Quantitative Genetic Models Research Articles

Interpreting selection when individuals interact

Summary A useful interpretation of quantitative genetic models of evolutionary change is that they (i) define a set of phenotypes that have a causal effect on fitness and on which selection acts, and (ii) define a set of breeding values that change as a correlated response to that selection because they covary with the phenotypes. When the expression of one trait causes variation in other traits then there are multiple paths by which a trait can cause fitness variation. Because of this, there are multiple ways in which selection can be defined, and still be consistent with a causal effect of traits on fitness. We use this result to show that genetical theories of natural/kin selection ignore causation and because of this we suggest they shed little light on the nature of selection. When traits expressed by an individual are affected by traits of their social partners (indirect genetic effects), we suggest a causal partitioning that allows selection to be cast in terms of Hamilton's costs and benefits. We show that previous attempts to understand Hamilton's rule in the context of indirect genetic effects either lack generality, or do not adequately describe all the ways in which an individual's actions constitute a cost to the individual or a benefit to its social partner(s). Our results allow us to explore Hamilton's rule in a multitrait setting. We show that evolution always increases inclusive fitness, and when the traits are measured in units of generalised genetic distance evolutionary change in the traits is in the direction in which inclusive fitness increases the fastest. However, we show that Hamilton's rule only holds in a multitrait context when the suite of traits are at equilibrium. When they are out of equilibrium, the conditions for altruism to evolve may be more or less stringent depending on genetic architecture and how costs and benefits are defined.

The Home Environment Shapes Emotional Eating.

Emotional overeating (EOE) is the tendency to eat more in response to negative emotions; its etiology in early life is unknown. We established the relative genetic and environmental influences on EOE in toddlerhood and early childhood. Data were from Gemini, a population-based cohort of 2,402 British twins born in 2007. EOE was measured using the "emotional overeating" scale of the Child Eating Behavior Questionnaire (CEBQ) at 16months and 5years. A longitudinal quantitative genetic model established that genetic influences on EOE were minimal; on the other hand, shared environmental influences explained most of the variance. EOE was moderately stable from 16months to 5years and continuing environmental factors shared by twin pairs at both ages explained the longitudinal association.

Vertebral Artery Diameter and Flow: Nature or Nurture.

In contrast with the carotid arteries, the vertebral arteries (VAs) show considerable variation in length, caliber, and vessel course. This study investigated whether the variation in diameter and flow characteristics of the VAs might be inherited. A total of 172 Italian twins from Padua, Perugia, and Terni (54 monozygotic, 32 dizygotic) recruited from the Italian Twin Registry underwent B-mode and pulsed-wave Doppler ultrasound assessment of their VAs. VA diameters, peak systolic velocity (PSV) and end diastolic velocity (EDV) were assessed at the level of a horizontal V2 segment. Univariate quantitative genetic modeling was performed. Fourteen percent of the sample had VA hypoplasia. Within pair correlation in monozygotic twins was higher than in dizygotics (.552 vs. .229) for VA diameter. Age- and sex-adjusted genetic effect, under the most parsimonious model, accounted for 54.7% (95% CI: 42.2-69.1%) of the variance of VA diameter, and unshared environmental effect for 45.3% (95% CI: 30.9-57.8%). No heritability was found for the PSV of VA, but shared (34.1%; 95% CI: 16.7-53.7%) and unshared (65.9%; 95% CI: 45.9-83.1%) environmental factors determined the variance. EDV of VA is moderately genetically influenced (42.4%; 95% CI: 16.1-64.9%) and also determined by the unshared environment (57.6%; 95% CI: 34.7-83.7%). The diameter of the VAs is moderately genetically determined. Different factors influence the PSV and EDV of VAs, which may highlight the complex hemodynamic background of VA flow and help to understand the vertebral flow anomalies found by ultrasound.

Determining Selection across Heterogeneous Landscapes: A Perturbation-Based Method and Its Application to Modeling Evolution in Space.

