Ecological Genetics of Mpi and Gpi Polymorphisms in the Acorn Barnacle and the Spatial Scale of Neutral and Non-neutral Variation

Different allozyme genotypes at the mannose phosphate isomerase(Mpi) locus in the northern acorn barnacle (Semibalanus balanoides)show a strong association with distinct intertidal microhabitats.In estuaries along the Maine Coast, the FF homozygote has higherfitness in exposed, high-tide level microhabitats while theSS homozygote has higher fitness under algal cover or at low-tidemicrohabitats. These patterns are consistent with a Levene (1953)model of balancing selection. In these same samples, polymorphismsat the glucose phosphate isomerase locus (Gpi) and mitochondrialDNA (mtDNA) show no fitness differences among microhabitats,providing intra-genomic controls supporting selection at ornear Mpi. Here we report a similar analysis of genotype-by-microhabitatassociations at sites in Narragansett Bay, Rhode Island, closeto the southern range limit of S. balanoides. Genotype zonationat Mpi between high- and low-tide microhabitats is significantlydifferent between Maine and Narragansett Bay due to oppositezonation patterns for the SF and FF genotypes. Enzyme activitydata are consistent with this "reverse" zonation. At Gpi, thereis significant microhabitat zonation in Narragansett Bay, whilethis locus behaves as a neutral marker in Maine. Mt DNA showsno significant microhabitat zonation in either Rhode Islandor Maine. The Mpi data suggest that Levene-type selection foralternative genotypes in alternative habitats may operate atscales of both 10's of meters and 100's of kilometers. The Gpidata show how an apparently neutral locus can exhibit non-neutralvariation under different environmental conditions. We arguethat both Mpi and Gpi provide important genetic variation foradaptation to environmental heterogeneity that is recruitedunder distinct conditions of stress and carbohydrate substrateavailability.     

ALLOZYME VARIATION IN A SNAIL (LITTORINA SAXATILIS)—DECONFOUNDING THE EFFECTS OF MICROHABITAT AND GENE FLOW

It is commonly observed that a restricted gene flow among populations of a species generates genetic differentiation in, for example, allozyme markers. However, recent studies suggest that microhabitat-specific variation may contribute to the total differentiation. To appreciate the relative contributions of geographic variation and habitat-specific variation, we sampled 42 subpopulations of the intertidal snail Littorina saxatilis from three different microhabitats (boulders, low and high rocky intertidal) on five small islands within a distance of 15 km. We used a modified orthogonal version of Nei's gene diversity analysis with a modified analysis of variance (ANOVA) that estimated the significance of habitat and geographic separation and the interaction between them. Between subpopulation differentiation (G_ST) was usually in the range of 5% to 10% but was exceptionally high in one locus (Aat; 53%). Genetic differentiation attributable to different habitats accounted for 10% to 81% (mean 35%) of the between subpopulation variation and was significant (P < 0.05) in six loci. Differentiation due to geographic separation accounted for 11% to 61% (mean 36%) and was significant (P < 0.05) in seven loci. Furthermore, three loci showed interactions between habitat and island, suggesting varying effects of habitat in different islands. Microhabitat-specific variation, probably through spatially varying fitness, seems particularly likely in Aat and Pgm-2. Moderate levels of habitat associated variation added to the observed differentiation due to gene flow in Pgi, Pnp, and Pgm-1, whereas in the remaining three loci either the habitat effect was confused by strong habitat-island interaction (Ark) or was virtually absent (Pep and Mpi).     

