two species of herpetofauna (spiny lizard and toad) were found to prefer habitat components characteristic of restored Tam‐Pop/Sal sites. Restored sites likely supported higher abundances of these species because restoration activities reduced canopy cover, increased native tree density, and restored surface water.     

Experimental and field evidence of behavioural habitat selection by juvenile Atlantic Acipenser oxyrinchus oxyrinchus and shortnose Acipenser brevirostrum sturgeons

The present work reports behavioural responses by young-of-the-year (21-30 cm) Atlantic sturgeon Acipenser oxyrinchus oxyrinchus and shortnose sturgeon Acipenser brevirostrum to nine binary combinations of dissolved oxygen saturation (40, 70 and 100%), temperature (12, 20 and 28°C) and salinity (1, 8 and 15). Both species showed no acclimation effects and similar discrimination and avoidance reactions to hypoxia (40% oxygen saturation), selecting higher dissolved oxygen choices in 71% of the tests. Acipenser oxyrinchus oxyrinchus and A. brevirostrum showed a similar preference for 20°C (>64% incidence), but differed in their responses to extreme temperature choices. Acipenser brevirostrum showed a significant avoidance behaviour to the 12°C but not to the 28°C choice. In contrast, A. o. oxyrinchus showed similar preference for 12 and 20°C, but avoided the 28°C choice in 71% of the tests where this temperature was included (P < 0·01). No significant preferences were observed among salinity choices, except between salinities 1 and 8, where A. o. oxyrinchus showed a significant preference for salinity 8. Behavioural responses matched expectations from bioenergetics in both species and were also consistent with the distribution of juvenile A. o. oxyrinchus capture locations in the Chesapeake Bay.     

Diel Migration and Spatial Distribution of Fish in a Small Stratified Lake

We used fishery surveys from 1954 to 1957 to determine the relationship between salinity and prairie stream-fish assemblage composition prior to the major drought of the 1950s and subsequent anthropogenic modifications. A total of 78,931 fishes were captured, representing 13 families and 44 species. Species were classified as having low, moderate, or high salinity tolerances based on k-means clustering of detrended correspondence scores. The proportion of species with high salinity tolerances was correlated positively (r = 0.74) with salinity, whereas the proportion of species with low (r = −0.69) or moderate (r = −0.36) tolerances was correlated strongly and negatively with salinity. Many of the low or moderate salinity tolerant species found in the 1950s were not collected in studies conducted 15 and 35 years later. Examination of these studies provides compelling evidence that salinity has been a dominant and persistent factor in affecting the structure of stream-fish assemblages for the past 50 years.     

Fish abundance and habitat relationships in forest and grassland streams, northern Hokkaido, Japan

The relationships between habitat variables and population densities of masu salmon (Oncorhynchus masou), rosyface dace (Leuciscus ezoe), Siberian stone loach (Noemacheilus barbatulus) and wrinklehead sculpin (Cottus nozawae) were examined by data collected at 55 reaches in forest and grassland streams in northern Hokkaido, Japan. Regression analysis suggested that salmon and dace densities were affected by water temperature (negative for salmon, positive for dace) and structural habitat factors (woody debris for salmon, pools for dace). Salmon density was higher in forest reaches than in grassland reaches, whereas dace density was higher in grassland reaches, suggesting that the removal of riparian forest had raised water temperature and allowed upstream invasions by dace. In contrast to salmon and dace, neither the density of loach nor sculpin differed between the forest and grassland reaches. For their densities, a negative effect of each on the other was most important, suggesting a strong effect of interspecific competition between loach and sculpin on their distributions. However, regression models also suggested that substrate heterogeneity mediated the outcome of their interspecific competition. On the basis of the results, a scenario is predicted for a fish-assemblage change with a typical land-development process in Hokkaido, and the importance of leaving or restoring riparian buffer for conservation and restoration of stream habitat is emphasized.