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1.
A previous genomewide association study (GWAS) identified SNP markers associated with propensity to migrate of rainbow and steelhead trout (Oncorhynchus mykiss) in a connected population with free access to the ocean in Upper Yakima River (UYR) and a population in Upper Mann Creek (UMC) that has been sequestered from its access to the ocean for more than 50 years. Applying genomic heritability estimation using the same dataset, we found that smoltification in the UYR population were almost completely determined by additive effects, with 95.5% additive heritability and 4.5% dominance heritability, whereas smoltification in the UMC population had substantial dominance effects, with 0% additive heritability and 39.3% dominance heritability. Dominance test detected one SNP marker (R30393) with significant dominance effect on smoltification (P = 1.98 × 10−7). Genomic-predicted additive effects completely separated migratory and nonmigratory fish in the UYR population, whereas genomic-predicted dominance effects achieved such complete separation in the UMC population. The UMC population had higher genomic additive and dominance correlations than the UYR population, and fish between these two populations had the least genomic correlations. These results suggested that blocking the free access to the ocean may have reduced genetic diversity and increased genomic similarity associated with the early life-history transition related to propensity to migrate. 相似文献
2.
Inbreeding is of concern in supportive breeding programmes in Pacific salmonids, Oncorhynchus spp, where the number of breeding adults is limited by rearing space or poor survival to adulthood, and large numbers are released to supplement wild stocks and fisheries. We reconstructed the pedigree of 6602 migratory hatchery steelhead (Oncorhynchus mykiss) over four generations, to determine the incidence and fitness consequences of inbreeding in a northwest USA programme. The hatchery maintained an effective population size, = 107.9 from F0 to F2, despite an increasing census size (N), which resulted in a decreasing Ne/N ratio (0.35 in F0 to 0.08 in F2). The reduced ratio was attributed to a small broodstock size, nonrandom transfers and high variance in reproductive success (particularly in males). We observed accumulation of inbreeding from the founder generation (in F4, percentage individuals with inbreeding coefficients Δf > 0 = 15.7%). Generalized linear mixed models showed that body length and weight decreased significantly with increasing Δf, and inbred fish returned later to spawn in a model that included father identity. However, there was no significant correlation between Δf and age at return, female fecundity or gonad weight. Similarly, there was no relationship between Δf and reproductive success of F2 and F3 individuals, which might be explained by the fact that reproductive success is partially controlled by hatchery mating protocols. This study is one of the first to show that small changes in inbreeding coefficient can affect some fitness‐related traits in a monitored population propagated and released to the wild. 相似文献
3.
Self-thinning patterns are frequently used to describe density dependence in populations on timescales shorter than the organism''s life span and have been used to infer carrying capacity of the environment. Among mobile animals, this concept has been used to document density dependence in stream salmonids, which compete over access to food and space. The carrying capacity, growth conditions, and initial cohort sizes often vary between streams and stream sections, which would influence the onset and strength of the density dependence. Despite much effort in describing habitat relationships in stream fishes, few studies have explicitly tested how the physical environment affects the slope of the thinning curves. Here, we investigate the prevalence and strength of self-thinning in juvenile stages of a steelhead (Oncorhynchus mykiss) population in Idaho, USA. Further, we investigate the roles of local physical habitat and metabolic constraints in explaining the variation in thinning curves among study sites in the watershed. Only yearling steelhead exhibited an overall significant thinning trend, but the slope of the mass–density relationship (−0.53) was shallower than predicted by theory and reported from empirical studies. There was no detectable relationship in subyearling steelhead. Certain abiotic factors explained a relatively large portion of the variation in the strength of the self-thinning among the study reaches. For subyearling steelhead, the slopes were negatively associated with the average water depth and flow velocity in the study sites, whereas slopes in yearlings were steeper in sites that incurred a higher metabolic cost. Our results show that the prevalence and strength of density dependence in natural fish populations can vary across heterogeneous watersheds and can be more pronounced during certain stages of a species'' life history, and that environmental factors can mediate the extent to which density dependence is manifested in predictable ways. 相似文献
4.
