Estimation of introgression in cutthroat trout populations using microsatellites

Introgressive hybridization, mediated by anthropogenic activity, poses a threat to numerous and diverse taxa. The management of introgressed individuals or populations within species of conservation concern is currently the subject of scientific and political debate. We investigate the utility of 10 non-diagnostic microsatellite loci for investigating admixture from introduced Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) and rainbow trout (O. mykiss) within 25 putative Rio Grande cutthroat trout (O. c. virginalis) populations. We apply five different approaches (correspondence analysis, maximum-likelihood assignment tests, an admixture estimator based on allele frequencies, an admixture estimator based on coalescent theory and an admixture estimator implementing a Bayesian method) and use two alternative O. c. virginalis reference samples. All approaches were capable of identifying one population that consisted entirely of introduced O. c. bouvieri, and three out of five approaches enabled us to discriminate those populations with relatively high levels of non-native introgression from those populations with little or none. Actual estimates of admixture coefficients within a test population, varied, however, with the approach and reference sample used. These results have important implications for policies dividing populations into different management categories according to the estimated proportion of non-native genetic material that they contain

Genetic diversity within fragmented cutthroat trout populations

Interior cutthroat trout Oncorhynchus clarkii have undergone severe declines over the past 150 years. Many subspecies now persist in a highly fragmented state, primarily within headwater streams. We used 12 microsatellites to investigate the population genetic characteristics of 22 remnant populations of Rio Grande cutthroat trout O. c. virginalis isolated in montane streams in New Mexico. Populations varied markedly in the amount of genetic diversity they contained. There was no significant relationship between estimated adult population size or habitat size and heterozygosity; however, populations occurring above natural barriers were significantly less diverse. Seven population samples exhibited significant deviations from Hardy-Weinberg equilibrium. Interlocus variance in the population inbreeding coefficient F-1S was correlated with habitat size, and several population samples exhibited a significantly higher variance in interindividual relatedness, or a significantly higher median individual inbreeding coefficient. than would be expected by chance. These results suggest that cutthroat trout populations in headwater streams consist of multiple partially discrete subpopulations in which only a small number of adults successfully reproduce. The potential for Such population substructure should be considered when planning management activities for stream-dwelling cutthroat trout

The social organization of fish shoals: a test of the predictive power of laboratory experiments for the field

By contrast with a multitude of laboratory studies on the social organization of fish, relatively little is known about the size, composition and dynamics of free-ranging fish shoals. We give an overview of the available information on fish shoals and assess to what degree the predictions made from laboratory studies are consistent with field data. The section on shoal choice behaviour in the laboratory is structured so that the evidence fur different shoaling preferences is discussed in the context of their mechanisms and functions. Predictions based on experiments in captivity regarding preferences for conspecifics, individuals of similar body length and unparasitized fish were highly consistent with field observations on free-ranging shoals whereas preferences for familiar conspecifics and kin remain to be conclusively demonstrated in the field. In general, there is a shortage of studies in which shoaling preferences have been investigated both in the laboratory) and the field, and field studies have so far been largely descriptive revealing little about the underlying mechanisms of observed patterns. Given their great importance of fish shoals both in fundamental and applied research, an advancement of our knowledge of their social organization should significantly contribute to a better understanding of a whole range of topics including reciprocal altruism, group-living and self-organization

Shoal choice in zebrafish, Danio rerio: the influence of shoal size and activity

Shoaling fish are expected, in many cases, to gain fitness benefits from being in a larger shoal and previous experiments have shown that fish are indeed capable of choosing between shoals of different sizes. We investigated the influence of shoal activity on shoal size preference in the zebrafish. We gave test fish the choice between shoals of one to four stimulus fish, presented at two different water temperatures, and so differing in their activity levels. Where all stimulus fish were in water of the same temperature, test fish generally preferred the larger shoal. However, this preference could be reduced by presenting the larger shoal in colder water and so reducing its activity. We discuss these findings with reference to the factors that may influence shoal activity, the effect of temperature on shoaling behaviour and the mechanisms that may be used by fish to discriminate shoal size. (C) 2001 The Association for the Study of Animal Behaviour

Population structure and genetic management of Rio Grande cutthroat trout (Oncorhynchus clarkii virginalis)

The Rio Grande cutthroat trout, Oncorhynchus clarkii virginalis, has declined precipitously over the past century, and currently exhibits a highly fragmented distribution within the Canadian, Pecos and Rio Grande river systems of the western United States. The relationships between populations in the three river drainages, and between O. c. virginalis and the closely related taxa O. c. pleuriticus and O. c. stomias, are not well understood. In order to guide management decisions for the subspecies, we investigated the distribution of variation at 12 micro-satellite loci and two regions of the mitochondrial genome. We observed a high level of genetic differentiation between O. c. virginalis populations occupying different headwater streams ( global F-st = 0.41). However, we found evidence for previous gene flow within the Rio Grande drainage, indicating that inter-population differentiation may have been exacerbated by the recent effects of population fragmentation. Despite large-scale anthropogenic movement of individuals from the Rio Grande into the Canadian and Pecos, the genetic signature of long-term evolutionary independence between the three drainages has been retained

Characterization of tetranucleotide microsatellites for Rio Grande cutthroat trout and rainbow trout, and their cross-amplification in other cutthroat trout subspecies

