Search

Patterns of genetic diversity and effective size should be predicted by life history traits (intrinsic), landscape properties (extrinsic), and population dynamics. Theoretical models portray complicated relationships among population subdivision, rates of extirpation and recolonization, and metapopulation genetic effective size (

Ecological speciation, which relies heavily on selection driving the emergence of new species, has become the primary paradigm through which rapid species radiations are understood. In this way, selection, particularly ecological selection, is assumed to be the driver of most species radiations. However, in many radiations, such as the radiation of Lake Malawi’s cichlids, the assumption of selection as the driver of speciation has rarely been explicitly tested, and drift, often, has completely been ignored as potential factor. In order to understand the forces driving the divergence of Lake Malawi cichlids at the microevolutionary level, we studied the genetic and phenotypic divergence of ten allopatric populations of Maylandia zebra. We estimated effective population sizes as proxy for drift. Further, we compared neutral genetic differentiation to divergence in three phenotypic traits: body size, body shape, and melanophore counts. We found small, yet significant, population differentiation in all the studied traits across most populations. Population sizes were small rendering the potential for drift to be high. However, phenotypic differentiation exceeded neutral expectations for all traits suggesting divergent local selection. Our data suggest that natural, and potentially also sexual, selection may be the dominant force driving population differentiation in Lake Malawi’s rock-dwelling cichlids, despite the potential for drift in small populations.

Movement is necessary for re-colonization of habitats following disturbance, but methods to estimate dispersal of small-bodied fishes are limited. We evaluated the efficacy of otolith microchemistry in identifying habitat origin of longfin dace Agosia chrysogaster in the Gila River, NM, USA. Additionally, we used this method to determine the source population of speckled dace Rhinichthys osculus that re-colonized a tributary reach following wildfire-induced extirpation. We determined otolith microchemical analysis was possible after finding elevated ambient water concentrations of Mg, Mn, and Sr in the disturbed tributary both before and after wildfire relative to other source streams. These water chemistry differences allowed us to test if speckled dace were derived from downstream populations, or from those potentially persisting within refugia in the fire-affected tributary. We found that otolith signatures consistently reflected water chemistry patterns for Mn and Sr, allowing us to classify individuals to known capture locations 86% (range = 74–100%) of the time. Otolith microchemistry techniques then revealed that 88% of speckled dace that re-colonized the fire-affected tributary reach were derived from refuge populations within the tributary. Our results indicated that otolith microchemistry could be an important tool for characterizing re-colonization dynamics of fish populations residing in chemically heterogeneous stream networks.

A peripheral population of mountain sucker, Pantosteus jordani, located in the Black Hills of South Dakota, USA, represents the eastern-most range of the species and is completely isolated from other populations. Over the last 50 years, mountain sucker populations have declined in the Black Hills, and now only occur in 40 % of the historic local range, with densities decreasing by more than 84 %.We used microsatellite DNA markers to estimate genetic diversity and to assess population structure across five streams where mountain suckers persist. We evaluated results in the context of recent ecological surveys to inform decisions about mountain sucker conservation. Significant allele frequency differences existed among sample streams (Global FST = 0.041) but there was no evidence of isolation by distance. Regionally, genetic effective size, Ne, was estimated to be at least 338 breeding individuals, but Ne within streams was expected to be less. Despite almost complete demographic isolation and reduced population size, there appears to be little evidence of inbreeding, but genetic drift and local isolation due to fragmentation probably best explains genetic structure in this peripheral mountain sucker population. Recommended strategies for population enhancement include restoration of stream connectivity and habitat improvement. Moreover, repatriation and assisted movement (i.e., gene flow) of fishes should maximize genetic diversity in stream fragments in the Black Hills region.

