The interaction of the xid and me genes

The murine "motheaten" (me) mutation has been bred onto the NFS background and combined with the X-linked immunodeficiency (xid) mutation to investigate the effect of the xid-induced B cell maturational block on the widespread immune dysfunction, high levels of autoantibodies, and early mortality found in the motheaten mice. The xid markedly reduced spontaneous IgM secretion by spleen cells, serum IgM, anti-ssDNA antibodies, anti-bromelain-treated-erythrocyte antibodies, and T cell binding (but not thymocytotoxic) antibodies; however, neither phenotype nor mortality was affected, suggesting that other factors are responsible for early death. Marked expansion of the Ly-1+ B cell pool was prevented by xid in the motheaten mouse leaving only a very small population of sIgM-positive B cells. This failure of non-Ly-1+ B cell development in me/me X xid mice suggests that me/me leads to inhibition of non-Ly-1+ B cells and preferential expansion of Ly-1+ B cells in motheaten mice, perhaps as a result of their high levels of maturation and activation factors.     

ANNUAL DIFFERENCES IN FEMALE REPRODUCTIVE SUCCESS AFFECT SPATIAL AND COHORT-SPECIFIC GENOTYPIC HETEROGENEITY IN PAINTED TURTLES

Long-term ecological data were used to evaluate the relative importance of movements, breeding structure, and reproductive ecological factors to the degree of spatial and age-specific variation in genetic characteristics of painted turtles (Chrysemys picta) on the E. S. George Reserve in southeastern Michigan. Estimates of the degree of spatial genetic structuring were based on the proportion of total genotypic variance partitioned within and between subpopulations (inferred from hierarchical F-statistics based on variation at 18 protein loci), and in terms of gene correlations (co-ancestry among individuals derived from reproductive data on full-sib families of females nesting at specific nesting areas). Little variation in allele frequency was observed among turtles from different marshes (F_mt = 0.003), though significant variation was observed among turtles from different nesting areas associated with each marsh (F_nm = 0.046). Gene correlations among individuals within nesting areas varied greatly over years (0.032-0.171; mean = 0.069) and were negatively correlated to the proportion of females that successfully nested during each year. General concordance between independent estimates of genotypic correlations (i.e., F_nm derived from protein electrophoretic variation vs. mean co-ancestry) suggests that allozyme data, when collected over spatial scales consistent with species behavioral characteristics and reproductive ecology, may accurately reflect the apportionment of gene diversity within and among subpopulations. The magnitude and patterning of allelic variation among nesting areas and individuals appears to be primarily a function of gametic correlations among members of full-sib families, irrespective of the degree of gene flow or female nesting-site fidelity. Comparisons of genetic characteristics among 11 cohorts (1974-1984) revealed that heterozygosity (H) and inbreeding coefficients (F) varied greatly. Cohort estimates of H and F were correlated to female nesting success and to estimates of co-ancestry for the same years. Results clearly reflect the concomitant importance of ecological factors (principally the proportion of the female population that successfully produce offspring during each year) in determining the magnitude and patterning of gene correlations within and among groups, and to the genotypic composition of offspring born during each year.     

Sampling Issues Affecting Accuracy of Likelihood-based Classification Using Genetical Data

We demonstrate the effectiveness of a genetic algorithm for discovering multi-locus combinations that provide accurate individual assignment decisions and estimates of mixture composition based on likelihood classification. Using simulated data representing different levels of inter-population differentiation (F_st～ 0.01 and 0.10), genetic diversities (four or eight alleles per locus), and population sizes (20, 40, 100 individuals in baseline populations), we show that subsets of loci can be identified that provide comparable levels of accuracy in classification decisions relative to entire multi-locus data sets, where 5, 10, or 20 loci were considered. Microsatellite data sets from hatchery strains of lake trout, Salvelinus namaycush, representing a comparable range of inter-population levels of differentiation in allele frequencies confirmed simulation results. For both simulated and empirical data sets, assignment accuracy was achieved using fewer loci (e.g., three or four loci out of eight for empirical lake trout studies). Simulation results were used to investigate properties of the ‘leave-one-out’ (L1O) method for estimating assignment error rates. Accuracy of population assignments based on L1O methods should be viewed with caution under certain conditions, particularly when baseline population sample sizes are low (<50).     

RAPTURE (RAD capture) panel facilitates analyses characterizing sea lamprey reproductive ecology and movement dynamics

Genomic tools are lacking for invasive and native populations of sea lamprey (Petromyzon marinus). Our objective was to discover single nucleotide polymorphism (SNP) loci to conduct pedigree analyses to quantify reproductive contributions of adult sea lampreys and dispersion of sibling larval sea lampreys of different ages in Great Lakes tributaries. Additional applications of data were explored using additional geographically expansive samples. We used restriction site‐associated DNA sequencing (RAD‐Seq) to discover genetic variation in Duffins Creek (DC), Ontario, Canada, and the St. Clair River (SCR), Michigan, USA. We subsequently developed RAD capture baits to genotype 3,446 RAD loci that contained 11,970 SNPs. Based on RAD capture assays, estimates of variance in SNP allele frequency among five Great Lakes tributary populations (mean F_ST 0.008; range 0.00–0.018) were concordant with previous microsatellite‐based studies; however, outlier loci were identified that contributed substantially to spatial population genetic structure. At finer scales within streams, simulations indicated that accuracy in genetic pedigree reconstruction was high when 200 or 500 independent loci were used, even in situations of high spawner abundance (e.g., 1,000 adults). Based on empirical collections of larval sea lamprey genotypes, we found that age‐1 and age‐2 families of full and half‐siblings were widely but nonrandomly distributed within stream reaches sampled. Using the genomic scale set of SNP loci developed in this study, biologists can rapidly genotype sea lamprey in non‐native and native ranges to investigate questions pertaining to population structuring and reproductive ecology at previously unattainable scales.     

