The complete mitochondrial genomes of two imperiled species endemic to the Southwestern United States: Peppered Chub () and Gila Trout ().

and are fish species endemic to the Southwestern United States. We present the complete mitochondrial genomes for these species. Each genome consisted of 13 protein-coding genes, two ribosomal (rRNA) genes, 22 transfer RNA (tRNA) genes, and the control region (D-loop).

Genetic erosion in an endangered desert fish during a megadrought despite long-term supportive breeding.

Human water use combined with a recent megadrought have reduced river and stream flow through the southwest United States and led to periodic drying of formerly perennial river segments. Reductions in snowmelt runoff and increased extent of drying collectively threaten short-lived, obligate aquatic species, including the endangered Rio Grande silvery minnow (Hybognathus amarus). This species is subject to boom-and-bust population dynamics, under which large fluctuations in abundance are expected to lower estimates of effective population size and erode genetic diversity over time.

Limited evidence for extensive genetic differentiation between X and Y chromosomes in Hybognathus amarus (Cypriniformes: Leuciscidae).

Sex determination systems and genetic sex differentiation across fishes are highly diverse but are unknown for most Cypriniformes, including Rio Grande silvery minnow (Hybognathus amarus). In this study, we aimed to detect and validate sex-linked markers to infer sex determination system and to demonstrate the utility of combining several methods for sex-linked marker detection in nonmodel organisms. To identify potential sex-linked markers, Nextera-tagmented reductively amplified DNA (nextRAD) libraries were generated from 66 females, 64 males, and 60 larvae of unknown sex.

Transitioning from microsatellites to SNP-based microhaplotypes in genetic monitoring programmes: Lessons from paired data spanning 20 years.

Many long-term genetic monitoring programmes began before next-generation sequencing became widely available. Older programmes can now transition to new marker systems usually consisting of 1000s of SNP loci, but there are still important questions about comparability, precision, and accuracy of key metrics estimated using SNPs. Ideally, transitioned programmes should capitalize on new information without sacrificing continuity of inference across the time series.

The complete mitochondrial genomes of three imperiled cyprinid fishes Bonytail (), Rio Grande Silvery Minnow () and Loach Minnow ().

, , and (Family Cyprinidae, Order Cypriniformes) are endemic and endangered fishes in the southwestern United States. We present complete mitochondrial genomes for each species. Each mitochondrion consisted of 13 protein-coding genes, 2 ribosomal (rRNA) genes, 22 transfer RNA (tRNA) genes, and a single control region (D-loop), and gene order was consistent with other cyprinid fishes.

Variance in Reproductive Success is Driven by Environmental Factors, not Mating System, in Bonytails.

Studying the reproductive ecology of aggregate broadcast spawning fishes is difficult because it generally is not feasible to sample all potential parents and unambiguously assign their offspring. We used molecular-based parentage analysis to gain insights into the reproductive ecology of the endangered Bonytail, and to evaluate whether protected off-channel habitats could be used as an alternative to hatchery production. By genotyping adults and offspring stocked (n = 4130) into two experimental backwaters across three years, we determined that most adults (82-97%) contributed to progeny production across years and backwaters, with one exception.

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.

Biogeography of "": intensive genetic sampling from the Pecos River 'melting pot' reveals a dynamic history and phylogenetic complexity.

Thorough sampling is necessary to delineate lineage diversity for polytypic "species" such as . We conducted extensive mtDNA sampling (cytochrome b and ND4) from the Pecos River, Rio Grande, and South Canadian River, New Mexico. Our study emphasized the Pecos River due to its complex geological history and potential to harbor multiple lineages.

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.

Genetic analysis of captive spawning strategies for the endangered Rio Grande Silvery Minnow.

Captive breeding and rearing are central elements in conservation, management, and recovery planning for many endangered species including Rio Grande Silvery Minnow, a North American freshwater cyprinid. Traditionally, the sole purpose of hatcheries was to produce as many fish as feasible for stocking and harvest. Production quotas are also an important consideration in hatchery programs for endangered species, but they must also maintain and maximize genetic diversity of fish produced through implementation of best breeding practices.

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.

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.

Genetic effective size, N(e), 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.

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 (N(e)), which is roughly equal to one-half the adult census size (N) in many organisms. However, N(e) 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.