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F W Allendorf

Publications and source records attributed to F W Allendorf.

At least 19 recordsLinked to original sources
PubMed2004

Genetic basis of variation in morphological and life-history traits of a wild population of pink salmon.

Understanding the genetic basis of phenotypic variation is essential for predicting the direction and rate of phenotypic evolution. We estimated heritabilities and genetic correlations of morphological (fork length, pectoral and pelvic fin ray counts, and gill arch raker counts) and life-history (egg number and individual egg weight) traits of pink salmon (Oncorhynchus gorbuscha) from Likes Creek, Alaska, in order to characterize the genetic basis of phenotypic variation in this species. Families were created from wild-caught adults, raised to the fry stage in the lab, released into the wild, and caught as returning adults and assigned to families using microsatellite loci and a growth hormone locus. Morphological traits were all moderately to highly heritable, but egg number and egg weight were not heritable, suggesting that past selection has eliminated additive genetic variation in egg number and egg weight or that there is high environmental variance in these traits. Genetic correlations were similar for nonadjacent morphological traits and adjacent traits. Genetic correlations predicted phenotypic correlations fairly accurately, but some pairs of traits with low genetic correlations had high phenotypic correlations, and vice versa, emphasizing the need to use caution when using phenotypic correlations as indices of genetic correlations. This is one of only a handful of studies to estimate heritabilities and genetic correlations for a wild population.

Animals↗
PubMed2004

Linkage disequilibrium between the pseudoautosomal PEPB-1 locus and the sex-determining region of chinook salmon.

Allele frequency differences between sexes and an excess of heterozygotes in males had suggested that the PEPB-1 locus is sex-linked in chinook salmon (Oncorhynchus tshawytscha). We here estimate less than 1% recombination between PEPB-1 and a growth hormone pseudogene known to be in the sex-determining region (SEX) in 374 progeny from eight experimental matings. We present modified maximum likelihood methods for estimating haplotype frequencies from population samples at a sex-linked locus in which functional alleles occur on both the X and Y chromosomes (pseudoautosomal loci). We find nearly complete linkage disequilibrium between PEPB-1 and SEX in 20 population samples from the Puget Sound region of Washington and southern British Columbia. However, allele frequencies at PEPB-1 were similar in males and females in 35 population samples from the coast of Washington and the Columbia River basin. Pseudoautosomal regions have been described in a broad taxonomic array of vertebrates and invertebrates, and they are likely candidate regions to find genes associated with differences in life history, morphology, or behavior between males and females.

Animals↗
PubMed2004

Founding events influence genetic population structure of sockeye salmon (Oncorhynchus nerka) in Lake Clark, Alaska.

Bottlenecks can have lasting effects on genetic population structure that obscure patterns of contemporary gene flow and drift. Sockeye salmon are vulnerable to bottleneck effects because they are a highly structured species with excellent colonizing abilities and often occupy geologically young habitats. We describe genetic divergence among and genetic variation within spawning populations of sockeye salmon throughout the Lake Clark area of Alaska. Fin tissue was collected from sockeye salmon representing 15 spawning populations of Lake Clark, Six-mile Lake, and Lake Iliamna. Allele frequencies differed significantly at 11 microsatellite loci in 96 of 105 pairwise population comparisons. Pairwise estimates of FST ranged from zero to 0.089. Six-mile Lake and Lake Clark populations have historically been grouped together for management purposes and are geographically proximate. However, Six-mile Lake populations are genetically similar to Lake Iliamna populations and are divergent from Lake Clark populations. The reduced allelic diversity and strong divergence of Lake Clark populations relative to Six-mile Lake and Lake Iliamna populations suggest a bottleneck associated with the colonization of Lake Clark by sockeye salmon. Geographic distance and spawning habitat differences apparently do not contribute to isolation and divergence among populations. However, temporal isolation based on spawning time and founder effects associated with ongoing glacial retreat and colonization of new spawning habitats contribute to the genetic population structure of Lake Clark sockeye salmon. Nonequilibrium conditions and the strong influence of genetic drift caution against using estimates of divergence to estimate gene flow among populations of Lake Clark sockeye salmon.

Alaska↗
PubMed2003

A consolidated linkage map for rainbow trout (Oncorhynchus mykiss).

Androgenetic doubled haploid progeny produced from a cross between the Oregon State University and Arlee clonal rainbow trout (Oncorhynchus mykiss) lines, used for a previous published rainbow trout map, were used to update the map with the addition of more amplified fragment length polymorphic (AFLP) markers, microsatellites, type I and allozyme markers. We have added more than 900 markers, bringing the total number to 1359 genetic markers and the sex phenotype including 799 EcoRI AFLPs, 174 PstI AFLPs, 226 microsatellites, 72 VNTR, 38 SINE markers, 29 known genes, 12 minisatellites, five RAPDs, and four allozymes. Thirty major linkage groups were identified. Synteny of linkage groups in our map with the outcrossed microsatellite map has been established for all except one linkage group in this doubled haploid cross. Putative homeologous relationships among linkage groups, resulting from the autotetraploid nature of the salmonid genome, have been revealed based on the placement of duplicated microsatellites and type I loci.