Spatial structure can decisively influence the way evolutionary processes unfold. To date, several methods have been used to study evolution in spatial systems, including population genetics, quantitative genetics, moment-closure approximations, and individual-based models. Here we extend the study of spatial evolutionary dynamics to eco-evolutionary models based on reaction-diffusion equations and adaptive dynamics. Specifically, we derive expressions for the strength of directional and stabilizing/disruptive selection that apply both in continuous space and to metacommunities with symmetrical dispersal between patches. For directional selection on a quantitative trait, this yields a way to integrate local directional selection across space and determine whether the trait value will increase or decrease. The robustness of this prediction is validated against quantitative genetics. For stabilizing/disruptive selection, we show that spatial heterogeneity always contributes to disruptive selection and hence always promotes evolutionary branching. The expression for directional selection is numerically very efficient and hence lends itself to simulation studies of evolutionary community assembly. We illustrate the application and utility of the expressions for this purpose with two examples of the evolution of resource utilization. Finally, we outline the domain of applicability of reaction-diffusion equations as a modeling framework and discuss their limitations.

A model for conditional male trimorphisms

Conditional dimorphisms are widespread in color, morphology, behavior, and life history. Such traits have been successfully modeled in game theory as conditional strategies, and in quantitative genetics as threshold traits. Conditional trimorphisms have recently been unveiled, and here we combine the rock-paper-scissors (RPS) model of game theory and the environmental threshold (ET) model of quantitative genetics to model trimorphisms that are environmentally induced and result from the expression of two thresholds. We investigated the tactic fitness structure for maintenance of alternative reproductive tactics in scarab dung beetles that constitute the first known examples of conditional male trimorphism. We parameterized a novel ternary fitness landscape that explains how conditional male trimorphism in these beetles can be maintained. We tracked changes in tactic frequencies in a wild population of Phanaeus triangularis and detected fitness intransitivity consistent with RPS dynamics. Quantitative predictions of our model compare favorably with corresponding observed parameters. The ternary landscape further reveals how geographic populations of these beetles can evolve between conditional trimorphism and dimorphism. The ternary model also suggests that polyphenic systems could potentially evolve between conditional and purely genetic mediation.

Bigger Is Fitter? Quantitative Genetic Decomposition of Selection Reveals an Adaptive Evolutionary Decline of Body Mass in a Wild Rodent Population.

In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions. Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called “stasis paradox” highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic environmental change. While the causes underlying the stasis paradox are hotly debated, comprehensive attempts aiming at a resolution are lacking. Here, we apply a quantitative genetic framework to individual-based long-term data for a wild rodent population and show that despite a positive association between body mass and fitness, there has been a genetic change towards lower body mass. The latter represents an adaptive response to viability selection favouring juveniles growing up to become relatively small adults, i.e., with a low potential adult mass, which presumably complete their development earlier. This selection is particularly strong towards the end of the snow-free season, and it has intensified in recent years, coinciding which a change in snowfall patterns. Importantly, neither the negative evolutionary change, nor the selective pressures that drive it, are apparent on the phenotypic level, where they are masked by phenotypic plasticity and a non causal (i.e., non genetic) positive association between body mass and fitness, respectively. Estimating selection at the genetic level enabled us to uncover adaptive evolution in action and to identify the corresponding phenotypic selective pressure. We thereby demonstrate that natural populations can show a rapid and adaptive evolutionary response to a novel selective pressure, and that explicitly (quantitative) genetic models are able to provide us with an understanding of the causes and consequences of selection that is superior to purely phenotypic estimates of selection and evolutionary change.

The effect of maternal glucocorticoid levels on juvenile docility in yellow-bellied marmots

Maternal effects can have significant and long-term consequences on offspring behavior and survival, while consistent individual differences (i.e., personality) can have profound impacts on individual fitness. Thus, both can influence population dynamics. However, the underlying mechanisms that determine variation in personality traits are poorly understood. Maternal effects are one potential mechanism that may explain personality variation. We capitalized on a long-term study of yellow-bellied marmots (Marmota flaviventris) to identify maternal effects on juvenile docility. To do so, we partitioned the variance in juvenile docility using a quantitative genetic modeling approach to isolate potential maternal effects. We also directly tested whether maternal stress, measured through fecal glucocorticoid metabolite levels during lactation of 82 mothers, was associated with offspring docility. Docility scores were estimated for 645 juveniles trapped between 2002 and 2012. We found an interaction between maternal glucocorticoid levels and dam age on juvenile docility. We also found significant maternal, litter, permanent environment, and year effects. These results suggest that a mother's life history stage interacts with stress to influence offspring personality. This early life influence can have long lasting effects on an individual's docility throughout life.

