Assortative mating but no evidence of genetic divergence in a species characterized by a trophic polymorphism.

Disruptive selection is a process that can result in multiple subgroups within a population, which is referred to as diversification. Foraging-related diversification has been described in many taxa, but many questions remain about the contribution of such diversification to reproductive isolation and potentially sympatric speciation. Here, we use stable isotope analysis of diet and morphological analysis of body shape to examine phenotypic divergence between littoral and pelagic foraging ecomorphs in a population of pumpkinseed sunfish (Lepomis gibbosus). We then examine reproductive isolation between ecomorphs by comparing the isotopic compositions of nesting males to eggs from their nests (a proxy for maternal diet) and use nine microsatellite loci to examine genetic divergence between ecomorphs. Our data support the presence of distinct foraging ecomorphs in this population and indicate that there is significant positive assortative mating based on diet. We did not find evidence of genetic divergence between ecomorphs, however, indicating that isolation is either relatively recent or is not strong enough to result in genetic divergence at the microsatellite loci. Based on our findings, pumpkinseed sunfish represent a system in which to further explore the mechanisms by which natural and sexual selection contribute to diversification, prior to the occurrence of sympatric speciation.

Predictability of multispecies competitive interactions in three populations of Atlantic salmon Salmo salar.

Juvenile Atlantic salmon Salmo salar from three allopatric populations (LaHave, Sebago and Saint-Jean) were placed into artificial streams with combinations of four non-native salmonids: brown trout Salmo trutta, rainbow trout Oncorhynchus mykiss, Chinook salmon Oncorhynchus tshawytscha and coho salmon Oncorhynchus kisutch. Non-additive effects, as evidenced by lower performance than predicted from weighted summed two-species competition trials, were detected for S. salar fork length (LF ) and mass, but not for survival, condition factor or riffle use. These data support emerging theory on niche overlap and species richness as factors that can lead to non-additive competition effects.

Diet and cannibalism in plainfin midshipman Porichthys notatus.

The macroscopic and microscopic diversity of potential food items available in the nests of plainfin midshipman Porichthys notatus were quantified and compared with items that were found in the stomach and intestine (digestive tract) of the guarding males. In this species, males occur as one of two possible reproductive morphs: guarder males that care for young and sneaker males that parasitize the courtship and care of guarder males. Although it was predicted that guarder males would have fewer feeding opportunities due to their confinement to the nest, they in fact had more food items in their digestive tracts than did sneaker males and females. Date in the breeding season (a proxy of care duration) and body condition were not correlated with the amount of food consumed by guarder males. The main type of food consumed was P. notatus embryos; 69% of all guarder males sampled had cannibalized offspring. By comparing the diet of both sexes and tactics, this study sheds light on some of the strategies designed to cope with the costs of providing parental care.

Genetic architecture of survival and fitness-related traits in two populations of Atlantic salmon.

The additive genetic effects of traits can be used to predict evolutionary trajectories, such as responses to selection. Non-additive genetic and maternal environmental effects can also change evolutionary trajectories and influence phenotypes, but these effects have received less attention by researchers. We partitioned the phenotypic variance of survival and fitness-related traits into additive genetic, non-additive genetic and maternal environmental effects using a full-factorial breeding design within two allopatric populations of Atlantic salmon (Salmo salar). Maternal environmental effects were large at early life stages, but decreased during development, with non-additive genetic effects being most significant at later juvenile stages (alevin and fry). Non-additive genetic effects were also, on average, larger than additive genetic effects. The populations, generally, did not differ in the trait values or inferred genetic architecture of the traits. Any differences between the populations for trait values could be explained by maternal environmental effects. We discuss whether the similarities in architectures of these populations is the result of natural selection across a common juvenile environment.

Quantitative genetic and translocation experiments reveal genotype-by-environment effects on juvenile life-history traits in two populations of Chinook salmon (Oncorhynchus tshawytscha).

Understanding the genetic architecture of phenotypic plasticity is required to assess how populations might respond to heterogeneous or changing environments. Although several studies have examined population-level patterns in environmental heterogeneity and plasticity, few studies have examined individual-level variation in plasticity. Here, we use the North Carolina II breeding design and translocation experiments between two populations of Chinook salmon to detail the genetic architecture and plasticity of offspring survival and growth. We followed the survival of 50,800 offspring through the larval stage and used parentage analysis to examine survival and growth through freshwater rearing. In one population, we found that additive genetic, nonadditive genetic and maternal effects explained 25%, 34% and 55% of the variance in larvae survival, respectively. In the second population, these effects explained 0%, 24% and 61% of the variance in larvae survival. In contrast, fry survival was regulated primarily by additive genetic effects, which indicates a shift from maternal to genetic effects as development proceeds. Fry growth also showed strong additive genetic effects. Translocations between populations revealed that offspring survival and growth varied between environments, the degree of which differed among families. These results indicate genetic differences among individuals in their degree of plasticity and consequently their ability to respond to environmental variation.