Animals↗
PubMed2003

Landscape location affects genetic variation of Canada lynx (Lynx canadensis).

The effect of a population's location on the landscape on genetic variation has been of interest to population genetics for more than half a century. However, most studies do not consider broadscale biogeography when interpreting genetic data. In this study, we propose an operational definition of a peripheral population, and then explore whether peripheral populations of Canada lynx (Lynx canadensis) have less genetic variation than core populations at nine microsatellite loci. We show that peripheral populations of lynx have fewer mean numbers of alleles per population and lower expected heterozygosity. This is surprising, given the lynx's capacity to move long distances, but can be explained by the fact that peripheral populations often have smaller population sizes, limited opportunities for genetic exchange and may be disproportionately affected by ebbs and flows of species' geographical range.

Alleles↗
PubMed2002

Insights into recently fragmented vole populations from combined genetic and demographic data.

We combined demographic and genetic data to evaluate the effects of habitat fragmentation on the population structure of the California red-backed vole (Clethrionomys californicus). We analysed variation in the mitochondrial DNA (mtDNA) control region and five nuclear microsatellite loci in small samples collected from two forest fragments and an unfragmented control site in 1990-91. We intensively sampled the same forest fragments and two different control sites in 1998 and 1999. Vole abundances fluctuated greatly at sizes below 50 individuals per fragment. Fragment populations had significantly lower mtDNA allelic diversity than controls, but not nuclear heterozygosity or numbers of alleles. The use of only trapping and/or mtDNA marker data would imply that fragment populations are at least partially isolated and vulnerable to inbreeding depression. In contrast, the abundance estimates combined with microsatellite data show that small fragment populations must be linked to nearby forests by high rates of migration. These results provide evidence for the usefulness of combining genetic and demographic data to understand nonequilibrium population structure in recently fragmented habitats.

Animals↗
PubMed2001

Heterozygosity-fitness correlations in rainbow trout: effects of allozyme loci or associative overdominance?

Previous studies with rainbow trout (Oncorhynchus mykiss) have shown that increased heterozygosity at allozyme loci is correlated with several phenotypic traits associated with fitness. We expected to find a similar effect of heterozygosity at other nuclear loci if these associations are due to loci in linkage disequilibrium with the allozyme loci (i.e., associative overdominance), rather than the allozymes themselves. We examined the association between multiple locus heterozygosity and condition factor at 10 allozyme and 10 microsatellite loci. Individuals that were more heterozygous at allozyme loci had significantly greater condition factor in two hatchery cohorts of rainbow trout (1996 P = 0.006; 1997 P < 0.001). In contrast, there was no evidence at microsatellite loci that increased heterozygosity was associated with greater condition factor. Our results suggest that the observed relationship between heterozygosity at allozyme loci and condition factor in rainbow trout appears to be due to the allozyme loci themselves, rather than associative overdominance. We cannot, however, rule out that differences in the mutation process between allozymes and microsatellites may be responsible for these observations. Regardless of the underlying mechanism, these results support the view that allozymes and microsatellites are differentially affected by natural selection.

Animals↗
PubMed2000

Concordance of genetic divergence among sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers.

We examined genetic variation at 21 polymorphic allozyme loci, 15 nuclear DNA loci, and mitochondrial DNA in four spawning populations of sockeye salmon (Oncorhynchus nerka) from Cook Inlet, Alaska, to test for differences in the patterns of divergence among different types of markers. We were specifically interested in testing the suggestion that natural selection at allozyme loci compromises the effectiveness of these markers for describing the amount and patterns of gene flow among populations. We found concordance among markers in the amount of genetic variation within and among populations, with the striking exception of one allozyme locus (sAH), which exhibited more than three times the amount of among-population differentiation as other loci. A consideration of reports of discordance between allozymes and other loci indicates that these differences usually result from one or two exceptional loci. We conclude that it is important to examine many loci when estimating genetic differentiation to infer historical amounts of gene flow and patterns of genetic exchange among populations. It is less important whether those loci are allozymes or nuclear DNA markers.

Animals↗
PubMed2000

Gene-centromere mapping of 312 loci in pink salmon by half-tetrad analysis.