Novel Candidate Genes Underlying Extreme Trophic Specialization in Caribbean Pupfishes.

The genetic changes responsible for evolutionary transitions from generalist to specialist phenotypes are poorly understood. Here we examine the genetic basis of craniofacial traits enabling novel trophic specialization in a sympatric radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas. This recent radiation consists of a generalist species and two novel specialists: a small-jawed "snail-eater" and a large-jawed "scale-eater." We genotyped 12 million single nucleotide polymorphisms (SNPs) by whole-genome resequencing of 37 individuals of all three species from nine populations and integrated genome-wide divergence scans with association mapping to identify divergent regions containing putatively causal SNPs affecting jaw size-the most rapidly diversifying trait in this radiation. A mere 22 fixed variants accompanied extreme ecological divergence between generalist and scale-eater species. We identified 31 regions (20 kb) containing variants fixed between specialists that were significantly associated with variation in jaw size which contained 11 genes annotated for skeletal system effects and 18 novel candidate genes never previously associated with craniofacial phenotypes. Six of these 31 regions showed robust signs of hard selective sweeps after accounting for demographic history. Our data are consistent with predictions based on quantitative genetic models of adaptation, suggesting that the effect sizes of regions influencing jaw phenotypes are positively correlated with distance between fitness peaks on a complex adaptive landscape.

When three traits make a line: evolution of phenotypic plasticity and genetic assimilation through linear reaction norms in stochastic environments

Genetic assimilation emerges from selection on phenotypic plasticity. Yet, commonly used quantitative genetics models of linear reaction norms considering intercept and slope as traits do not mimic the full process of genetic assimilation. We argue that intercept-slope reaction norm models are insufficient representations of genetic effects on linear reaction norms and that considering reaction norm intercept as a trait is unfortunate because the definition of this trait relates to a specific environmental value (zero) and confounds genetic effects on reaction norm elevation with genetic effects on environmental perception. Instead, we suggest a model with three traits representing genetic effects that, respectively, (i) are independent of the environment, (ii) alter the sensitivity of the phenotype to the environment and (iii) determine how the organism perceives the environment. The model predicts that, given sufficient additive genetic variation in environmental perception, the environmental value at which reaction norms tend to cross will respond rapidly to selection after an abrupt environmental change, and eventually becomes equal to the new mean environment. This readjustment of the zone of canalization becomes completed without changes in genetic correlations, genetic drift or imposing any fitness costs of maintaining plasticity. The asymptotic evolutionary outcome of this three-trait linear reaction norm generally entails a lower degree of phenotypic plasticity than the two-trait model, and maximum expected fitness does not occur at the mean trait values in the population.

Climate change, hydrology, and fish morphology: predictions using phenotype-environment associations

Phenotype-environment associations (PEAs) describe relationships between the mean phenotypes of a set of populations and the environmental values of the areas in which they inhabit. We show how these PEAs can be used to determine the ability of populations to adapt to future environmental changes, using relationships between fish body shape and stream flow rates as an example. First, we establish that fish in high-flow habitats have more streamlined body shapes than those in low-flow habitats. Then, using future estimates of flow rates obtained from landscape hydrologic models, we predict body shapes of stream fish in the year 2055. Lastly, we use simulations based on a quantitative population genetics model to determine each fish population’s ability to alter its phenotype to the predicted body shape in 2055. While some fish populations were predicted to be able to reach the predicted body shape, others were identified as vulnerable to changing flow rates and may need human assistance to persist into the mid-century. The simulations introduced here combine correlative and mechanistic methods to predict future adaptation to environmental change and are applicable to a wide range of taxa.

Cytoplasmic inheritance of parent-offspring cell structure in the clonal diatom Cyclotella meneghiniana.