Selection at the MHC class IIB locus across guppy (Poecilia reticulata) populations.

The highly diverse genes of the major histocompatibility complex (MHC) are important in the adaptive immune system and are expected to be under selection from pathogens. Thus, the MHC genes provide an exceptional opportunity to investigate patterns of selection within and across populations. In this study, we analyzed genetic variation at the MHC class IIB gene and six microsatellite loci across 10 populations of guppies (Poecilia reticulata) in the northern range of Trinidad. We found a high level of diversity at the MHC, with a total of 43 alleles in 142 individuals. At the population level, we found that neutral evolution could not fully account for the variability found at the MHC. Instead, we found that MHC F(ST) statistics were lower than F(ST) derived from the microsatellite loci; 33 of 45 population pairwise estimates for the MHC were significantly lower than those for the microsatellite loci, and MHC F(ST) estimates were consistently lower than those predicted by a coalescent model of neutral evolution. These results suggest a similar selection acting across populations, and we discuss the potential roles of directional and balancing selection. At the sequence level, we found evidence for both positive and purifying selection. Furthermore, positive selection was detected within and adjacent to the putative peptide-binding region (PBR) of the MHC. Surprisingly, we also found a purifying selection at two sites within the putative PBR. Overall, our data provide evidence for selection for functional diversity at the MHC class IIB gene at both the population and nucleotide levels of guppy populations.

MHC genetic structure and divergence across populations of Chinook salmon (Oncorhynchus tshawytscha).

The major histocompatibility complex (MHC) is thought to be under strong selection pressure because of its integral role in pathogen recognition. Consequently, patterns of MHC genetic variation should reflect selection pressures across the landscape. We examined genetic variation and population genetic structure at the MHC class I-A1 and class II-B1 exons in five Chinook salmon (Oncorhynchus tshawytscha) populations from two geographic regions in British Columbia, Canada. We then compared estimates of population structure at the MHC genes with neutral estimates based on microsatellites to examine the potential for local adaptation at the MHC. Chinook salmon are in decline throughout much of their native range and understanding the degree of local adaptation exhibited by the MHC may be important in conservation planning. Comparisons among populations yielded higher G'(ST) estimates for the MHC class I than expected under neutrality based on the microsatellites. In contrast, the MHC class II tended to exhibit lower G'(ST) values than did the microsatellites. These results suggest that across populations unique selection pressures are driving allele frequency differences at the MHC class I but that the MHC class II may be the subject of homogenizing selection. Rates of nonsynonymous versus synonymous substitutions found in codons associated within the MHC class I and II peptide-binding regions provided strong evidence of positive selection. Together, these results support the hypothesis that selection is influencing genetic variation at the MHC, but suggest that selection pressures may vary at the two classes of loci both at the sequence and population levels.

Dietary carotenoid levels affect carotenoid and retinoid allocation in female Chinook salmon Oncorhynchus tshawytscha.

This study examined the effect of dietary carotenoid availability on carotenoid and retinoid concentrations in the flesh, plasma, skin and eggs of female Chinook salmon Oncorhynchus tshawytscha. Carotenoid concentrations in all tissues were closely related to dietary availability. Early in the breeding season, carotenoids were stored primarily in the muscle, with a flesh carotenoid concentration of 9.9 microg g(-1) in fish fed a high carotenoid diet compared with 1.9 microg g(-1) in fish fed a low carotenoid diet. During the breeding season, carotenoid reserves were mobilized predominantly to the eggs and also to the skin. By the end of the breeding season, carotenoid concentrations in the eggs were 17.9 microg g(-1) in fish fed a high carotenoid diet and 3.9 microg g(-1) in fish fed a low carotenoid diet. Conversely, egg retinoid concentrations were only c. 20% lower in fish fed a low v. high carotenoid diet, which suggests that retinoid concentrations were not limited by the availability of carotenoid precursors. Egg carotenoid concentrations were not correlated with either skin carotenoid concentration or colouration, which suggests that female carotenoid displays are not a reliable signal that males can use to evaluate egg carotenoid resources.