Adaptive maintenance of genetic polymorphism in an intertidal barnacle: habitat- and life-stage-specific survivorship of Mpi genotypes

In the northern acorn barnacle, Semibalanus balanoides, genotype frequencies of three genetic markers were tracked over time in four types of intertidal habitats. These habitats were selected to represent natural variation in several environmental parameters, specifically the degree of physical stress experienced by barnacles. Frequencies for one allozyme locus (Gpi) and a presumably neutral mtDNA marker were homogeneous among habitats in each temporal sample. Similarly, no temporal stratification in genotype frequencies was evident across the five sampling intervals: from planktonic larvae sampled in March to juveniles collected at the end of June. In contrast to the Gpi and mtDNA loci, Mpi genotypes significantly changed in frequency in two habitats in the high intertidal zone. On exposed substrate, the Mpi-FF homozygote increased in frequency, whereas the alternative homozygote, Mpi-SS, significantly decreased in frequency. Barnacles that were protected from environmental stress at high intertidal heights by the Ascophyllum nodosum algal canopy demonstrated the opposite pattern. In both habitats, the change in frequency of the heterozygote was intermediate to that of the homozygous genotypes. Furthermore, these patterns of genotype-by-environment association reflected a pulse of genotype-specific mortality that occurred over a two-week interval subsequent to metamorphosis from the larval to the adult form. These data indicate that each Mpi homozygote is the highest fitness genotype in some portion of the intertidal environment. Using the Levene (1953) model to evaluate the spatial variation in genotypic fitness, the stable maintenance of the Mpi polymorphism is predicted under certain subsets of conditions. Environmental heterogeneity in the intertidal zone translates to spatial variation in selection pressures, which may result in the active maintenance of the Mpi polymorphism in this species.     

Adult survival and reproductive rate are linked to habitat preference in territorial,year‐round resident Song Sparrows Melospiza melodia

Individual animal fitness can be strongly influenced by the ability to recognize habitat features which may be beneficial. Many studies focus on the effects of habitat on annual reproductive rate, even though adult survival is typically a greater influence on fitness and population growth in vertebrate species with intermediate to long lifespans. Understanding the effects of preferred habitat on individuals over the annual cycle is therefore necessary to predict its influences on individual fitness. This is particularly true in species that are resident and territorial year‐round in the temperate zone, which may face potential trade‐offs between habitat that maximizes reproduction and that which maximizes non‐breeding season (‘over‐winter’) survival. We used a 37‐year study of Song Sparrows Melospiza melodia residing territorially year‐round on a small island to examine what habitat features influenced adult over‐winter survival, how site‐specific variation in adult survival vs. annual reproductive rate influenced long‐term habitat preference, and if preferred sites on average conferred higher individual fitness. Habitat features such as area of shrub cover and exposure to intertidal coastline predicted adult over‐winter survival independent of individual age or sex, population size, or winter weather. Long‐term habitat preference (measured as occupation rate) was better predicted by site‐specific annual reproductive rate than by expected over‐winter survival, but preferred sites maximized fitness on average over the entire annual cycle,. Although adult over‐winter survival had a greater influence on population growth (λ) than did reproductive rate, the influence of reproductive rate on λ increased in preferred sites because site‐specific variation in reproductive rate was higher than variation in expected over‐winter survival. Because preferred habitats tended to have higher mean site‐specific reproductive and adult survival rates, territorial birds in this population do not appear to experience seasonal trade‐offs in preferred habitat but are predicted to incur substantial fitness costs of settling in less‐preferred sites.     

COUNTERVAILING SELECTION IN DIFFERENT FITNESS COMPONENTS IN FEMALE RED DEER

In individually monitored red deer (Cervus elaphus) living in the North Block of the Isle of Rhum, Scotland, juvenile survival is related to the genotype at the enzyme loci Mpi and Idh-2 (each with two alleles, f and s). To establish whether other fitness components also are related to genetic differences, we examined whether age at first breeding, fecundity, and adult survival of females were related to genotype at the same loci. Fertility in females shot outside the study area was also analyzed in relation to Mpi and Idh-2 genotype. The analyses controlled for phenotypic and environmental factors affecting female reproductive performance. At Mpi, f-carrying females in the study area bred earlier than ss individuals and tended to be more fecund. However, no association was found between Mpi genotype and adult survival. In culled females, Mpi f-carriers were more likely to be pregnant than ss females. At Idh-2, homozygous females in the study area started breeding earlier than heterozygous females. Idh-2 fs and ss females were more fecund than ff females though this relationship was complicated by an interaction with spring temperature in the year of birth. When the population was at high density, adult survival of Idh-2 ss females was better than survival of ff females, which was, in turn, better than survival of fs females. No association was found between Idh-2 genotype and fertility in culled females. Overall, the associations found in female reproductive measures favor those genotypes that survive particularly badly over the first two years of life. This result supports the idea that countervailing selection in different fitness components (antagonistic pleiotropy) is a common and powerful force maintaining polymorphism in natural populations. It may also explain how fitness components can have large heritabilities while overall fitness may have a low heritability.     