Author(s): Pilger, Tyler J.; Peterson, Matthew L.; Lee, Dana; Fuller, Andrea; Demko, Doug | Abstract: Conservation and management of culturally and economically important species rely on monitoring programs to provide accurate and robust estimates of population size. Rotary screw traps (RSTs) are often used to monitor populations of anadromous fish, including fall-run Chinook Salmon (Oncorhynchus tshawytscha) in California’s Central Valley. Abundance estimates from RST data depend on estimating a trap's efficiency via mark-recapture releases. Because efficiency estimates are highly variable and influenced by many factors, abundance estimates can be highly uncertain. An additional complication is the multiple accepted methods for how to apply a limited number of trap efficiency estimates, each from discrete time-periods, to a population’s downstream migration, which can span months. Yet, few studies have evaluated these different methods, particularly with long-term monitoring programs. We used 21 years of mark-recapture data and RST catch of juvenile fall-run Chinook Salmon on the Stanislaus River, California, to investigate factors associated with trap efficiency variability across years and mark-recapture releases. We compared annual abundance estimates across five methods that differed in treatment of trap efficiency (stratified versus modeled) and statistical approach (frequentist versus Bayesian) to assess the variability of estimates across methods, and to evaluate whether method affected trends in estimated abundance. Consistent with short-term studies, we observed negative associations between estimated trap efficiency and river discharge as well as fish size. Abundance estimates were robust across all methods, frequently having overlapping confidence intervals. Abundance trends, for the number of increases and decreases from year to year, did not differ across methods. Estimated juvenile abundances were significantly related to adult escapement counts, and the relationship did not depend on estimation method. Understanding the sources of uncertainty related to abundance estimates is necessary to ensure that high-quality estimates are used in life cycle and stock-recruitment modeling.

Climate change and fire suppression have altered fire regimes globally, leading to larger, more frequent, and more severe wildfires. Responses of coldwater stream biota to single wildfires are well studied, but measured responses to consecutive wildfires in warmwater systems that often include mixed assemblages of native and nonnative taxa are lacking. We quantified changes in physical habitat, resource availability, and biomass of cold- and warmwater oligochaetes, insects, crayfish, fishes, and tadpoles following consecutive megafires (covering >100 km2) in the upper Gila River, New Mexico, USA. We were particularly interested in comparing responses of native and nonnative fishes that might have evolved under different disturbance regimes. Changes in habitat and resource availability were related to cumulative fire effects, fire size, and postfire precipitation. The 2nd of 2 consecutive wildfires in the basin was larger and, coupled with moderate postfire discharge, resulted in increased siltatio...

Conservation genetic studies are challenged by the fact that populations of many imperiled species have experienced declines and fragmentation to the degree they no longer exhibit natural, self-sustaining metapopulation processes; characteristics of great importance to managers charged with their protection. Genetic patterns of species from minimally impacted systems can inform management practices for populations in more modified and fragmented systems. We assessed spatial and temporal patterns of intraspecific genetic diversity and differentiation using microsatellites for three imperiled fishes of the unfragmented upper Gila River, New Mexico, USA. Estimates of contemporary effective size were low for these species, but we observed little genetic evidence of inbreeding. Overall genetic structure was low (all species FST

Ash flows and flooding associated with wildfires represent important but understudied sources of disturbance for fish populations. Knowledge concerning these disturbances is especially limited for larger streams where warm water species dominate. Fire-related disturbances have been hypothesised to differentially affect native and non-native fishes, although this hypothesis has only been tested for salmonids. The objective of our research was to contrast effects of uncharacteristically large wildfires followed by flooding on metapopulations of native and non-native fishes in the Gila River of southwest New Mexico. Probabilities of occupancy, colonisation and local extinction of fishes were calculated across sites before and during disturbance and were also measured across a broader spatial scale during disturbance to identify potential refuge locations. Occupancy was higher for native fishes than non-natives, but multiple wildfire and flood events increased extinction probabilities of native species. Responses of non-native species to wildfires were mixed; extinction of non-native salmonids increased during disturbance, while extinction of several warm water species remained unchanged or decreased. Several undisturbed sites were poor refugia for natives as they were impacted by non-native piscivores, dewatering, and fragmentation. However, despite exposure to multiple disturbances, sites located in large tributary and valley reaches were consistently occupied by native species, suggesting these habitats provided refugia. We suggest that management actions (forest thinning; prescribed burning) that restore a more natural disturbance regime of small and less severe fires coupled with habitat remediation activities (non-native removal; decreased water withdrawal; improved connectivity) might diminish extinction risk for native fishes exposed to wildfire disturbance.

In the late 1940s, Rio Grande Sucker Pantosteus plebeius was reported in tributaries of the Gila River in the Colorado Basin and presumed to be introduced because of its absence in mid-19th century...