We estimated recombination rates between 312 loci and their centromeres in gynogenetic diploid pink salmon (Oncorhynchus gorbuscha) that we produced by initiating development with irradiated sperm and blocking the maternal second meiotic division. Amplified fragment length polymorphisms (AFLPs) were significantly more centromeric than loci identified by three other techniques (allozymes, microsatellites, and PCR using primer sequences from interspersed nuclear elements). The near absence of AFLPs in distal regions could limit their utility in constructing linkage maps. A large proportion of loci had frequency of second division segregation (y) values approaching 1.0, indicating near complete crossover interference on many chromosome arms. As predicted from models of chromosomal evolution in salmonids based upon results with allozyme loci, all duplicated microsatellite loci that shared alleles (isoloci) had y values of nearly 1.0.

Animals↗
PubMed1999

Small effective population size in the long-toed salamander.

The effective population sizes (Ne) of six populations of the long-toed salamander (Ambystoma macrodactylum) from Montana and Idaho, USA were estimated from allozyme data from samples collected in 1978, 1996 and 1997 using the temporal allele frequency method. Five of the six estimates ranged from 23 to 207 (mean = 123 +/- 79); one estimate was indistinguishable from infinity. In order to infer the actual Ne of salamander populations, we compared the frequency distribution of our observed Ne estimates with distributions obtained from simulated populations of known Ne. Our observed Ne estimate distribution was consistent with distributions from simulated populations with Ne values of 10, 25, and 50, suggesting an actual Ne for each of the six salamander populations of less than 100. This Ne estimate agrees with most other Ne estimates for amphibians. We conclude by discussing the conservation implications of small Ne values in amphibians in the context of increasing isolation of populations due to habitat fragmentation.

Alleles↗
PubMed1998

Usefulness of molecular markers for detecting population bottlenecks via monitoring genetic change.

It is important to detect population bottlenecks in threatened and managed species because bottlenecks can increase the risk of population extinction. Early detection is critical and can be facilitated by statistically powerful monitoring programs for detecting bottleneck-induced genetic change. We used Monte Carlo computer simulations to evaluate the power of the following tests for detecting genetic changes caused by a severe reduction in a population's effective size (Ne): a test for loss of heterozygosity, two tests for loss of alleles, two tests for change in the distribution of allele frequencies, and a test for small Ne based on variance in allele frequencies (the 'variance test'). The variance test was most powerful; it provided an 85% probability of detecting a bottleneck of size Ne = 10 when monitoring five microsatellite loci and sampling 30 individuals both before and one generation after the bottleneck. The variance test was almost 10-times more powerful than a commonly used test for loss of heterozygosity, and it allowed for detection of bottlenecks before 5% of a population's heterozygosity had been lost. The second most powerful tests were generally the tests for loss of alleles. However, these tests had reduced power for detecting genetic bottlenecks caused by skewed sex ratios. We provide guidelines for the number of loci and individuals needed to achieve high-power tests when monitoring via the variance test. We also illustrate how the variance test performs when monitoring loci that have widely different allele frequency distributions as observed in five wild populations of mountain sheep (Ovis canadensis).

Alleles↗
PubMed1997

Secondary tetrasomic segregation of MDH-B and preferential pairing of homeologues in rainbow trout.

We examined the inheritance of allelic variation at an isozyme locus, MDH-B, duplicated by ancestral polyploidy in salmonid fishes. We detected only disomic segregation in females. Segregation ratios in males were best explained by a mixture of disomic and tetrasomic inheritance. We propose a two-stage model of pairing in male meiosis in which, first, homologous chromosomes pair and recombine in the proximal region of the chromosome. Next, homeologous chromosomes pair and recombine distally. We suggest that this type of tetrasomic inheritance in which centromeres segregate disomically should be referred to as "secondary tetrasomy" to distinguish it from tetrasomy involving entire chromosomes (i.e., "primary tetrasomy"). Differences in segregation ratios between males indicate differences between individuals in the amount of recombination between homeologous chromosomes. We also consider the implication of these results for estimation of allele frequencies at duplicated loci in salmonid populations.

Alleles↗
PubMed1995

Microsatellite evolution in congeneric mammals: domestic and bighorn sheep.

We compared genotypes at eight (AC)n microsatellite loci in domestic sheep (Ovis aries) and wild Rocky Mountain bighorn sheep (O. canadensis). The domestic sheep had greater genetic variation, higher allele-size variances, and larger allele sizes than the wild sheep. Accumulating evidence from higher taxonomic comparisons shows that these parameters are biased if microsatellite loci are selected in one taxon and used in another. Our results demonstrate similar biases between congeneric species. We compared standard measures of genetic variation, differentiation, and distance within and between species (H, D, FST) to newer measures based on allele-size variance (SW, SB, RST). The size-based distances better detected species-level divergence, but standard measures better distinguished allopatric populations. Empirical calibration of these measures at the subspecies level is needed to establish their useful ranges.