The effects of diet and physiological stress on the evolutionary dynamics of an enzyme polymorphism

In the northern acorn barnacle Semibalanus balanoides, polymorphism at the mannose-6-phosphate isomerase (Mpi) locus appears to be maintained by distinct selection regimes that vary between intertidal microhabitats. The goal of the present experiment was to elucidate the mechanism of selection at the Mpi locus by examining the relationship between genotype and fitness-related life-history traits in laboratory manipulations. When barnacles were cultured on a mannose-supplemented diet and exposed to thermal stress, different Mpi genotypes exhibited differences in the rate of growth that predicted survivorship. In contrast, no such relationship was observed in control or fructose-supplemented dietary treatments either in the presence or in the absence of stress. Similarly, the phenotype and survivorship of genotypes at another allozyme locus and a presumably neutral mitochondrial DNA marker were homogeneous across all treatments and unaffected by experimental manipulations. These results suggest that the differential survivorship of Mpi genotypes in the field and laboratory results from a differential ability to process mannose-6-phosphate through glycolysis. The widespread polymorphism at Mpi observed in marine taxa may reflect the interaction between dietary composition and environmental heterogeneity in intertidal habitats.     

A second case of genetic host races in Rhagoletis? A population genetic comparison of sympatric host populations in the European cherry fruit fly,Rhagoletis cerasi

Despite an increasing acceptance in the biological community for sympatric speciation as a mode of species formation, well documented examples of sympatrically evolved ‘incipient species’ remain rare. The sympatric host races of apple maggot, Rhagoletis pomonella (Walsh), represent one of the most prominent case studies for sympatric speciation via a host shift. The European cherry fruit fly, R. cerasi (L.), shows strong ecological similarities to R. pomonella: (1) infestation of two different host plants, Lonicera xylosteum L. and Prunus avium L., and (2) divergent phenological and behavioral adaptations of flies on different hosts. The population genetic study presented here addresses whether the host associated populations of R. cerasi also represent genetically differentiated true host races. Out of a total of 29 allozyme loci examined, six were polymorphic and used to analyze six sympatric pairs of R. cerasi populations on Lonicera and Prunus from Switzerland and Germany. A direct comparison of allele frequencies between sympatric sites showed no pattern indicative of host races in R. cerasi. However, the hierarchical F‐statistic for one locus, mannose 6‐phosphate isomerase (Mpi), showed significant population differentiation that was in accordance with host race differentiation. Mpi is one of several loci that are also diagnostic for host race differentiation in R. pomonella. Results from Mpi suggest the formation of sympatric host races in R. cerasi, but additional polymorphic markers are necessary.     

The role of habitat choice in micro‐evolutionary dynamics: An experimental study on the Mediterranean killifish Aphanius fasciatus (Cyprinodontidae)

Habitat choice is defined as a nonrandom distribution of genotypes in different microhabitats. Therefore, it could exert a great impact on the genetic variance of natural populations by promoting genetic divergence, local adaptation, and may even lead to sympatric speciation. Despite this potential role in micro‐ and macro‐evolutionary processes, there is little empirical evidence that the various genotypes within a population may differ in habitat choice‐related behaviors. Here, we tested whether habitat choice may have contributed to genetic divergence within a local population of the Mediterranean killifish Aphanius fasciatus, which emerged between groups inhabiting microhabitats with different oxygen concentrations during previous field studies. In a first experiment, we studied the distribution of individuals in conditions of hypoxia and normoxia to test whether they had a different ability to shy away from a hypoxic environment; in a second experiment, we analyzed the individual behavior of fish separately in the two conditions, to verify whether they showed peculiar behavioral responses linked to a possible differential distribution. We then analyzed the six allozyme loci, whose allelic and genotypic frequencies were significantly divergent in the previous studies. In the first test, we found that the distribution of the two homozygote genotypes of the glucose‐6‐phosphate isomerase‐1 locus (GPI‐1) was significantly different between the hypoxic and the normoxic conditions. During the second test, all individuals were more active in hypoxic conditions, but the two GPI‐1 homozygotes showed a significant difference in time spent performing surface breathing, which was consistent with their distribution observed in the first experiment. These results provide evidence that individual behavioral traits, related to genetic features, may lead to a nonrandom distribution of genotypes in heterogeneous although contiguous microhabitats and, consequently, that habitat choice can play a significant role in driving the micro‐evolutionary dynamics of this species.     