Environmentally Enriched Male Mink Gain More Copulations than Stereotypic,Barren-Reared Competitors

Wild carnivores in zoos, conservation breeding centres, and farms commonly live in relatively small, unstimulating enclosures. Under these captive conditions, in a range of species including giant pandas, black-footed ferrets, and European mink, male reproductive abilities are often poor. Such problems have long been hypothesized to be caused by these animals'' housing conditions. We show for the first time that rearing under welfare-improving (i.e., highly valued and stress-reducing) environmental enrichments enhances male carnivores'' copulatory performance: in mate choice competitions, enriched male American mink (Neovison vison) mated more often than non-enriched males. We screened for several potential mediators of this effect. First was physiological stress and its impact on reproductive physiology; second, stress-mediated changes in morphology and variables related to immunocompetence that could influence male attractiveness; and third, behavioural changes likely to affect social competence, particularly autistic-like excessive routine and repetition (‘perseveration’) as is reflected in the stereotypies common in captive animals. Consistent with physiological stress, excreted steroid metabolites revealed that non-enriched males had higher cortisol levels and lower androgen levels than enriched conspecifics. Their os penises (bacula) also tended to be less developed. Consistent with reduced attractiveness, non-enriched males were lighter, with comparatively small spleens and a trend to greater fluctuating asymmetry. Consistent with impaired social competence, non-enriched males performed more stereotypic behaviour (e.g., pacing) in their home cages. Of all these effects, the only significant predictor of copulation number was stereotypy (a trend suggesting that low bodyweights may also be influential): highly stereotypic males gained the fewest copulations. The neurophysiological changes underlying stereotypy thus handicap males sexually. We hypothesise that such males are abnormally perseverative when interacting with females. Investigating similar problems in other taxa would be worthwhile, since many vertebrates, wild and domestic, live in conditions that cause stereotypic behaviour and/or impair neurological development.     

Post‐hatch dispersal of lake sturgeon (Acipenser fulvescens,Rafinesque, 1817) yolk‐sac larvae in relation to substrate in an artificial stream

Knowledge of the effects of environment and genotype on behavior during early ontogenetic stages of many fish species including lake sturgeon (Acipenser fulvescens) is generally lacking. Understanding these effects is particularly important at a time when human activities are fundamentally altering habitats and seasonal and diel physical and biotic stream features. Artificial stream channels were used in a controlled experiment to quantify lake sturgeon yolk‐sac larvae dispersal distance and stream substrate preference from different females (N = 2) whose eggs were incubated at different temperatures (10 and 18°C) that simulated stream conditions during early and late spawning and incubation periods in the Black River, Michigan. Data revealed that yolk‐sac larvae exhibited considerable variability in dispersal distance as a function of family (genotype), temperature experienced during previous (embryonic) ontogenetic stages, and environmental ‘grain’. Yolk‐sac larvae dispersal distance varied as a function of the juxtaposition of substrate to location of egg hatch. Lake sturgeon yolk‐sac larvae dispersed from mesh screens attached to bricks and settled exclusively in gravel substrate. Dispersal distance also varied as a function of family and egg incubation temperatures, reflecting differences in offspring body size and levels of endogenous yolk reserves (yolk sac area) at hatch. Expression of plasticity in dispersal behavior may be particularly important to individual survival and population levels of recruitment contingent upon the location, size, and degree of fragmentation of suitable (gravel) habitats between adult spawning and yolk‐sac larvae rearing areas.     

18S rRNA metabarcoding diet analysis of a predatory fish community across seasonal changes in prey availability

Predator–prey relationships are important ecological interactions, affecting biotic community composition and energy flow through a system, and are of interest to ecologists and managers. Morphological diet analysis has been the primary method used to quantify the diets of predators, but emerging molecular techniques using genetic data can provide more accurate estimates of relative diet composition. This study used sequences from the 18S V9 rRNA barcoding region to identify prey items in the gastrointestinal (GI) tracts of predatory fishes. Predator GI samples were taken from the Black River, Cheboygan Co., MI, USA (n = 367 samples, 12 predator species) during periods of high prey availability, including the larval stage of regionally threatened lake sturgeon (Acipenser fulvescens Rafinesque 1817) in late May/early June of 2015 and of relatively lower prey availability in early July of 2015. DNA was extracted and sequenced from 355 samples (96.7%), and prey DNA was identified in 286 of the 355 samples (80.6%). Prey were grouped into 33 ecologically significant taxonomic groups based on the lowest taxonomic level sequences that could be identified using sequences available on GenBank. Changes in the makeup of diet composition, dietary overlap, and predator preference were analyzed comparing the periods of high and low prey abundance. Some predator species exhibited significant seasonal changes in diet composition. Dietary overlap was slightly but significantly higher during the period of high prey abundance; however, there was little change in predator preference. This suggests that change in prey availability was the driving factor in changing predator diet composition and dietary overlap. This study demonstrates the utility of molecular diet analysis and how temporal variability in community composition adds complexity to predator–prey interactions.