E. Quillet F. Krieg N. Dechamp C. Hervet A. Bérard P. Le Roy R. Guyomard P. Prunet T. G. Pottinger 《Animal genetics》2014,45(2):223-234
Better understanding of the mechanisms underlying interindividual variation in stress responses and their links with production traits is a key issue for sustainable animal breeding. In this study, we searched for quantitative trait loci (QTL) controlling the magnitude of the plasma cortisol stress response and compared them to body size traits in five F2 full‐sib families issued from two rainbow trout lines divergently selected for high or low post‐confinement plasma cortisol level. Approximately 1000 F2 individuals were individually tagged and exposed to two successive acute confinement challenges (1 month interval). Post‐stress plasma cortisol concentrations were determined for each fish. A medium density genome scan was carried out (268 markers, overall marker spacing less than 10 cM). QTL detection was performed using qtlmap software, based on an interval mapping method ( http://www.inra.fr/qtlmap ). Overall, QTL of medium individual effects on cortisol responsiveness (<10% of phenotypic variance) were detected on 18 chromosomes, strongly supporting the hypothesis that control of the trait is polygenic. Although a core array of QTL controlled cortisol concentrations at both challenges, several QTL seemed challenge specific, suggesting that responses to the first and to a subsequent exposure to the confinement stressor are distinct traits sharing only part of their genetic control. Chromosomal location of the steroidogenic acute regulatory protein (STAR) makes it a good potential candidate gene for one of the QTL. Finally, comparison of body size traits QTL (weight, length and body conformation) with cortisol‐associated QTL did not support evidence for negative genetic relationships between the two types of traits. 相似文献
5.
Stefan Reiser Dominique Marie Pohlmann Udo Koops Joachim Paul Grger Ulfert Focken 《Zeitschrift fur angewandte Ichthyologie》2019,35(2):465-472
Environmental enrichment aims for a deliberate increase in structural complexity in otherwise plain rearing units, helping to reduce aberrant traits and promote welfare of fish kept in captivity. Before putting enrichment protocols into practice, however, practitioners like hatchery managers need clear guidelines on enrichment measures and on the substrates used. In the present study, we used rainbow trout as a model species for salmonid rearing and investigated the use of a single layer of three different gravel types, i.e., small (4–8 mm), medium (8–16 mm) and large (16–32 mm), for environmental enrichment during egg incubation, endogenous and first feeding of rainbow trout and compared this to a barren control. From the egg stage onwards, we determined mortality, fungal prevalence as well as growth of larvae and fingerlings. We found that gravel size significantly affected mortality and fungal prevalence with the smallest gravel size and the control showing the lowest incidents. Growth of larvae and fingerlings was not affected by gravel, both when compared between gravel types and to the barren control. When using gravel for environmental enrichment in salmonid hatcheries, a small gravel size should be used. Small gravel provides the fish with a more natural environment without compromising practical feasibility of enrichment in hatcheries, still allowing for easy visual inspection and manual control of the reared fish. 相似文献
6.
Martin C. Arostegui Thomas P. Quinn Lisa W. Seeb James E. Seeb Garrett J. McKinney 《Molecular ecology》2019,28(6):1412-1427
Migratory behaviour patterns in animals are controlled by a complex genetic architecture. Rainbow trout (Oncorhynchus mykiss) is a salmonid fish that spawns in streams but exhibits three primary life history pathways: stream‐resident (fluvial), lake‐migrant (adfluvial) and ocean‐migrant (anadromous). Previous studies examining fluvial and anadromous O. mykiss have identified several genes associated with life history divergence including the presence of an inversion complex within chromosome 5 (Omy05) that appears to maintain a suite of linked genes controlling migratory behaviour. However, adfluvial trout are migratory without being anadromous, and the genetic basis for this life history has not been investigated from evolutionary perspectives. We sampled wild, native nonanadromous rainbow trout occupying connected stream and lake habitats in a southwest Alaskan watershed to determine whether these fish exhibit genetic divergence between fluvial and adfluvial ecotypes, and whether that divergence parallels that documented in fluvial and anadromous O. mykiss. Data from restriction site‐associated DNA (RAD) sequencing revealed an association between frequencies of both the Omy05 inversion complex and other single nucleotide polymorphisms (SNPs) with habitat type (stream or lake), supporting the genetic divergence of fluvial and adfluvial individuals in sympatry. The presence of a genetic basis for migration into lakes, analogous to that documented for anadromy, indicates that the adfluvial ecotype must be recognized separately from the fluvial form of O. mykiss even though neither is anadromous. These results highlight the genetic architecture underlying migration and the importance of chromosomal inversions in promoting and sustaining intraspecific diversity. 相似文献
7.