Environmental heterogeneity and balancing selection in the acorn barnacle Semibalanus balanoides

The northern acorn barnacle Semibalans banlanoides occupies several intertidal microhabitats which vary greatly in their degree of physical stress. This environmental heterogeneity creates distinct selection regimes which can maintain genetic variation in natural populations. Despite considerable attention placed on the link between spatial variation in fitness and balancing selection at specific loci, experimental manipulations and fitness estimates for molecular polymorphisms have rarely been conducted in the wild. The aim of this transplant experiment was to manipulate the level of physical stress experienced by a cohort of barnacles in the field and then investigate the spatial variation in fitness for genotypes at three loci: two candidate allozymes and the mitochondrial DNA control region. The viability of mannose-6-phosphate isomerase (Mpi) genotypes was dependent on the level of physical stress experienced in the various treatments; alternative homozygotes were favoured in alternative high stress-low stress environments. In contrast, the fitness of genotypes at other loci was equivalent among treatments and unaffected by the manipulation. Evaluated in the light of balancing selection models, these data indicate that the presence of multiple environmental niches is sufficient to promote a stable Mpi polymorphism in barnacle populations and that allelic variation at this locus reflects the process of adaptation to the heterogeneous intertidal landscape.     

Flight and Oviposition Behavior of the Adult Maritime Ringlet (Coenonympha nipisiquit McDunnough) Females in Response to Microhabitat

Maritime ringlet butterflies (Coenonympha nipisiquit McDunnough), an endangered species in Canada, inhabit salt marshes, which consist of microhabitat mosaics with varied larval survival rate. These microhabitats may influence the movement and reproductive behaviors of females, which in turn may affect population dynamics. I recorded behaviors and locations of females every minute with a GPS rover and calculated their move lengths and turning angles. Move lengths did not change in response to microhabitats, although turning angles became larger near bodies of water with sparse vegetation. Females spent a longer time in one location and oviposited more often where the principal larval host, Spartina patens (Aiton) Muhl., is abundant, regardless of larval survival rate. Older females tended to initiate flight more readily than younger females and spent more time flying and nectaring. Younger females were more fecund and spent a longer time at one location. Because young females tend to be less mobile and more fecund, the majority of oviposition should take place near eclosion sites. However, some eggs will be laid away from microhabitats favorable to larval survival when older females become mobile and move out of their natal microhabitats. Because it seems to have little potential to colonize new habitat on its own, monitoring population dynamics and habitat quality will be crucial for the persistence and recovery of this rare species.     

Evolution in fine-grained environments. II. Habitat selection as a homeostatic mechanism

