Megan J. Osborne

Fragmentation and dewatering transform Great Plains stream fish communities

Biodiversity in stream networks is threatened globally by interactions between habitat fragmentation and altered hydrologic regimes. In the Great Plains of North America, stream networks are fragmented by >19 000 anthropogenic barriers, and flow regimes are altered by surface water retention and groundwater extraction. We documented the distribution of anthropogenic barriers and dry stream segments in five basins covering the central Great Plains to assess effects of broad-scale environmental change on stream fish community structure and distribution of reproductive guilds. We used an information-theoretic approach to rank competing models in which fragmentation, discharge magnitude, and percentage of time streams had zero flow (a measure of desiccation) were included to predict effects of environmental alterations on the distribution of fishes belonging to different reproductive guilds. Fragmentation caused by anthropogenic barriers was most common in the eastern Great Plains, but stream desiccation beca...

Life history and environmental variation interact to determine effective population to census size ratio

Successful recovery and sustainability of threatened and exploited species depends in part on retention and maintenance of genetic diversity. Theory indicates that genetic diversity is lost at a rate inversely proportional to the genetically effective population size (Ne), which is roughly equal to one-half the adult census size (N) in many organisms. However, Ne has been reported to be up to five orders of magnitude lower than N in species with life histories that result in type III survivorship (high fecundity, but heavy mortality in early life stages, e.g. bony fishes), prompting speculation that low values of Ne may be a general feature of such organisms despite sometimes vast abundances. Here, we compared Ne and the ratio Ne/N across three ecologically similar fish species from the arid southwestern United States, all with type III life histories but with differing expectations of egg and larval survivorship that correlate with the degree of human-imposed habitat fragmentation. Our study indicates that type III life history may be necessary, but this alone is insufficient to account for extraordinarily low values of Ne/N. Rather, life history interacts with environmentally imposed mortality to determine the rate and magnitude of change in genetic diversity in these desert fish species.

Genetic effective size, Ne, tracks density in a small freshwater cyprinid, Pecos bluntnose shiner (Notropis simus pecosensis)

Genetic monitoring tracks changes in measures of diversity including allelic richness, heterozygosity and genetic effective size over time, and has emerged as an important tool for understanding evolutionary consequences of population management. One proposed application of genetic monitoring has been to estimate abundance and its trajectory through time. Here, genetic monitoring was conducted across five consecutive year for the Pecos bluntnose shiner, a federally threatened minnow. Temporal changes in allele frequencies at seven microsatellite DNA loci were used to estimate variance effective size (NeV) across adjacent years in the time series. Likewise, effective size was computed using the linkage disequilibrium method (NeD) for each sample. Estimates of Ne were then compared to estimates of adult fish density obtained from traditional demographic monitoring. For Pecos bluntnose shiner, density (catch‐per‐unit‐effort), NeV and NeD were positively associated across this time series. Results for Pecos bluntnose shiner were compared to a related and ecologically similar species, the Rio Grande silvery minnow. In this species, density and NeV were negatively associated, which suggested decoupling of abundance and effective size trajectories. Conversely, density and NeD were positively associated. For Rio Grande silvery minnow, discrepancies among estimates of Ne and their relationships with adult fish density could be related to effects of high variance in reproductive success in the wild and/or effects of supplementation of the wild population with captive‐bred and reared fish. The efficacy of Ne as a predictor of density and abundance may depend on intrinsic population dynamics of the species and how these dynamics are influenced by the landscape features, management protocols and other factors.