Catalina Monzón‐Argüello Carlos Garcia de Leaniz Gonzalo Gajardo Sofia Consuegra 《Ecology and evolution》2013,3(10):3359-3368
The ability of invasive species to adapt to novel conditions depends on population size and environmental mismatch, but also on genetic variation. Away from their native range, invasive species confronted with novel selective pressures may display different levels of neutral versus functional genetic variation. However, the majority of invasion studies have only examined genetic variation at neutral markers, which may reveal little about how invaders adapt to novel environments. Salmonids are good model systems to examine adaptation to novel pressures because they have been translocated all over the world and represent major threats to freshwater biodiversity in the Southern Hemisphere, where they have become invasive. We examined patterns of genetic differentiation at seven putatively neutral (microsatellites) loci and one immune‐related major histocompatibility complex (MHC class II‐β) locus among introduced rainbow trout living in captivity (farmed) or under natural conditions (naturalized) in Chilean Patagonia. A significant positive association was found between differentiation at neutral and functional markers, highlighting the role of neutral evolutionary forces in shaping genetic variation at immune‐related genes in salmonids. However, functional (MHC) genetic diversity (but not microsatellite diversity) decreased with time spent in the wild since introduction, suggesting that there was selection against alleles associated with captive rearing of donor populations that do not provide an advantage in the wild. Thus, although high genetic diversity may initially enhance fitness in translocated populations, it does not necessarily reflect invasion success, as adaptation to novel conditions may result in rapid loss of functional MHC diversity. 相似文献
8.
Catalina Monzn‐Argüello Sofia Consuegra Gonzalo Gajardo Francisco Marco‐Rius Daniel M. Fowler Jacquelin DeFaveri Carlos Garcia de Leaniz 《Evolutionary Applications》2014,7(8):921-936
Invasion success may be expected to increase with residence time (i.e., time since first introduction) and secondary releases (i.e., those that follow the original introduction), but this has rarely been tested in natural fish populations. We compared genetic and phenotypic divergence in rainbow trout and brown trout in Chile and the Falkland Islands to test the prediction that adaptive divergence, measured as PST/FST, would increase with residence time and secondary releases. We also explored whether interspecific competition between invaders could drive phenotypic divergence. Residence time had no significant effect on genetic diversity, phenotypic divergence, effective population size, or signatures of expansion of invasive trout. In contrast, secondary releases had a major effect on trout invasions, and rainbow trout populations mostly affected by aquaculture escapees showed significant divergence from less affected populations. Coexistence with brown trout had a positive effect on phenotypic divergence of rainbow trout. Our results highlight an important role of secondary releases in shaping fish invasions, but do not support the contention that older invaders are more differentiated than younger ones. They also suggest that exotic trout may not have yet developed local adaptations in these recently invaded habitats, at least with respect to growth‐related traits. 相似文献
9.