In cytoplasmic inheritance, structural states of a parent cell could be transmitted to offspring cells via two mechanisms. The first is referred to as the hangover of parent structure, where the structure itself remains and faithfully transmits within offspring cells; the second is structural inheritance, wherein the parent structure functions as a template for development of new offspring structure. We estimated to what extent the parent structure affects the development of offspring structure by structural inheritance, using a clone of the diatom Cyclotella meneghiniana The cell has two siliceous valves (a cell wall part at both cell poles): one is inherited from the parent and the other is newly formed. We estimated cytoplasmic heritability by comparing valve traits (central fultoportulae (CTFP), striae, central area, and cell diameter) of parent and new offspring valves, using single-cell isolation and valve labelling. Parent-offspring valve trait regressions showed that all traits, except CTFP, were significantly correlated. We formulated a quantitative genetic model considering the diatom inheritance system and revealed short-term rapid evolution compared with other inheritance systems. Diatom structural inheritance will have evolved to enable clonal populations to rapidly acquire and maintain suitable structures for temporal changes in environments and life-cycle stages.

Accounting for genetic differences among unknown parents in microevolutionary studies: how to include genetic groups in quantitative genetic animal models.

Summary Quantifying and predicting microevolutionary responses to environmental change requires unbiased estimation of quantitative genetic parameters in wild populations. ‘Animal models’, which utilize pedigree data to separate genetic and environmental effects on phenotypes, provide powerful means to estimate key parameters and have revolutionized quantitative genetic analyses of wild populations.However, pedigrees collected in wild populations commonly contain many individuals with unknown parents. When unknown parents are non‐randomly associated with genetic values for focal traits, animal model parameter estimates can be severely biased. Yet, such bias has not previously been highlighted and statistical methods designed to minimize such biases have not been implemented in evolutionary ecology.We first illustrate how the occurrence of non‐random unknown parents in population pedigrees can substantially bias animal model predictions of breeding values and estimates of additive genetic variance, and create spurious temporal trends in predicted breeding values in the absence of local selection. We then introduce ‘genetic group’ methods, which were developed in agricultural science, and explain how these methods can minimize bias in quantitative genetic parameter estimates stemming from genetic heterogeneity among individuals with unknown parents.We summarize the conceptual foundations of genetic group animal models and provide extensive, step‐by‐step tutorials that demonstrate how to fit such models in a variety of software programs. Furthermore, we provide new functions in r that extend current software capabilities and provide a standardized approach across software programs to implement genetic group methods.Beyond simply alleviating bias, genetic group animal models can directly estimate new parameters pertaining to key biological processes. We discuss one such example, where genetic group methods potentially allow the microevolutionary consequences of local selection to be distinguished from effects of immigration and resulting gene flow.We highlight some remaining limitations of genetic group models and discuss opportunities for further development and application in evolutionary ecology. We suggest that genetic group methods should no longer be overlooked by evolutionary ecologists, but should become standard components of the toolkit for animal model analyses of wild population data sets.

High evolutionary constraints limited adaptive responses to past climate changes in toad skulls.

Interactions among traits that build a complex structure may be represented as genetic covariation and correlation. Genetic correlations may act as constraints, deflecting the evolutionary response from the direction of natural selection. We investigated the relative importance of drift, selection, and constraints in driving skull divergence in a group of related toad species. The distributional range of these species encompasses very distinct habitats with important climatic differences and the species are primarily distinguished by differences in their skulls. Some parts of the toad skull, such as the snout, may have functional relevance in reproductive ecology, detecting water cues. Thus, we hypothesized that the species skull divergence was driven by natural selection associated with climatic variation. However, given that all species present high correlations among skull traits, our second prediction was of high constraints deflecting the response to selection. We first extracted the main morphological direction that is expected to be subjected to selection by using within- and between-species covariance matrices. We then used evolutionary regressions to investigate whether divergence along this direction is explained by climatic variation between species. We also used quantitative genetics models to test for a role of random drift versus natural selection in skull divergence and to reconstruct selection gradients along species phylogeny. Climatic variables explained high proportions of between-species variation in the most selected axis. However, most evolutionary responses were not in the direction of selection, but aligned with the direction of allometric size, the dimension of highest phenotypic variance in the ancestral population. We conclude that toad species have responded to selection related to climate in their skulls, yet high evolutionary constraints dominated species divergence and may limit species responses to future climate change.

Food fussiness and food neophobia share a common etiology in early childhood.

