Conservation Genetics at the Interface of Theory and Application

Understanding the ecological mechanisms responsible for patterns of spatial genetic structure and diversity is a central issue to evolutionary ecology and biodiversity conservation. The Anthropocene has seen a mass extinction only previously observed through geological records, and freshwater fishes of North America have not been spared owing to large-scale modification of freshwater habitats and introduction of nonnative species. Concomitant with reduced numbers of species is a rapid reduction in genetic diversity within species; this diversity that is required for species to adapt to rapidly changing environments of human dominated landscapes. However, understanding why species exhibit different patterns of spatial genetic structure and genetic diversity requires substantial ecological data and knowledge of species life histories. This body of research incorporates both ecological and genetic data to address key issues related to the conservation of native fishes of the upper Gila River, NM, USA, and evaluates how differences in ecology among species influences their evolutionary trajectories (i.e., genetic diversity and structuring). Chapter 1 adopted a conservation genetics approach to evaluate the genetic health and long-term maintenance of genetic diversity of three imperiled species protected by New Mexico State and United States Federal laws. Estimates of contemporary effective size were low for these species, as were estimates of genetic structure (all species FST \u3c 0.025) suggesting moderate to high gene flow for all species. Chapter 2 broadened the scope of focal species by including most of the fish community and increasing life history variation to evaluate how dispersal and life history influence patterns of genetic structure within a shared riverscape (i.e., attributes of a landscape specifically related to networks of streams and rivers). A key result was that genetic patterns were highly variable among species and related to life history and abundance. Across species, overall genetic differentiation (FST) was not strongly predicted by species traits, but fecundity was negatively associated with effect of distance on genetic structure (measured by Mantel\u27s r). Chapter 3 examined the relationship between metapopulation processes and species evolutionary trajectories. Metapopulation genetic effective size was reduced by temporal instability (extirpation/recolonization), but high abundance appeared to counter balance effects of temporal instability. These results indicate that ecological trade-offs related to life-history strategies (e.g., fecundity, body size, parental investment, etc.) also influence individual species\u27 evolutionary responses (i.e., genetic diversity and differentiation) to landscape factors and threats to persistence

The Magnitude of Global Marine Species Diversity

Background: The question of how many marine species exist is important because it provides a metric for how much we do and do not know about life in the oceans. We have compiled the first register of the marine species of the world and used this baseline to estimate how many more species, partitioned among all major eukaryotic groups, may be discovered. Results: There are ∼226,000 eukaryotic marine species described. More species were described in the past decade (∼20,000) than in any previous one. The number of authors describing new species has been increasing at a faster rate than the number of new species described in the past six decades. We report that there are ∼170,000 synonyms, that 58,000–72,000 species are collected but not yet described, and that 482,000–741,000 more species have yet to be sampled. Molecular methods may add tens of thousands of cryptic species. Thus, there may be 0.7–1.0 million marine species. Past rates of description of new species indicate there may be 0.5 ± 0.2 million marine species. On average 37% (median 31%) of species in over 100 recent field studies around the world might be new to science. Conclusions: Currently, between one-third and two-thirds of marine species may be undescribed, and previous estimates of there being well over one million marine species appear highly unlikely. More species than ever before are being described annually by an increasing number of authors. If the current trend continues, most species will be discovered this century

Data from: Spatio-temporal variation in parasite communities maintains diversity at the major histocompatibility complex class IIβ in the endangered Rio Grande Silvery Minnow

Climate change will strongly impact aquatic ecosystems particularly in arid and semi-arid regions. Fish-parasite interactions will also be affected by predicted altered flow and temperature regimes, and other environmental stressors. Hence, identifying environmental and genetic factors associated with maintaining diversity at immune genes is critical for understanding species’ adaptive capacity. Here we combine genetic (MHC Class IIβ and microsatellites), parasitological and ecological data to explore the relationship between these factors in the remnant wild Rio Grande silvery minnow (Hybognathus amarus) population, an endangered species found in the southwestern United States. Infections with multiple parasites on the gills were observed and there was spatio-temporal variation in parasite communities and patterns of infection among individuals. Despite its highly endangered status and chronically low genetic effective size, Rio Grande silvery minnow had high allelic diversity at MHC Class IIβ with more alleles recognised at the presumptive DAB1 locus compared to the DAB3 locus. We identified significant associations between specific parasites and MHC alleles against a backdrop of generalist parasite prevalence. We also found that individuals with higher individual neutral heterozygosity and higher amino acid divergence between MHC alleles, had lower parasite abundance and diversity. Taken together, these results suggest a role for fluctuating selection imposed by spatio-temporal variation in pathogen communities and divergent allele advantage in maintenance of high MHC polymorphism. Understanding the complex interaction of habitat, pathogens and immunity in protected species will require integrated experimental, genetic and field studies