Suzanne J. Kelson Michael R. Miller Tasha Q. Thompson Sean M. O&#x;Rourke Stephanie M. Carlson 《Molecular ecology》2020,29(5):870-885
Landscape permeability is often explored spatially, but may also vary temporally. Landscape permeability, including partial barriers, influences migratory animals that move across the landscape. Partial barriers are common in rivers where barrier passage varies with streamflow. We explore the influence of partial barriers on the spatial and temporal distribution of migration‐linked genotypes of Oncorhynchus mykiss, a salmonid fish with co‐occurring resident and migratory forms, in tributaries to the South Fork Eel River, California, USA, Elder and Fox Creeks. We genotyped >4,000 individuals using RAD‐capture and classified individuals as resident, heterozygous or migratory genotypes using life history‐associated loci. Across four years of study (2014–2017), the permeability of partial barriers varied across dry and wet years. In Elder Creek, the largest waterfall was passable for adults migrating up‐river 4–39 days each year. In this stream, the overall spatial pattern, with fewer migratory genotypes above the waterfall, remained true across dry and wet years (67%–76% of migratory alleles were downstream of the waterfall). We also observed a strong relationship between distance upstream and proportion of migratory alleles. In Fox Creek, the primary barrier is at the mouth, and we found that the migratory allele frequency varied with the annual timing of high flow events. In years when rain events occurred during the peak breeding season, migratory allele frequency was high (60%–68%), but otherwise it was low (30% in two years). We highlight that partial barriers and landscape permeability can be temporally dynamic, and this effect can be observed through changing genotype frequencies in migratory animals. 相似文献
10.
《Evolutionary Applications》2017,10(2):146-160
Effective population size (Ne) is among the most important metrics in evolutionary biology. In natural populations, it is often difficult to collect adequate demographic data to calculate Ne directly. Consequently, genetic methods to estimate Ne have been developed. Two Ne estimators based on sibship reconstruction using multilocus genotype data have been developed in recent years: sibship assignment and parentage analysis without parents. In this study, we evaluated the accuracy of sibship reconstruction using a large empirical dataset from five hatchery steelhead populations with known pedigrees and using 95 single nucleotide polymorphism (SNP) markers. We challenged the software COLONY with 2,599,961 known relationships and demonstrated that reconstruction of full‐sib and unrelated pairs was greater than 95% and 99% accurate, respectively. However, reconstruction of half‐sib pairs was poor (<5% accurate). Despite poor half‐sib reconstruction, both estimators provided accurate estimates of the effective number of breeders (Nb) when sample sizes were near or greater than the true Nb and when assuming a monogamous mating system. We further demonstrated that both methods provide roughly equivalent estimates of Nb. Our results indicate that sibship reconstruction and current SNP panels provide promise for estimating Nb in steelhead populations in the region. 相似文献
11.
M. Segoli R. Stouthamer C. M. Stouthamer P. Rugman‐Jones J. A. Rosenheim 《Journal of evolutionary biology》2013,26(12):2716-2720
Wolbachia is a widespread endosymbiont that induces dramatic manipulations of its host's reproduction. Although there has been substantial progress in the developing theory for Wolbachia–host interactions and in measuring the effects of Wolbachia on host fitness in the laboratory, there is a widely recognized need to quantify the effects of Wolbachia on the host fitness in the field. The wasp Anagrus sophiae, an egg parasitoid of planthoppers, carries a Wolbachia strain that induces parthenogenesis, but its effects on the fitness of its Anagrus host are unknown. We developed a method to estimate the realized lifetime reproductive success of female wasps by collecting them soon after they die naturally in the field, counting the number of eggs remaining in their ovaries and quantifying Wolbachia density in their body. We sampled from a highly infected A. sophiae population and found no evidence for Wolbachia virulence and possible evidence for positive effects of Wolbachia on realized reproductive success. 相似文献
12.