A model of genotype specific habitat selection is developed for an organism subject to within-lifetime environmental fluctuations. Habitat selection is first overlaid upon both hard and soft selection Levene models with either discrete or continuous habitats. It is shown that even if all genotypes have identical physiological and fitness responses within a habitat, habitat selection can still maintain a polymorphism. In other words, physiological divergence is not a necessary prerequisite for divergence in habitat preferences. Within-lifetime environmental variability is then assumed to occur within each chosen habitat. It is shown that habitat selection acts as an evolutionary filter that can enhance the fitness impact of some niches and effectively eliminate the impact of others such that it generally increases the chances for a polymorphism under soft selection. However, density-dependent effects obscure the relationship between physiological fitness and evolutionary outcome. Indeed, it is possible for selection to favor an allele causing its bearers to preferentially go to the niche to which they are least physiologically adapted. Hence, changes in habitat preference can evolve before an organism has completely adapted physiologically to a new habitat. The fitness impact of habitat selection interacts with both homeostatic avoidance mechanisms (i.e., short-term buffering) and with tolerance (long-term) mechanisms. In general, habitat selection will be most favored in those organisms deficient in long-term tolerance. Moreover, habitat selection tends to accentuate selection favoring short-term avoidance mechanisms. Thus, organisms displaying much habitat selection should have poor physiological long-term tolerances but effective physiological short-term avoidance mechanisms. Finally, if the fitness costs associated with habitat selection are too large to be ignored and are comparable for all genotypes, habitat selection directs the selective pressures back onto the physiological homeostatic capabilities. Hence, the very existence and extent of habitat selection depends critically upon the physiological capabilities of the organism.     

An ‘ecological trap’ for yellow warbler nest microhabitat selection

Contrary to assumptions of habitat selection theory, field studies frequently detect ‘ecological traps’, where animals prefer habitats conferring lower fitness than available alternatives. Evidence for traps includes cases where birds prefer breeding habitats associated with relatively high nest predation rates despite the importance of nest survival to avian fitness. Because birds select breeding habitat at multiple spatial scales, the processes underlying traps for birds are likely scale‐dependent. We studied a potential ecological trap for a population of yellow warblers Dendroica petechia while paying specific attention to spatial scale. We quantified nest microhabitat preference by comparing nest‐ versus random‐site microhabitat structure and related preferred microhabitat features with nest survival. Over a nine‐year study period and three study sites, we found a consistently negative relationship between preferred microhabitat patches and nest survival rates. Data from experimental nests described a similar relationship, corroborating the apparent positive relationship between preferred microhabitat and nest predation. As do other songbirds, yellow warblers select breeding habitat in at least two steps at two spatial scales; (1) they select territories at a coarser spatial scale and (2) nest microhabitats at a finer scale from within individual territories. By comparing nest versus random sites within territories, we showed that maladaptive nest microhabitat preferences arose during within‐territory nest site selection (step 2). Furthermore, nest predation rates varied at a fine enough scale to provide individual yellow warblers with lower‐predation alternatives to preferred microhabitats. Given these results, tradeoffs between nest survival and other fitness components are unlikely since fitness components other than nest survival are probably more relevant to territory‐scale habitat selection. Instead, exchanges of individuals among populations facing different predation regimes, the recent proliferation of the parasitic brown‐headed cowbird Molothrus ater, and/or anthropogenic changes to riparian vegetation structure are more likely explanations.     

Genetic structure,allozyme-habitat associations and reproductive fitness in Gypsophila fastigiata (Caryophyllaceae)

Relationships between allozyme differentiation, habitat variation and individual reproductive success were examined in local populations of a perennial herb, Gypsophila fastigiata, on the Baltic island of Öland (Sweden). Relatively little (c. 2%) of the total allozyme diversity in this largely outcrossing species is explained by differentiation between sites tens of kilometres apart. The low level of geographic differentiation suggests that gene flow between sites is, or has recently been, extensive. Yet the component of allozyme diversity due to differentiation between plots (only tens of meters apart) within sites is 3 times larger than the between-site component of diversity. Allozyme variation, especially at the Pgi-2 locus, is significantly associated with habitat variation within sites. Different allele x habitat combinations for the Pgi-2 locus are associated with differences in individual reproductive fitness. Differential selection in different local habitats may thus contribute to the fine-scale structuring of genetic diversity within sites.     