Dendritic ecological network (DEN) architecture can be a strong predictor of spatial genetic patterns in theoretical and simulation studies. Yet, interspecific differences in dispersal capabilities and distribution within the network may equally affect species’ genetic structuring. We characterized patterns of genetic variation from up to ten microsatellite loci for nine numerically dominant members of the upper Gila River fish community, New Mexico, USA. Using comparative landscape genetics, we evaluated the role of network architecture for structuring populations within species (pairwise FST) while explicitly accounting for intraspecific demographic influences on effective population size (Ne). Five species exhibited patterns of connectivity and/or genetic diversity gradients that were predicted by network structure. These species were generally considered to be small-bodied or habitat specialists. Spatial variation of Ne was a strong predictor of pairwise FST for two species, suggesting patterns of connectivity may also be influenced by genetic drift independent of network properties. Finally, two study species exhibited genetic patterns that were unexplained by network properties and appeared to be related to nonequilibrium processes. Properties of DENs shape community-wide genetic structure but effects are modified by intrinsic traits and nonequilibrium processes. Further theoretical development of the DEN framework should account for such cases.

As with many endangered, long-lived iteroparous fishes, survival of razorback sucker depends on a management strategy that circumvents recruitment failure that results from predation by non-native fishes. In Lake Mohave, AZ-NV, management of razorback sucker centers on capture of larvae spawned in the lake, rearing them in off-channel habitats, and subsequent release ("repatriation") to the lake when adults are sufficiently large to resist predation. The effects of this strategy on genetic diversity, however, remained uncertain. After correction for differences in sample size among groups, metrics of mitochondrial DNA (mtDNA; number of haplotypes, N H , and haplotype diversity, H D ) and microsatellite (number of alleles, N A , and expected heterozygosity, H E ) diversity did not differ significantly between annual samples of repatriated adults and larval year-classes or among pooled samples of repatriated adults, larvae, and wild fish. These findings indicate that the current management program thus far maintained historical genetic variation of razorback sucker in the lake. Because effective population size, N e , is closely tied to the small census population size (N c = ~1500-3000) of razorback sucker in Lake Mohave, this population will remain at risk from genetic, as well as demographic risk of extinction unless N c is increased substantially.

North American freshwater mussels of the Order Unionoida are critically imperiled, primarily due to stream habitat modifications and fragmentation by reservoirs. Whereas many species respond negatively to impoundments, some species benefit by increases in lentic habitat. During winter drawdown of Tuttle Creek Reservoir, KS in 2006–2007, we collected freshwater mussel shells to characterize spatial variation in assemblage structure within the reservoir and compare reservoir assemblages to stream assemblages within the surrounding drainage basin. Of the 22 unionid species that occurred in the basin, six were found in Tuttle Creek Reservoir. Species richness in the reservoir did not differ from that found in both small and large streams. Species composition in streams varied along a gradient from small to large (1st-7th) order streams, and mussel assemblages in the reservoir were most similar to that of large order streams. This study identified the subset of stream-dwelling unionid species that are...

The upper Gila River basin is one of the few unimpounded drainage basins west of the Continental Divide, and as such is a stronghold for endemic fishes in the region. Nevertheless, multiple nonindigenous fishes potentially threaten the persistence of native fishes, and little is known of the trophic ecology of either native or nonnative fishes in this system. Gut contents and stable isotopes ( 13 C and 15 N) were used to identify trophic relationships, trophic niche overlap and evaluate potential interactions among native and nonnative fishes. Both native and nonnative fishes fed across multiple trophic levels. In general, adult native suckers had lower 15 N signatures and consumed more algae and detritus than smaller native fish, including juvenile suckers. Adult nonnative smallmouth bass (Micropterus dolomieu), yellow bullhead (Ameiurus natalis) and two species of trout preyed on small-bodied fishes and predaceous aquatic invertebrates leading to significantly higher trophic positions than small and large-bodied native fishes. Thus, the presence of these nonnative fishes extended community food-chain lengths by foraging at higher trophic levels. Although predation on juvenile native fishes might threaten persistence of native fishes, the high degree of omnivory suggests that impacts of nonnative predators may be lessened and dependent on environmental variability.