Anders Pape Møller Juan J. Soler Jan Tøttrup Nielsen Ismael Galván 《Ecology and evolution》2015,5(8):1676-1685
Pathogenic bacteria constitute a serious threat to viability of many organisms. Because growth of most bacteria is favored by humid and warm environmental conditions, earlier reproducers in seasonal environments should suffer less from the negative consequences of pathogenic bacteria. These relationships, and the effects on reproductive success, should be particularly prominent in predators because they are frequently exposed to pathogenic microorganisms from sick prey. Here, we presented and tested this hypothesis by sampling bacteria on adult and nestling goshawks Accipiter gentilis. We predicted that early breeders and their offspring should have fewer bacteria than those reproducing later during the breeding season. Adult goshawks with a high abundance of Staphylococcus on their beak and claws were easier to capture and their laying date was delayed. Moreover, goshawks that laid their eggs later had offspring with more Staphylococcus on their beaks and claws. The strength of the association between laying date and bacterial density of nestlings was stronger during the warm spring of 2013, when nestlings suffered from a higher abundance of pathogenic bacteria. Hatching failure and fledging failure were more common in nests with a higher abundance of Staphylococcus independently of the number of years occupied, laying date, and age of the female nest owner. These findings imply that timing of reproduction may be under the influence of pathogenic bacteria. Because early breeding goshawks produce more recruits than later breeders, our results suggest a role for pathogenic bacteria in the optimal timing of reproduction. 相似文献
13.
14.
Charlotte Depeux Jean‐Franois Lemaître Jrme Moreau Franois‐Xavier Dechaume‐Moncharmont Tiffany Laverre Hlne Pauhlac Jean‐Michel Gaillard Sophie Beltran‐Bech 《Journal of evolutionary biology》2020,33(9):1256-1264
Reproductive senescence is the decrease of reproductive performance with increasing age and can potentially include trans‐generational effects as the offspring produced by old parents might have a lower fitness than those produced by young parents. This negative effect may be caused either by the age of the father, mother or the interaction between the ages of both parents. Using the common woodlouse Armadillidium vulgare, an indeterminate grower, as a biological model, we tested for the existence of a deleterious effect of parental age on fitness components. Contrary to previous findings reported from vertebrate studies, old parents produced both a higher number and larger offspring than young parents. However, their offspring had lower fitness components (by surviving less, producing a smaller number of clutches or not reproducing at all) than offspring born to young parents. Our findings strongly support the existence of trans‐generational senescence in woodlice and contradict the belief that old individuals in indeterminate growers contribute the most to recruitment and correspond thereby to the key life stage for population dynamics. Our work also provides rare evidence that the trans‐generational effect of senescence can be stronger than direct reproductive senescence in indeterminate growers. 相似文献
15.
In this study, we documented the breeding system of a wild population of Atlantic salmon (Salmo salar L.) by genetically sampling every returning adult and assessed the determinants of individual fitness. We then quantified the impacts of catch and release (C&R) on mating and reproductive success. Both sexes showed high variance in individual reproductive success, and the estimated standardized variance was higher for males (2.86) than for females (0.73). We found a weak positive relationship between body size and fitness and observed that fitness was positively correlated with the number of mates, especially in males. Mature male parr sired 44% of the analysed offspring. The impact of C&R on the number of offspring was size dependent, as the reproductive success of larger fish was more impaired than smaller ones. Also, there was an interactive negative effect of water temperature and air exposure time on reproductive success of C&R salmon. This study improves our understanding of the complex reproductive biology of the Atlantic salmon and is the first to investigate the impact of C&R on reproductive success. Our study expands the management toolbox of appropriate C&R practices that promote conservation of salmon populations and limit negative impacts on mating and reproductive success. 相似文献
16.
《Evolutionary Applications》2017,10(5):485-497
Human‐driven evolution can impact the ecological role and conservation value of impacted populations. Most evolutionary restoration approaches focus on manipulating gene flow, but an alternative approach is to manipulate the selection regime to restore historical or desired trait values. Here we examined the potential utility of this approach to restore anadromous migratory behavior in coastal California steelhead trout (Oncorhynchus mykiss) populations. We evaluated the effects of natural and anthropogenic environmental variables on the observed frequency of alleles at a genomic marker tightly associated with migratory behavior across 39 steelhead populations from across California, USA. We then modeled the potential for evolutionary restoration at sites that have been impacted by anthropogenic barriers. We found that complete barriers such as dams are associated with major reductions in the frequency of anadromy‐associated alleles. The removal of dams is therefore expected to restore anadromy significantly. Interestingly, accumulations of large numbers of partial barriers (passable under at least some flow conditions) were also associated with significant reductions in migratory allele frequencies. Restoration involving the removal of partial barriers could be evaluated alongside dam removal and fishway construction as a cost‐effective tool to restore anadromous fish migrations. Results encourage broader consideration of in situ evolution during the development of habitat restoration projects. 相似文献
17.