Genetic Effects of Hatchery Propagation and Rearing in the Endangered Rio Grande Silvery Minnow, Hybognathus amarus

The Rio Grande silvery minnow, Hybognathus amarus, is a federally endangered cyprinid now confined to the middle Rio Grande, New Mexico, in a fraction of its former range. The precipitous decline of the remaining wild population and lack of recruitment in the summer of 2000 prompted collection and placement of eggs and wild fish in propagation facilities. The aim of this study was to assess the genetic effects of hatchery propagation in the Rio Grande silvery minnow using 10 microsatellite loci and partial mitochondrial ND4 sequences. Three hatchery stocks (2001, 2002, and 2003) and the wild source population (collected in 2001–2002) were considered. Principal findings were; (i) captively spawned and reared Rio Grande silvery minnow had depleted levels of allelic diversity but similar levels of heterozygosity to the wild population, and (ii) fish raised from wild-caught eggs maintained similar levels of allelic diversity but had higher inbreeding coefficients than the wild source stock. With the repatriation of over 500,000 Rio Grande silvery minnow to the Rio Grande, the genetic effects of propagation are likely to impact the remaining wild population, especially as numbers in the wild continue to decline.

Genetic and ecological dynamics of species replacement in an arid-land river system.

Museum records indicate that Hybognathus placitus was introduced into the Pecos River, New Mexico during the early 1960s. Approximately 10 years later, a congener, Hybognathus amarus, was extirpated from the system. We used microsatellite and mtDNA data, ecological data and modelling, and a computer simulation approach to reconstruct the history of invasion and species replacement. To identify the potential role of hybridization and introgression, we genetically screened H. amarus (n = 389) from the Rio Grande, New Mexico, and H. placitus (n = 424) from the Pecos River, New Mexico using four nuclear microsatellites and a partial fragment of the mtDNA ND4 gene. Assignment tests excluded hybridization as a primary factor in species replacement and suggested a role for interspecific competition. Genetic analyses showed that H. placitus were introduced into the Pecos River from at least two genetically distinct source populations in the Canadian and Red rivers, Oklahoma. Lotka–Volterra models of interspecific competition indicated that the number of founding individuals could have been as few as 20 for H. placitus to have competitively displaced H. amarus in the Pecos River in 10 to 15 generations. Observed differences of allele frequencies between source and founder populations indicated that between 32 and 115 H. placitus individuals founded the Pecos River. Genetic and ecological data suggest that interspecific competition could have led to species replacement in this arid‐land river system.

Genetic monitoring and complex population dynamics: insights from a 12-year study of the Rio Grande silvery minnow

The endangered Rio Grande silvery minnow persists as a remnant population in a highly fragmented and regulated arid‐land river system. The species is subject to dramatic annual fluctuations in density. Since 2003, the wild population has been supplemented by hatchery‐reared fish. We report on a 12‐year (1999–2010) monitoring study of genetic diversity and effective population size (Ne) of wild and hatchery stocks. Our goals were to evaluate how genetic metrics responded to changes in wild fish density and whether they corresponded to the number and levels of diversity of hatchery‐reared repatriates. Genetic diversity and all measures of Ne in the wild population did not correlate with wild fish density until hatchery supplementation began in earnest. Estimates of variance and inbreeding effective size were not correlated. Our results suggest source–sink dynamics where captive stocks form a genetically diverse source and the wild population behaves as a sink. Nevertheless, overall genetic diversity of silvery minnow has been maintained over the last decade, and we attribute this to a well‐designed and executed propagation management plan. When multiple factors like environmental fluctuation and hatchery supplementation act simultaneously on a population, interpretation of genetic monitoring data may be equally complex and require considerable ecological data.

Comparative riverscape genetics reveals reservoirs of genetic diversity for conservation and restoration of Great Plains fishes

We used comparative landscape genetics to examine the relative roles of historical events, intrinsic traits and landscape factors in determining the distribution of genetic diversity of river fishes across the North American Great Plains. Spatial patterns of diversity were overlaid on a patch‐based graphical model and then compared within and among three species that co‐occurred across five Great Plains watersheds. Species differing in reproductive strategy (benthic vs. pelagic‐spawning) were hypothesized to have different patterns of genetic diversity, but the overriding factor shaping contemporary patterns of diversity was the signature of past climates and geological history. Allelic diversity was significantly higher at southern latitudes for Cyprinella lutrensis and Hybognathus placitus, consistent with northward expansion from southern Pleistocene refugia. Within the historical context, all species exhibited lowered occupancy and abundance in heavily fragmented and drier upstream reaches, particularly H. placitus; a pelagic‐spawning species, suggesting rates of extirpation have outpaced losses of genetic diversity in this species. Within most tributary basins, genetically diverse populations of each species persisted. Hence, reconnecting genetically diverse populations with those characterized by reduced diversity (regardless of their position within the riverine network) would provide populations with greater genetic and demographic resilience. We discuss cases where cross‐basin transfer may be appropriate to enhance genetic diversity and mitigate negative effects of climate change. Overall, striking similarities in genetic patterns and in response to fragmentation and dewatering suggest a common strategy for genetic resource management in this unique riverine fish assemblage.