Intense predation on larval and juvenile fishes by introduced piscivores can be detrimental to recruitment of threatened and endangered native fishes. Introduced largemouth bass (Micropterus salmoides) in the San Juan River, New Mexico, Colorado, and Utah, rarely are collected as adults; however, juveniles (,200 mm total length) often occur in the same habitats as young-of-the-year native fishes. To evaluate the prevalence of native fishes in the diet of juvenile largemouth bass, stomach samples from juveniles were collected from the San Juan River in New Mexico during July and August 2005, when young-of-the-year native and nonnative fishes were present. Stomach contents of largemouth bass were identified as native catostomids, native cyprinids, or nonnative cyprinids based on pharyngeal teeth. Although nonnative fishes comprised .80% of the potential prey base, significantly more native fishes were identified in stomachs than nonnative fishes. The disproportional abundance of native fishes in the diet of juvenile largemouth bass suggests greater susceptibility of young-of-the-year natives to predation by largemouth bass in the San Juan River. RESUMEN—La depredacion intensa sobre peces en estadio larval y juvenil por pisco ´voros introducidos puede ser perjudicial para el reclutamiento de las especies nativas amenazadas o en peligro de extincion. El pez introducido lobina negra (Micropterus salmoides )e n el ro San Juan de los estados de Nuevo Mexico, Colorado y Utah es raramente recolectado como adulto; sin embargo, los juveniles (,200 mm TL) a menudo viven en los mismos habitats de otros peces nativos jovenes-del-ano. Para evaluar la prevalencia de los peces nativos en la dieta de los juveniles de la lobina negra se colectaron muestras del contenido estomacal de juveniles del ro ´o San Juan en Nuevo Mexico durante los meses de julio y agosto del 2005, cuando los jovenes-del-ano de peces nativos y no nativos estuvieron presentes. Basado en la dentadura faringueal, el contenido estomacal del pez lobina negra fue identificado como catostomido nativo, cipro ´nido nativo y cipro ´nido no nativo. Aunque los peces no nativos comprendieron .80% de las presas potenciales, significativamente mas peces nativos fueron identificados en los estomagos que peces no nativos. La abundancia desproporcionada de los peces nativos en la dieta de los juveniles de la lobina negra sugiere mas susceptibilidad de los peces nativos jovenes-del-ano a la depredacion de la lobina negra en el ro ´o San Juan.

We isolated and characterized 16 microsatellite DNA loci in Longfin Dace, Agosia chrysogaster, a minnow native to Sonoran Desert streams (southwestern US and northwestern Mexico). After optimization, all primer pairs produced consistently scorable products. Genetic diversity metrics were determined for each locus using 50 individuals from two populations in the Gila River basin, New Mexico. Allelic richness ranged from 2 to 37 and observed heterozygosity ranged from 0.08 to 0.95 across loci. These microsatellites offer a powerful tool to study effects of habitat fragmentation, dewatering, and climate change on population connectivity and genetic diversity in this species. Moreover, Longfin Dace co-occurs with more geographically restricted and endangered desert fish species. Genetic information for Longfin Dace could provide an important comparative dataset to assist conservation and management of other imperiled fishes in the region.

Human-induced eutrophication degrades freshwater systems worldwide by reducing water quality and altering ecosystem structure and function. We compared current total nitrogen (TN) and phosphorus (TP) concentrations for the U.S. Environmental Protection Agency nutrient ecoregions with estimated reference conditions. In all nutrient ecoregions, current median TN and TP values for rivers and lakes exceeded reference median values. In 12 of 14 ecoregions, over 90% of rivers currently exceed reference median values. We calculated potential annual value losses in recreational water usage, waterfront real estate, spending on recovery of threatened and endangered species, and drinking water. The combined costs were approximately $2.2 billion annually as a result of eutrophication in U.S. freshwaters. The greatest economic losses were attributed to lakefront property values ($0.3-2.8 billion per year, although this number was poorly constrained) and recreational use ($0.37-1.16 billion per year). Our evaluation likely underestimates economic losses incurred from freshwater eutrophication. We document potential costs to identify where restoring natural nutrient regimes can have the greatest economic benefits. Our research exposes gaps in current records (e.g., accounting for frequency of algal blooms and fish kills) and suggests further research is necessary to refine cost estimates.