Winter microhabitat selection of a threatened pond amphibian in constructed urban wetlands

Mitigating the threat of habitat loss requires actions such as restoring and creating new habitat. In order to effectively achieve this, species habitat requirements and use patterns need to be understood. While many studies have been conducted on the habitat choice of species, these generally focused on habitat use during periods of high activity and detection probability without considering seasonal shifts in habitat use. Understanding habitat selection by frogs during the winter season of low activity may be crucial since it may differ from that used during the summer and may be overlooked as important for population success. We describe the microhabitat use of the threatened green and golden bell frog (Litoria aurea) using radio tracking methods during winter when detection is low and knowledge is limited. We followed 26 individuals between May and July, 2011 to determine whether they selected specific overwintering microhabitats and related this to levels of individual exposure to predators, distance from the edge of the water and temperature of microhabitats. We found that overwintering bell frogs inhabited reeds and rock gabions more frequently than expected and that females used a reduced subset of microhabitats compared to males. Additionally, microhabitats used were more likely to conceal an individual from view, and the majority of overwintering sites were located within 5 m of the edge of the water which may be important for reducing the risk of predation and desiccation. Rock gabions had significantly warmer (1.2°C–1.8°C) mean temperatures than the other microhabitats used. The information presented here can be used in habitat creation and reintroduction programmes to provide habitat which is suitable during both the breeding and non‐breeding season for the conservation of other populations.     

A model of polymorphism with several seasons and several habitats, and its application to the mosquito Aedes aegypti

Polymorphism has been shown to be possible but unlikely with a different selection intensity in each of several niches, or with varying selection intensity during successive generations. We show that polymorphism is likely with the combination of several niches and several seasons. The model contains two seasons, three habitats, many generations per season, habitat selection, positive assortative mating, movement between habitats, and different fitnesses of each genotype in each habitat. It is a stepping stone model with differential migration of genotypes. It is applied to the polymorphism of the indoor and the outdoor genotypes of the yellow fever mosquito Aedes aegypti. Matrix methods and simple models of population genetics comprised the computer model. Polymorphism is likely with most reasonable values of the parameters. Fitnesses and rate of movement are the most important parameters influencing the character and likelihood of polymorphism; habitat selection and positive assortative mating have much less effect. The model indicates that polymorphism of A. aegypti in east Africa results from: (1) the presence of a dry season when breeding occurs only in the human habitat; (2) greater fitness of the indoor ecotype in the human habitat and of the outdoor ecotype in the natural habitat; and (3) less than random movement between human and natural habitats.     

The composition and density of fauna utilizing burrow microhabitats created by a non-native burrowing crustacean (<Emphasis Type="Italic">Sphaeroma quoianum</Emphasis>)

The non-native isopod, Sphaeroma quoianum, has invaded many estuaries of the Pacific coast of North America. It creates extensive burrow microhabitats in intertidal and subtidal substrata that provide habitat for estuarine organisms. We sampled burrows to determine the effects of substratum type on the community of inquilines (burrow inhabitants). The density of inquilines was higher in wood and sandstone than marsh banks. Inquilines, representing 58 species from seven phyla, were present in 86% of samples. Inquilines equaled or outnumbered S. quoianum in 49% of the samples. Non-native fauna comprised 29% of the species and 35% of the abundance of inquilines, which is higher than other estuarine habitats in Coos Bay. Sessile non-native species were found living within burrows at tidal heights higher than their typical range. Thus, the novel habitat provided by burrows of S. quoianum may alter the densities and intertidal distribution of both native and non-native estuarine fauna.     

Fatal errors in set as a cost of dispersal and the influence of intertidal flora on set of barnacles

Summary Cyprid larvae of Balanus cariosus settle preferentially on slate plates with a biota characteristic of the lower intertidal shore, and the cyprids also prefer plates with more algae. Cyprid larvae of Balanus glandula had the same preferences in two out of three experiments. We conclude that some component of the flora guides both species during settling and metamorphosis. Data on vertical distribution and fecundity of B. glandula show that the preference for the lower shore decreases fitness of B. glandula at the site of the settling experiments and at most other sites sampled in or near the San Juan Islands, though in some restricted habitats in the San Juans and extensive areas in the adjacent regions of Puget Sound a preference for the lower shore is appropriate. Extensive dispersal among sites is possible in the planktonic period of 2 to 4 weeks. This example supports the hypothesis that a cost to large scale dispersal is lower fitness at many sites within a species' range. In this case the cost is through poorer correlation between stimuli guiding choice of habitat and favorability of habitat.     