Rio Grande Sucker Gila basin

Microsatellite data is provided for 10 loci in GenAlEx format. Population information is provided in column two of speadsheet--usats. Mitochondrial DNA haplotype information is provided for the 526 base pair fragment of ND4 and the 303 base pair fragment of cyt-b, samples are in the same order as the microsatellite fil

Evaluation of Long-Term Mark-Recapture Data for Estimating Abundance of Juvenile Fall-Run Chinook Salmon on the Stanislaus River from 1996 to 2017

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.

Diets of Native and Non-Native Piscivores in the Stanislaus River, California, Under Contrasting Hydrologic Conditions

The fish communities of the Sacramento–San Joaquin Delta and its tributaries in California’s Central Valley have been irreparably altered through introductions of numerous fish species, including Striped Bass (Morone saxatilis), black bass (Micropterus spp.), and catfishes (Ameiurus spp. and Ictalurus spp.). Research into how predation by non-native piscivores affects native anadromous species has focused on the Sacramento and San Joaquin river mainstems and Delta habitats, through which all anadromous species must pass. Yet, the ranges of non-native fishes extend into upstream tributaries. We collected diets from native and non-native piscivores in the Stanislaus River, a tributary to the San Joaquin River and a remaining stronghold for native fishes. Piscivorous fishes primarily consumed invertebrates and the native species fall-run Chinook Salmon (Oncorhynchus tshawytscha) and Pacific Lamprey (Entosphenus tridentatus). Juvenile Chinook Salmon and Pacific Lamprey were consumed at higher frequencies than any other potential fish prey species, particularly by Striped Bass and black bass. The frequency of native fishes in predator diets was similar across years, despite contrasting hydrologic conditions; 2019 (wet year), 2020 (dry year), and 2021 (critically dry year). Our results show that Pacific Lamprey were frequently consumed by native and non-native piscivores, and that juvenile Chinook Salmon experience substantial predation early in their migration, regardless of hydrologic conditions

Counting the Parts to Understand the Whole: Rethinking Monitoring of Steelhead in California’s Central Valley

Steelhead (Oncorhynchus mykiss expressing an anadromous life history) in the Sacramento and San Joaquin rivers and their tributaries in California’s Central Valley (CCV) belong to a Distinct Population Segment (DPS) that is listed as threatened under the US Endangered Species Act. Although contemporary management and recovery plans include numerous planned and ongoing efforts seeking to aid in DPS recovery—such as gravel augmentation, manipulation of spring flows, and restoration of rearing and spawning habitat—a paucity of data precludes the possibility of evaluating the effect of these actions on populations of Steelhead in CCV streams. Knowledge gaps relating to historic and current abundance, population-specific ratios of resident and anadromous life-history expression, and the influence of hatchery-reared fish remain largely unaddressed. This is partly a result of aspects of Steelhead biology that make them difficult to monitor, including the multitude of factors that contribute to the expression of anadromy, polymorphic populations, and migration periods that coincide with challenging field conditions. However, these gaps in understanding are also partly the result of an institutional focus on Chinook Salmon (Oncorhynchus tshawytscha) and a pervasive notion that actions benefiting Chinook populations will also benefit Steelhead populations. To evaluate these gaps and to suggest approaches for assessing DPS recovery actions, we review available data and existing monitoring efforts, and consider the actions necessary to inform the development of targeted O. mykiss monitoring programs. Current management and recovery goals focus on abundance estimates of Steelhead only, yet current monitoring is insufficient for reliable estimates. We argue that a reallocation of monitoring resources to better understand the interaction between resident O. mykiss and Steelhead would provide better data to estimate the vital rates needed to evaluate the effects of recovery actions

Genetic Structure of a Disjunct Peripheral Population of Mountain Sucker Pantosteus Jordani in the Black Hills, South Dakota, USA

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

Data from: River network architecture, genetic effective size and distributional patterns predict differences in genetic structure across species in a dryland stream fish community

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