Alleles↗
PubMed1994

One of two growth hormone genes in coho salmon is sex-linked.

Salmonid fishes have two growth hormone genes resulting from their polyploid ancestry. We used the polymerase chain reaction to examine genetic variation in the third intron (C) of both of these genes in coho salmon (Oncorhynchus kisutch). A polymorphism in the length of intron C in GH-1 is due to a variable number of copies of a 31-nt repeat that is absent from GH-1 of the closely related chinook salmon (Oncorhynchus tshawytscha) and rainbow trout (Oncorhynchus mykiss). Thus, this tandem repeat sequence has become established in the genome of coho salmon since the separation of this species from its closest relatives. All male coho salmon examined have an allele at the second growth hormone gene, GH-2, that is not found in females. GH-2 is thus on the sex chromosome and there is no recombination between GH-2 and the sex-determining locus (SEX). Sequences of intron C indicate much greater divergence between the X chromosome-specific allele and the Y chromosome-specific allele within coho salmon than between the X chromosome-specific alleles of coho and the closely related chinook salmon. Thus, absence of recombination between GH-2 and SEX apparently predates separation of these two species.

Alleles↗
PubMed1994

Sex-linkage of two enzyme loci in Oncorhyncus mykiss (rainbow trout)

We report the first sex-linked loci in Oncorhynchus mykiss (rainbow trout). Previous cytological and breeding experiments have demonstrated an XX/XY sex determining system in this and other salmonid species. Joint segregation data from fathers indicated an average of 8.1 per cent recombination between HEX-2 and the sex determining locus (SEX). The average recombination between HEX-2 and sSOD-1 in fathers was 26.8 per cent. No evidence of non-random segregation of HEX-2 and sSOD-1 was found in mothers; this difference in recombination rates between males and females is concordant with previous studies with rainbow trout and other salmonid species. These results also suggest the possibility that proper chromosomal pairing and segregation in salmonid males does not require a crossover event. Unlike the extreme XX/XY heteromorphy in mammals, functional alleles for HEX-2 and sSOD-1 occur on both the X and Y chromosomes. Significant non-random associations (i.e. gametic disequilibrium) occur between genotypes at HEX-2 and SEX in the hatchery population used for the inheritance study. This gametic disequilibrium has resulted in large changes in allele frequency at HEX-2 from one generation to the next and an excess of heterozygotes in comparison to expected binomial (i.e. Hardy-Weinberg) proportions.

Animals↗
PubMed1991

Genetic analysis of androgenetic rainbow trout.

We analyzed a number of genetic characteristics in androgenetic rainbow trout (Oncorhynchus mykiss) and their progeny. The androgenetic progeny of individual androgenetic males appeared genetically identical to each other based on eight enzyme loci. Their viability was no higher than that of androgenetic progeny of outbred males. Homozygous androgenetic female rainbow trout produced very poor quality eggs. When common eggs and sperm from outbred individuals were used to produce androgenetic and gynogenetic progeny, the yield of gynogenetic progeny was higher but some were heterozygous at protein loci, while no androgenetic progeny were heterozygous. Some androgenetic diploid rainbow trout were successfully produced from cryopreserved sperm. The progeny of some androgenetic males crossed to normal females were virtually all males, while the progeny of other males were virtually all females. This suggests that both XX and YY androgenetic individuals may develop as males. Androgenesis is likely to be useful for generating homozygous clones for research and for recovering strains from cryopreserved sperm.

Animals↗
PubMed1988

Developmental rate and viability of rainbow trout with a null allele at a lactate dehydrogenase locus.

We show that a previously described isozyme polymorphism in rainbow trout (Salmo gairdneri) is the result of an enzymatically inactive (i.e., null) allele (n). Ldh3 null homozygotes (n/n) and heterozygotes (100/n) have reductions of about 20 and 12% in total lactate dehydrogenase (LDH) activity at hatching, respectively. As juveniles, (100/n) fish have reductions in LDH activity of 15, 37, and 21% in brain, heart, and white muscle, respectively. Embryos with different Ldh3 phenotypes from 11 families do not differ significantly in either survival or hatching time. However, a second measure of developmental rate, the amount of malate dehydrogenase (MDH) and phosphoglucomutase (PGM) activity in 33-day-old embryos, suggests that (100/n) embryos develop more slowly than (100/100) embryos. In three of four families examined, (100/n) embryos have significantly lower amounts of total MDH activity (8-10%). In one of these, (100/n) embryos also have significantly lower total PGM activity (15%). These data suggest that the reduction in total LDH activity is associated with small but detectable delays in developmental rate but nondetectable differences in survival to hatching.

Aging↗