An experimental analysis of the relationships between fitness components and malic enzyme genotypes inTribolium confusum

The hypothesis that natural selection is capable of maintaining allozyme variation in natural populations was tested using a species of flour beetles,Tribolium confusum. We selected a polymorphic locus (a locus encoding variation for malic enzyme) in an experimental population ofT. confusum and scored the genotypes at this locus for a series of fitness components on different flour types. Measurements included survival rate, development time, fecundity, and rate of egg cannibalism. Flour type had significant effects on most traits. Significant differences among genotypes for fecundity and rates of egg cannibalism and the presence of genotype × flour type interactions for development time were demonstrated. Thus, changes in allele frequencies at the malic enzyme locus could in part be under the influence of natural selection. The existence of genotype × flour type interactions suggests that environmental heterogeneity could maintain allozyme variation at the malic enzyme locus.     

Is local adaptation in Mimulus guttatus caused by trade‐offs at individual loci?

Local adaptation is considered to be the result of fitness trade‐offs for particular phenotypes across different habitats. However, it is unclear whether such phenotypic trade‐offs exist at the level of individual genetic loci. Local adaptation could arise from trade‐offs of alternative alleles at individual loci or by complementary sets of loci with different fitness effects of alleles in one habitat but selective neutrality in the alternative habitat. To evaluate the genome‐wide basis of local adaptation, we performed a field‐based quantitative trait locus (QTL) mapping experiment on recombinant inbred lines (RILs) created from coastal perennial and inland annual races of the yellow monkeyflower (Mimulus guttatus) grown reciprocally in native parental habitats. Overall, we detected 19 QTLs affecting one or more of 16 traits measured in two environments, most of small effect. We identified 15 additional QTL effects at two previously identified candidate QTLs [DIV ERGENCE (DIV)]. Significant QTL by environment interactions were detected at the DIV loci, which was largely attributable to genotypic differences at a single field site. We found no detectable evidence for trade‐offs for any one component of fitness, although DIV2 showed a trade‐off involving different fitness traits between sites, suggesting that local adaptation is largely controlled by non‐overlapping loci. This is surprising for an outcrosser, implying that reduced gene flow prevents the evolution of individuals adapted to multiple environments. We also determined that native genotypes were not uniformly adaptive, possibly reflecting fixed mutational load in one of the populations.     

Genomics meets applied ecology: Characterizing habitat quality for sloths in a tropical agroecosystem

Understanding how habitat quality in heterogeneous landscapes governs the distribution and fitness of individuals is a fundamental aspect of ecology. While mean individual fitness is generally considered a key to assessing habitat quality, a comprehensive understanding of habitat quality in heterogeneous landscapes requires estimates of dispersal rates among habitat types. The increasing accessibility of genomic approaches, combined with field‐based demographic methods, provides novel opportunities for incorporating dispersal estimation into assessments of habitat quality. In this study, we integrated genomic kinship approaches with field‐based estimates of fitness components and approximate Bayesian computation (ABC) procedures to estimate habitat‐specific dispersal rates and characterize habitat quality in two‐toed sloths (Choloepus hoffmanni) occurring in a Costa Rican agricultural ecosystem. Field‐based observations indicated that birth and survival rates were similar in a sparsely shaded cacao farm and adjacent cattle pasture–forest mosaic. Sloth density was threefold higher in pasture compared with cacao, whereas home range size and overlap were greater in cacao compared with pasture. Dispersal rates were similar between the two habitats, as estimated using ABC procedures applied to the spatial distribution of pairs of related individuals identified using 3,431 single nucleotide polymorphism and 11 microsatellite locus genotypes. Our results indicate that crops produced under a sparse overstorey can, in some cases, constitute lower‐quality habitat than pasture–forest mosaics for sloths, perhaps because of differences in food resources or predator communities. Finally, our study demonstrates that integrating field‐based demographic approaches with genomic methods can provide a powerful means for characterizing habitat quality for animal populations occurring in heterogeneous landscapes.