Mate choice for nonadditive genetic benefits and the maintenance of genetic diversity in song sparrows.

The lek paradox asserts that strong directional selection via female choice should deplete additive genetic variation in fitness and consequently any benefit to females expressing the preference. Recently, we have provided a novel resolution to the paradox by showing that nonadditive genetic effects such as overdominance can be inherited from parent to offspring, and populations with females that express a mating preference for outbred males maintain higher genetic variation than populations with females that mate randomly. Here, we test our dynamic model using empirical data previously published from a small island population of song sparrows (Melospiza melodia). The model assumes that fitness and male trait expression display overdominance effects. The results demonstrate that female choice for outbred males mediated by directional selection on song repertoire size provides a heritable benefit to offspring through reduced inbreeding depression. Within the population, we estimate the heritability of the inbreeding coefficient to be 0.18 +/- 0.08 (SD). Furthermore, we show that mate choice for outbred males increases fitness-related genetic variation in the population by 12% and thereby reduces inbreeding depression by 1% per generation in typical years and upwards of 15% in severe years. Thus, mate choice may help to stave off population extinction in this and other small populations.

Microsatellite genetic differentiation among populations of the Trinidadian guppy.

Insight into the processes of evolutionary change can be obtained by studying the distribution of genetic diversity among populations. Such diversity can be shaped by historical colonization events, population connectivity and adaptation to local selection pressures. Here we examine genetic differentiation of Trinidadian guppies, Poecilia reticulata, by genotyping 373 individuals from 15 populations located in three drainages (northern coast, Caroni and Oropouche) with 7 microsatellite loci. Our data provide little evidence to support previous claims of two major genetic lineages of guppies in northern Trinidad but instead suggest a more complex pattern of gene flow among populations from different drainages. First, some of the populations in the Caroni drainage show genetic signatures similar to those in the Oropouche drainage. Second, the populations in the northern coast are all highly differentiated from those in either the Caroni or Oropouche drainages. Despite differing selection regimes owing to predation pressure, populations from upstream and downstream locales typically cluster together, albeit upstream populations consistently have less genetic variability than the corresponding downstream population. There is, however, no overall pattern of isolation by distance. We also find evidence that an artificially transplanted population from the Caroni drainage is successfully invading into other populations within the Oropouche system. Our analysis details the genetic and phylogeographic structure of Trinidadian guppies in the northern range and provides insight into evolutionary processes at different timescales that have shaped genetic heterogeneity in this fish.

Kinship affects innate responses to a predator in bluegill Lepomis macrochirus larvae.

Naïve kin groups and mixed-family groups of bluegill Lepomis macrochirus larvae were exposed to a novel predator cue. The larvae responded by increasing shoal cohesiveness in kin groups but not in mixed-family groups; moreover, larvae sired by males of the 'cuckolder' life history tended to have an enhanced ability to respond to direct cues of kinship v. larvae sired by males of the 'parental' life history, which instead appeared to respond to cues of life history rather than relatedness per se. The increased shoal cohesion among related individuals probably confers a survival benefit and indicates that the antipredatory shoaling response is innate in L. macrochirus.

MHC class IIB additive and non-additive effects on fitness measures in the guppy Poecilia reticulata.

The genetic architecture of fitness at the class IIB gene of the major histocompatibility complex (MHC) in the guppy Poecilia reticulata was analysed. Diversity at the MHC is thought to be maintained by some form of balancing selection; heterozygote advantage, frequency-dependent selection or spatially and temporally fluctuating selection. Here these hypotheses are evaluated by using an algorithm that partitions the effect of specific MHC allele and genotypes on fitness measures. The effect of MHC genotype on surrogate measures of fitness was tested, including growth rate (at high and low bulk food diets), parasite load following a parasite challenge and survival. The number of copies of the Pore_a132 MHC allele was inversely related to infection by Gyrodactylus flukes and it appeared to be positively related to faster growth. Also, genotypes combining the Pore_a132 or other relatively common alleles paired with rare MHC alleles produced both advantageous and detrimental non-additive effects. Thus, the genetic architecture underlying fitness at the MHC is complex in the P. reticulata.

The MHC and non-random mating in a captive population of Chinook salmon.