We describe the isolation and characterization of 12 tetranucleotide microsatellites for Rio Grande cutthroat trout (Oncorhynchus clarkii virginalis) and rainbow trout (Oncorhynchus mykiss), and subsequently investigate their performance in Colorado River cutthroat trout (Oncorhynchus clarkii pleuriticus), greenback cutthroat trout (Oncorhynchus clarkii stomias) and Yellowstone cutthroat trout (Oncorhynchus clarki bouvieri). All 12 loci are polymorphic in all subspecies of O. clarkii examined

Interpopulation hybridization results in widespread viability selection across the genome in Tigriopus californicus

Background: Genetic interactions within hybrids influence their overall fitness. Understanding the details of these interactions can improve our understanding of speciation. One experimental approach is to investigate deviations from Mendelian expectations (segregation distortion) in the inheritance of mapped genetic markers. In this study, we used the copepod Tigriopus californicus, a species which exhibits high genetic divergence between populations and a general pattern of reduced fitness in F2 interpopulation hybrids. Previous studies have implicated both nuclear-cytoplasmic and nuclear-nuclear interactions in causing this fitness reduction. We identified and mapped population-diagnostic single nucleotide polymorphisms (SNPs) and used these to examine segregation distortion across the genome within F2 hybrids.Results: We generated a linkage map which included 45 newly elucidated SNPs and 8 population-diagnostic microsatellites used in previous studies. The map, the first available for the Copepoda, was estimated to cover 75% of the genome and included markers on all 12 T. californicus chromosomes. We observed little segregation distortion in newly hatched F2 hybrid larvae (fewer than 10% of markers at p < 0.05), but strikingly higher distortion in F2 hybrid adult males (45% of markers at p < 0.05). Hence, segregation distortion was primarily caused by selection against particular genetic combinations which acted between hatching and maturity. Distorted markers were not distributed randomly across the genome but clustered on particular chromosomes. In contrast to other studies in this species we found little evidence for cytonuclear coadaptation. Instead, different linkage groups exhibited markedly different patterns of distortion, which appear to have been influenced by nuclear-nuclear epistatic interactions and may also reflect genetic load carried within the parental lines.Conclusion: Adult male F2 hybrids between two populations of T. californius exhibit dramatic segregation distortion across the genome. Distorted loci are clustered within specific linkage groups, and the direction of distortion differs between chromosomes. This segregation distortion is due to selection acting between hatching and adulthood

Across the great divide: genetic forensics reveals misidentification of endangered cutthroat trout populations

Accurate assessment of species identity is fundamental for conservation biology. Using molecular markers from the mitochondrial and nuclear genomes, we discovered that many putatively native populations of greenback cutthroat trout (Oncorhynchus clarkii stomias) comprised another subspecies of cutthroat trout, Colorado River cutthroat trout (Oncorhynchus clarkii pleuriticus). The error can be explained by the introduction of Colorado River cutthroat trout throughout the native range of greenback cutthroat trout in the late 19th and early 20th centuries by fish stocking activities. Our results suggest greenback cutthroat trout within its native range is at a higher risk of extinction than ever before despite conservation activities spanning more than two decades

Regulatory Architecture of Gene Expression Variation in the Threespine Stickleback Gasterosteus aculeatus

Much adaptive evolutionary change is underlain by mutational variation in regions of the genome that regulate gene expression rather than in the coding regions of the genes themselves. An understanding of the role of gene expression variation in facilitating local adaptation will be aided by an understanding of underlying regulatory networks. Here, we characterize the genetic architecture of gene expression variation in the threespine stickleback (Gasterosteus aculeatus), an important model in the study of adaptive evolution. We collected transcriptomic and genomic data from 60 half-sib families using an expression microarray and genotyping-by-sequencing, and located expression quantitative trait loci (eQTL) underlying the variation in gene expression in liver tissue using an interval mapping approach. We identified eQTL for several thousand expression traits. Expression was influenced by polymorphism in both cis- and trans-regulatory regions. Transe-QTL clustered into hotspots. We did not identify master transcriptional regulators in hotspot locations: rather, the presence of hotspots may be driven by complex interactions between multiple transcription factors. One observed hotspot colocated with a QTL recently found to underlie salinity tolerance in the threespine stickleback. However, most other observed hotspots did not colocate with regions of the genome known to be involved in adaptive divergence between marine and freshwater habitats

Single nucleotide polymorphisms to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees

Many wild Atlantic salmon (Salmo salar) populations are threatened by introgressive hybridization from domesticated fish that have escaped from aquaculture facilities. A detailed understanding of the hybridization dynamics between wild salmon and aquaculture escapees requires discrimination of different hybrid classes; however, markers currently available to discriminate the two types of parental genome have limited power to do this. Using a high-density Atlantic salmon single nucleotide polymorphism (SNP) array, in combination with pooled-sample allelotyping and an F-st outlier approach, we identified 200 SNPs that differentiated an important Atlantic salmon stock from the escapees potentially hybridizing with it. By simulating multiple generations of wild-escapee hybridization, involving wild populations in two major phylogeographic lineages and a genetically diverse set of escapees, we showed that both the complete set of SNPs and smaller subsets could reliably assign individuals to different hybrid classes up to the third hybrid (F3) generation. This set of markers will be a useful tool for investigating the genetic interactions between native wild fish and aquaculture escapees in many Atlantic salmon populations