Genetic heterogeneity among pelagic egg samples and variance in reproductive success in an endangered freshwater fish, Hybognathus amarus (Cyprinidae)

SynopsisA sweepstakes–mismatch process whereby reproduction is poorly coordinated with appropriate resources for larval development and recruitment can result in large variance in reproductive success among individuals and spawning aggregations. This process has been proposed to explain low ratio of genetic effective population size (Ne) to adult census size (N) ratios in marine species with high fecundity, pelagic spawning, and extensive mortality in early life stages. This process is also hypothesized to also account for very low Ne/N (≈ 0.001) observed in the federally endangered Rio Grande silvery minnow, Hybognathus amarus. This species is a freshwater fish that shares life-history features with marine pelagic spawners. We tested two key predictions of the sweepstakes–mismatch hypothesis using molecular data: (i) that temporally distinct samples of eggs differ in genetic composition and, (ii) that egg samples do not comprise a random subset of potential adult breeders. We present genetic data that supports both predictions and that are consistent with the hypothesis that high variance in reproductive success among adult breeders is an important factor that lowers Ne/N in H. amarus. This study highlights the importance of understanding the interaction of early life history and fragmentation in devising conservation plans for endangered aquatic organisms.

Microsatellite markers for the endangered razorback sucker, Xyrauchen texanus , are widely applicable to genetic studies of other catostomine fishes

We developed 10 polymorphic microsatellite markers for the federally endangered razorback sucker, Xyrauchen texanus. PCR optimization and cross-species amplification experiments indicated that these markers will be useful for analysis of fine-scale population structure in razorback and two other sucker species; the white sucker, Catostomus commersonii and the Rio Grande sucker, C. plebeius. Alleles at locus Xte4 did not overlap when compared between razorback and bluehead (C. discobolus) suckers and permits detection of F1 hybrids. These microsatellite markers appear widely applicable for identifying genetic consequences of population decline, hatchery rearing and release, and hybridization in razorback and other castostomine suckers.

Isolation and characterization of major histocompatibility class IIβ genes in an endangered North American cyprinid fish, the Rio Grande silvery minnow (Hybognathus amarus)

The major histocompatibility complex (MHC) is a critical component of the adaptive immune response in vertebrates. Due to the role that MHC plays in immunity, absence of variation within these genes may cause species to be vulnerable to emerging diseases. The freshwater fish family Cyprinidae comprises the most diverse and species-rich group of freshwater fish in the world, but some are imperiled. Despite considerable species richness and the long evolutionary history of the family, there are very few reports of MHC sequences (apart from a few model species), and no sequences are reported from endemic North American cyprinids (subfamily Leuciscinae). Here we isolate and characterize the MH Class II beta genes from complementary DNA and genomic DNA of the non-model, endangered Rio Grande silvery minnow (Hybognathus amarus), a North American cyprinid. Phylogenetic reconstruction revealed two groups of divergent MH alleles that are paralogous to previously described loci found in deeply divergent cyprinid taxa including common carp, zebrafish, African large barb and bream. Both groups of alleles were under the influence of diversifying selection yet not all individuals had alleles belonging to both allelic groups. We concluded that the general organization and pattern of variation of MH class II genes in Rio Grande silvery minnow is similar to that identified in other cyprinid fishes studied to date, despite distant evolutionary relationships and evidence of a severe genetic bottleneck.