Detailed analysis of variation in reproductive success can provide an understanding of the selective pressures that drive the evolution of adaptations. Here, we use experimental spawning channels to assess phenotypic and genotypic correlates of reproductive success in Chinook salmon (Oncorhynchus tshawytscha). Groups of 36 fish in three different sex ratios (1:2, 1:1 and 2:1) were allowed to spawn and the offspring were collected after emergence from the gravel. Microsatellite genetic markers were used to assign parentage of each offspring, and the parents were also typed at the major histocompatibility class IIB locus (MHC). We found that large males, and males with brighter coloration and a more green/blue hue on their lateral integument sired more offspring, albeit only body size and brightness had independent effects. There was no similar relationship between these variables and female reproductive success. Furthermore, there was no effect of sex ratio on the strength or significance of any of the correlations. Females mated non-randomly at the MHC, appearing to select mates that produced offspring with greater genetic diversity as measured by amino-acid divergence. Females mated randomly with respect to male genetic relatedness and males mated randomly with respect to both MHC and genetic relatedness. These results indicate that sexual selection favours increased body size and perhaps integument coloration in males as well as increases genetic diversity at the MHC by female mate choice.

Microsatellite evolution in vertebrates: inference from AC dinucleotide repeats.

We analyze published data from 592 AC microsatellite loci from 98 species in five vertebrate classes including fish, reptiles, amphibians, birds, and mammals. We use these data to address nine major questions about microsatellite evolution. First, we find that larger genomes do not have more microsatellite loci and therefore reject the hypothesis that microsatellites function primarily to package DNA into chromosomes. Second, we confirm that microsatellite loci are relatively rare in avian genomes, but reject the hypothesis that this is due to physical constraints imposed by flight. Third, we find that microsatellite variation differs among species within classes, possibly relating to population dynamics. Fourth, we reject the hypothesis that microsatellite structure (length, number of alleles, allele dispersion, range in allele sizes) differs between poikilotherms and homeotherms. The difference is found only in fish, which have longer microsatellites and more alleles than the other classes. Fifth, we find that the range in microsatellite allele size at a locus is largely due to the number of alleles and secondarily to allele dispersion. Sixth, length is a major factor influencing mutation rate. Seventh, there is a directional mutation toward an increase in microsatellite length. Eighth, at the species level, microsatellite and allozyme heterozygosity covary and therefore inferences based on large-scale studies of allozyme variation may also reflect microsatellite genetic diversity. Finally, published microsatellite loci (isolated using conventional hybridization methods) provide a biased estimate of the actual mean repeat length of microsatellites in the genome.

Dynamic adjustment of parental care in response to perceived paternity.

Theories of parental care evolution predict that genetic relatedness will be an important variable in the amount of care a parent provides. However, current inferences of relatedness-based parental investment from studies in humans and birds remain challenged. No study has yet demonstrated parental care adjustment in a manner uncomplicated by life-history correlates or experimental design. We now present a unique test that controls for individual life histories and demonstrates paternity-related dynamic adjustments in parental care. Brood-rearing male bluegill sunfish (Lepomis macrochirus) that are cuckolded to a varying degree will either increase or decrease their parental investment in response to changing information on paternity during brood development. Specifically, as parental males detect paternity lost to cuckolders and, hence, a reduction in the value of their brood, they adaptively lower their level of parental care. Conversely, if they detect that their paternity is higher than previously assessed, they adaptively raise their level of parental care. This dynamic adjustment during brood rearing indicates the importance of genetic relatedness in parental investment decisions and provides needed empirical support for theoretical predictions.

Tactic-specific success in sperm competition.

Sperm competition is a major force in sexual selection, but its implications for mating-system and life-history evolution are only beginning to be understood. The well-known sneak-guard model predicts that sneaks will win in sperm competition. We now provide empirical confirmation of this prediction. Bluegill sunfish (Lepomis macrochirus) have both sneak (cuckolder) and guard (parental) males. Guards make nests, court females and provide solitary parental care for the embryos. Sneaks include small cuckolders, which are termed 'sneakers', that dart in and out of nests in order to ejaculate between the spawning pair and larger cuckolders, which are termed 'satellites', that mimic females in order to ejaculate between the spawning pair. Using field behavioural data, genetic data and new mathematical models for paternity analyses, we show, for the first time to the authors' knowledge, that sneaks fertilize more eggs than guards during sperm competition. In addition, we show that sneakers are superior to satellites in sperm competition and, thus, that even among sneaks there are tactic-specific differences in competitive success.

Genetic life history effects on juvenile survival in bluegill.