Accurate estimates of heritability () are necessary to assess adaptive responses of populations and evolution of fitness‐related traits in changing environments. For plants, estimates generally rely on maternal progeny designs, assuming that offspring are either half‐sibs or unrelated. However, plant mating systems often depart from half‐sib assumptions, this can bias estimates. Here, we investigate how to accurately estimate in nonmodel species through the analysis of sibling designs with a moderate genotyping effort. We performed simulations to investigate how microsatellite marker information available for only a subset of offspring can improve estimates based on maternal progeny designs in the presence of nonrandom mating, inbreeding in the parental population or maternal effects. We compared the basic family method, considering or not adjustments based on average relatedness coefficients, and methods based on the animal model. The animal model was used with average relatedness information, or with hybrid relatedness information: associating one‐generation pedigree and family assumptions, or associating one‐generation pedigree and average relatedness coefficients. Our results highlighted that methods using marker‐based relatedness coefficients performed as well as pedigree‐based methods in the presence of nonrandom mating (i.e. unequal male reproductive contributions, selfing), offering promising prospects to investigate in situ heritabilities in natural populations. In the presence of maternal effects, only the use of pairwise relatednesses through pedigree information improved the accuracy of estimates. In that case, the amount of father‐related offspring in the sibling design is the most critical. Overall, we showed that the method using both one‐generation pedigree and average relatedness coefficients was the most robust to various ecological scenarios. 相似文献
18.
The use of alternative reproductive tactics (ARTs) is widespread in animals. Males of some species may change tactics depending on age, body condition and social environment. Many bat species are polygynous where a fraction of males only have access to fertile females. For polygynous bats, knowledge of the reproductive success of males using different ARTs is scarce, and it remains unclear how age of males is related to switching decisions between social statuses. We studied a large captive population of Carollia perspicillata, where males are either harem holders, bachelors or peripheral males. Using a multistate procedure, we modelled the age‐related switches in reproductive tactics and in survival probability. From the model, we calculated the reproductive success and the frequencies of males displaying different reproductive tactics. As in mammals, the switch between social statuses is often related to age, we predicted that the transition probability of bachelor and peripheral males to harem status would increase with age. We show, however, that social status transition towards a harem holding position was not related to age. Reproductive success changed with age and social status. Harem males had a significantly higher reproductive success than bachelor males except between a short period from 3.8 to 4.4 years of age where success was similar, and a significantly higher reproductive success than peripheral males between 2.6 and 4.4 years of age. Harem males showed a clear decrease in the probability of maintaining social status with age, which suggests that senescence reduces resource holding potential. 相似文献
19.
Todd R. Seamons Lorenz Hauser Kerry A. Naish Thomas P. Quinn 《Evolutionary Applications》2012,5(7):705-719
Two strategies have been proposed to avoid negative genetic effects of artificially propagated individuals on wild populations: (i) integration of wild and captive populations to minimize domestication selection and (ii) segregation of released individuals from the wild population to minimize interbreeding. We tested the efficacy of the strategy of segregation by divergent life history in a steelhead trout, Oncorhynchus mykiss, system, where hatchery fish were selected to spawn months earlier than the indigenous wild population. The proportion of wild ancestry smolts and adults declined by 10–20% over the three generations since the hatchery program began. Up to 80% of the naturally produced steelhead in any given year were hatchery/wild hybrids. Regression model selection analysis showed that the proportion of hatchery ancestry smolts was lower in years when stream discharge was high, suggesting a negative effect of flow on reproductive success of early‐spawning hatchery fish. Furthermore, proportions of hybrid smolts and adults were higher in years when the number of naturally spawning hatchery‐produced adults was higher. Divergent life history failed to prevent interbreeding when physical isolation was ineffective, an inadequacy that is likely to prevail in many other situations. 相似文献