Background‘Food fussiness’ (FF) is the tendency to be highly selective about which foods one is willing to eat, and emerges in early childhood; ‘food neophobia’ (FN) is a closely related characteristic but specifically refers to rejection of unfamiliar food. These behaviors are associated, but the extent to which their etiological architecture overlaps is unknown. The objective of this study was to quantify the relative contribution of genetic and environmental influences to variation in FF and FN in early childhood; and to establish the extent to which they share common genetic and environmental influences.MethodParticipants were 1,921 families with 16‐month‐old twins from the Gemini birth cohort. Parents completed the Child Eating Behaviour Questionnaire which included three FF items and four FN items. Bivariate quantitative genetic modeling was used to quantify: (a) genetic and environmental contributions to variation in FF and FN; and (b) the extent to which genetic or environmental influences on FF and FN are shared across the traits.ResultsFood fussiness and FN were strongly correlated (r = .72, p < .001). Proportions of variation in FF were equally explained by genetic (.46; 95% CI: 0.41–0.52) and shared environmental influences (.46; 95% CI: 0.41–0.51). Shared environmental effects accounted for a significantly lower proportion of variation in FN (.22; 95% CI: 0.14–0.30), but genetic influences were not significantly different from those on FF (.58, 95% CI: 0.50–0.67). FF and FN largely shared a common etiology, indicated by high genetic (.73; 95% CI: 0.67–0.78) and shared environmental correlations (.78; 95% CI: 0.69–0.86) across the two traits.ConclusionsFood fussiness and FN both show considerable heritability at 16 months but shared environmental factors, for example the home environment, influenced more interindividual differences in the expression of FF than in FN. FF and FN largely share a common etiology.

Sensation seeking and impulsive traits as personality endophenotypes for antisocial behavior: Evidence from two independent samples

Sensation seeking and impulsivity are personality traits that are correlated with risk for antisocial behavior (ASB). This paper uses two independent samples of twins to (a) test the extent to which sensation seeking and impulsivity statistically mediate genetic influence on ASB, and (b) compare this to genetic influences accounted for by other personality traits. In Sample 1, delinquent behavior, as well as impulsivity, sensation seeking and Big Five personality traits, were measured in adolescent twins from the Texas Twin Project. In Sample 2, adult twins from the Australian Twin Registry responded to questionnaires that assessed individual differences in Eysenck's and Cloninger's personality dimensions, and a structured telephone interview that asked participants to retrospectively report DSM-defined symptoms of conduct disorder. Bivariate quantitative genetic models were used to identify genetic overlap between personality traits and ASB. Across both samples, novelty/sensation seeking and impulsive traits accounted for larger portions of genetic variance in ASB than other personality traits. We discuss whether sensation seeking and impulsive personality are causal endophenotypes for ASB, or merely index genetic liability for ASB.

Disentangling evolutionary, plastic and demographic processes underlying trait dynamics: a review of four frameworks

Summary Biologists are increasingly interested in decomposing trait dynamics into underlying processes, such as evolution, plasticity and demography. Four important frameworks that allow for such a decomposition are the quantitative genetic animal model (AM), the ‘Geber’ method (GM), the age‐structured Price equation (APE) and the integral projection model (IPM). However, as these frameworks have largely been developed independently, they differ in the assumptions they make, the data they require, as well as their outcomes and interpretation. Here, we evaluate how each framework decomposes trait dynamics into underlying processes. To do so, we apply them to simulated data for a hypothetical animal population. Individual body size was affected by, among others, genes, maternal effects and food intake. We simulated scenarios with and without selection on body size and with high and low heritability. The APE and IPM provided similar results, as did the AM and GM, with important differences between the former and the latter. All frameworks detected positive contributions of selection in the high but not in the low selection scenarios. However, only the AM and GM distinguished between the high and low heritability scenarios. Furthermore, the AM and GM revealed a high contribution of plasticity. The APE and IPM attributed most of the change in body size to ontogenetic growth and inheritance, where the latter captures the combined effects of plasticity, maternal effects and heritability. We show how these apparent discrepancies are mostly due to differences in aims and definitions. For example, the APE and IPM capture selection, whereas the AM and GM focus on the response to selection. Furthermore, the frameworks differ in the processes that are ascribed to plasticity and in how they take into account demography. We conclude that no single framework provides the ‘true’ contributions of evolution, plasticity and demography. Instead, different research questions require different frameworks. A thorough understanding of the different definitions of their components is necessary for selecting the most appropriate framework for the question at hand and for making biologically meaningful inferences. This work thus supports both future analysis and the careful interpretation of existing work.