Foraging behaviour under the risk of predation has important consequences on an individual's survivorship and fitness. In bluegill (Lepomis macrochirus), we have recently shown that offspring sired by males of alternative life histories differ in their foraging behaviour. Specifically, offspring sired by 'cuckolder' males take fewer risks during foraging than do offspring sired by 'parental' males. This behavioural difference can have important consequences on the fitness of the two life histories and thus the underlying evolutionary mechanism. Here, we examine the consequences of this behavioural variation on growth rate, condition and survivorship during early development of juveniles. We used split in vitro fertilization to generate maternal half-sibs that differed in sire life history. The resulting 18 455 larvae from 50 families were released into a microcosm with safe and risky foraging areas for approximately 2 months. A total of 262 juveniles (1.4%) survived of which parentage was unambiguously determined using microsatellite genetic markers for 254 (97%). Although we found significant dam effects, there was no difference in apparent growth rate or condition of juveniles sired by males of the two life histories. Of the 25 paired half-sib families, 15 had higher survivorship when sired by a cuckolder male, seven had higher survivorship when sired by a parental male and three had no surviving offspring from either sire. Thus, although growth was similar between the two offspring types, survivorship was not. Combining the differential survivorship estimate with paternity data from natural nests and the frequency of males adopting each life history, we calculated that the cuckolder life history has 1.87 times higher fitness than the parental life history. As such, the life histories likely are not governed by a genetic polymorphism.

Sperm competition in a fish with external fertilization: the contribution of sperm number, speed and length.

The role of sperm number and quality in male competitiveness was investigated using in vitro fertilization experiments with bluegill (Lepomis macrochirus). Bluegill males use one of three mating tactics: 'sneakers', which streak spawn; 'satellites', which mimic females; and 'parentals', which are territorial. The in vitro experiments mimicked natural spawning by incorporating these males' mean proximity to eggs and timing of sperm release. Using a maximum-likelihood algorithm, raffle equations were fit to paternity data, which revealed a strong effect of sperm number on male competitiveness. There was no difference in sperm flagellum length, curvilinear swim speed or path linearity among the three male mating types, and these traits did not explain any additional variation in male competitiveness. It was estimated that, given closer proximity to eggs, satellites need release only 0.34 times as many sperm as parentals to obtain equal paternity. Despite being farther from the eggs and releasing sperm about half a second after parentals, sneakers need only release 0.58 times as many sperm as parentals to obtain equal paternity. Thus, the increased competitiveness of sneakers' sperm must come from a component of sperm quality other than speed or length.

Mean d(2) and divergence time: transformations and standardizations.

The fitness consequences of inbreeding and outbreeding have intrigued biologists for a long time. Recently a measure of relatedness of parental haplotypes has been proposed called mean d(2). This measure is based on a stepwise mutational process and therefore is tailored to microsatellite genetic markers. Theoretical work suggests that mean d(2) typically is less suited for measuring fitness consequences due to close inbreeding rather than heterozygosity. However, mean d(2) may be more appropriate than heterozygosity for measuring divergence times over longer time scales and thus for detecting outbreeding depression. Here, simulations are used to (1). identify appropriate standardization coefficients and transformations for mean d(2), and (2). evaluate mean d(2) as a measure of divergence time of parental lineages over time scales up to 10000 generations. Results show that mean d(2) is a linear predictor of divergence time. The coefficient of variation of mean d(2) approaches a constant value with increasing divergence time and therefore logarithm transformation is appropriate to restore homoscedasticity. When mutation rates and sizes are known for each locus they can be incorporated into a standardization coefficient to increase the precision of mean d(2). As few as 10 loci can explain more than 70% of the variation in divergence time between lineages. While heterozygosity outperforms mean d(2) at detecting differences in divergence time over relative short time periods (or=1000 generations). However, gene flow of as little as 1% per generation can significantly reduce the ability of either mean d(2) or heterozygosity to estimate divergence time.

Genetic paternity analysis and breeding success in bluegill sunfish (Lepomis macrochirus).

Fish have some of the most complex mating systems known in the animal kingdom. With the advent of powerful genetic markers and an emerging mathematical framework to calculate parentage, it is now possible to analyze genetic relatedness and gene flow in these systems. An important example is the bluegill sunfish (Lepomis macrochirus) which consists of parental males that provide sole care for the young, cuckolder males that parasitize the parentals, and females that actively choose among males within dense breeding colonies. In this article genetic markers for bluegill are characterized and their utility in parentage studies is demonstrated by calculating the genetic relatedness of parental males to their broods for an entire natural breeding colony. A novel Monte Carlo simulation is developed to calculate the confidence in the relatedness estimates and these data are used to provide an estimate of the mean breeding success of parental and cuckolder males. Finally, the applications of genetic analyses to understanding mating systems, parental care, and life-history evolution in bluegill are discussed.