Pollen dispersal slows geographical range shift and accelerates ecological niche shift under climate change

Species may survive climate change by migrating to track favorable climates and/or adapting to different climates. Several quantitative genetics models predict that species escaping extinction will change their geographical distribution while keeping the same ecological niche. We introduce pollen dispersal in these models, which affects gene flow but not directly colonization. We show that plant populations may escape extinction because of both spatial range and ecological niche shifts. Exact analytical formulas predict that increasing pollen dispersal distance slows the expected spatial range shift and accelerates the ecological niche shift. There is an optimal distance of pollen dispersal, which maximizes the sustainable rate of climate change. These conclusions hold in simulations relaxing several strong assumptions of our analytical model. Our results imply that, for plants with long distance of pollen dispersal, models assuming niche conservatism may not accurately predict their future distribution under climate change.

Testing for biases in selection on avian reproductive traits and partitioning direct and indirect selection using quantitative genetic models

Key life history traits such as breeding time and clutch size are frequently both heritable and under directional selection, yet many studies fail to document microevolutionary responses. One general explanation is that selection estimates are biased by the omission of correlated traits that have causal effects on fitness, but few valid tests of this exist. Here, we show, using a quantitative genetic framework and six decades of life-history data on two free-living populations of great tits Parus major, that selection estimates for egg-laying date and clutch size are relatively unbiased. Predicted responses to selection based on the Robertson-Price Identity were similar to those based on the multivariate breeder's equation (MVBE), indicating that unmeasured covarying traits were not missing from the analysis. Changing patterns of phenotypic selection on these traits (for laying date, linked to climate change) therefore reflect changing selection on breeding values, and genetic constraints appear not to limit their independent evolution. Quantitative genetic analysis of correlational data from pedigreed populations can be a valuable complement to experimental approaches to help identify whether apparent associations between traits and fitness are biased by missing traits, and to parse the roles of direct versus indirect selection across a range of environments.

What Explains the Heritability of Completed Fertility? Evidence from Two Large Twin Studies.

In modern societies, individual differences in completed fertility are linked with genotypic differences between individuals. Explaining the heritability of completed fertility has been inconclusive, with alternative explanations centering on family formation timing, pursuit of education, or other psychological traits. We use the twin subsample from the Midlife Development in the United States study and the TwinsUK study to examine these issues. In total, 2606 adult twin pairs reported on their completed fertility, age at first birth and marriage, level of education, Big Five personality traits, and cognitive ability. Quantitative genetic Cholesky models were used to partition the variance in completed fertility into genetic and environmental variance that is shared with other phenotypes and residual variance. Genetic influences on completed fertility are strongly related to family formation timing and less strongly, but significantly, with psychological traits. Multivariate models indicate that family formation, demographic, and psychological phenotypes leave no residual genetic variance in completed fertility in either dataset. Results are largely consistent across U.S. and U.K. sociocultural contexts.

High-throughput sequencing and graph-based cluster analysis facilitate microsatellite development from a highly complex genome.

Despite recent advances in high‐throughput sequencing, difficulties are often encountered when developing microsatellites for species with large and complex genomes. This probably reflects the close association in many species of microsatellites with cryptic repetitive elements. We therefore developed a novel approach for isolating polymorphic microsatellites from the club‐legged grasshopper (Gomphocerus sibiricus), an emerging quantitative genetic and behavioral model system. Whole genome shotgun Illumina MiSeq sequencing was used to generate over three million 300 bp paired‐end reads, of which 67.75% were grouped into 40,548 clusters within RepeatExplorer. Annotations of the top 468 clusters, which represent 60.5% of the reads, revealed homology to satellite DNA and a variety of transposable elements. Evaluating 96 primer pairs in eight wild‐caught individuals, we found that primers mined from singleton reads were six times more likely to amplify a single polymorphic microsatellite locus than primers mined from clusters. Our study provides experimental evidence in support of the notion that microsatellites associated with repetitive elements are less likely to successfully amplify. It also reveals how advances in high‐throughput sequencing and graph‐based repetitive DNA analysis can be leveraged to isolate polymorphic microsatellites from complex genomes.