Experimental evidence that matching habitat choice drives local adaptation in a wild population

Unraveling Adaptive Evolutionary Divergence at Microgeographic Scales

AbstractStriking examples of local adaptation at fine geographic scales are increasingly being documented in natural populations. However, the relative contributions made by natural selection, phenotype-dependent dispersal (when individuals disperse with respect to a habitat preference), and mate preference in generating and maintaining microgeographic adaptation and divergence are not well studied. Here, we develop quantitative genetics models and individual-based simulations (IBSs) to uncover the evolutionary forces that possibly drive microgeographic divergence. We also perform Bayesian estimation of the parameters in our IBS using empirical data on habitat-specific variation in bill morphology in the island scrub-jay (Aphelocoma insularis) to apply our models to a natural system. We find that natural selection and phenotype-dependent dispersal can generate the patterns of divergence we observe in the island scrub-jay. However, mate preference for a mate with similar bill morphology, even though observed in the species, does not play a significant role in driving divergence. Our modeling approach provides insights into phenotypic evolution occurring over small spatial scales relative to dispersal ranges, suggesting that adaptive divergence at microgeographic scales may be common across a wider range of taxa than previously thought. Our quantitative genetic models help to inform future theoretical and empirical work to determine how selection, habitat preference, and mate preference contribute to local adaptation and microgeographic divergence.

Crypsis by background matching and disruptive coloration as drivers of substrate occupation in sympatric Amazonian bark praying mantises

Background matching and disruptive coloration are common camouflage strategies in nature, but few studies have accurately measured their protective value in living organisms. Amazon's Bark praying mantises exhibit colour patterns matching whitish and greenish-brown tree trunks. We tested the functional significance of background matching and disruptive coloration of different praying mantis morphospecies (white, grey and green) detected by DNA barcoding. Through image analysis, avian visual models and field experiments using humans as potential predators, we explored whether the background occupation of mantises provides camouflage against predation. Data were obtained for individuals against their occupied tree trunks (whitish or greenish-brown) and microhabitats (lichen or bryophyte patches), compared to non-occupied trunks. White and grey mantises showed lower colour contrasts against occupied trunks at the scale of tree trunk, with no differences in luminance contrasts. Conversely, green mantises showed lower colour and luminance contrasts against microhabitats and also exhibited high edge disruption against greenish-brown trunks. The camouflage of white and green mantis models against colour-matching trunks increased search time and reduced encounter distance of human predators. We highlight the importance of camouflage strategies at different spatial scales to enhance individual survival against predators. Specifically, we present a stunning study system to investigate the relationship of phylogenetically related species that use camouflage in sympatry.

A generalised approach to the study and understanding of adaptive evolution

Evolutionary theory has made large impacts on our understanding and management of the world, in part because it has been able to incorporate new data and new insights successfully. Nonetheless, there is currently a tension between certain biological phenomena and mainstream evolutionary theory. For example, how does the inheritance of molecular epigenetic changes fit into mainstream evolutionary theory? Is niche construction an evolutionary process? Is local adaptation via habitat choice also adaptive evolution? These examples suggest there is scope (and perhaps even a need) to broaden our views on evolution. We identify three aspects whose incorporation into a single framework would enable a more generalised approach to the understanding and study of adaptive evolution: (i) a broadened view of extended phenotypes; (ii) that traits can respond to each other; and (iii) that inheritance can be non-genetic. We use causal modelling to integrate these three aspects with established views on the variables and mechanisms that drive and allow for adaptive evolution. Our causal model identifies natural selection and non-genetic inheritance of adaptive parental responses as two complementary yet distinct and independent drivers of adaptive evolution. Both drivers are compatible with the Price equation; specifically, non-genetic inheritance of parental responses is captured by an often-neglected component of the Price equation. Our causal model is general and simplified, but can be adjusted flexibly in terms of variables and causal connections, depending on the research question and/or biological system. By revisiting the three examples given above, we show how to use it as a heuristic tool to clarify conceptual issues and to help design empirical research. In contrast to a gene-centric view defining evolution only in terms of genetic change, our generalised approach allows us to see evolution as a change in the whole causal structure, consisting not just of genetic but also of phenotypic and environmental variables.

Social phenotype-dependent selection of social environment in wild great and blue tits: an experimental study

There is growing evidence that individuals actively assess the match between their phenotype and their environment when making habitat choice decisions (so-called matching habitat choice). However, to our knowledge, no studies have considered how the social environment may interact with social phenotype in determining habitat choice, despite habitat choice being an inherently social process and growing evidence for individual variation in sociability. We conducted an experiment using wild great and blue tits to understand how birds integrate their social phenotype and social environment when choosing where and how to feed. We used programmable feeders to (i) record social interactions and estimate social phenotype, and (ii) experimentally manipulate the local density experienced by birds of differing social phenotype. By tracking feeder usage, we estimated how social environment and social phenotype predicted feeder choice and feeding behaviour. Both social environment and social phenotype predicted feeder usage, but a bird's decision to remain in a particular social environment did not depend on their social phenotype. By contrast, for feeding behaviour, responses to the social environment depended on social phenotype. Our results provide rare evidence of matching habitat choice and shed light on the dependence of habitat choice on between-individual differences in social phenotype.

Visual Background Choice and Light Environment Affect Male Guppy Visual Contrast

Male guppies (Poecilia reticulata) have multiple colored spots and perform courtship displays near the edges of streams in Trinidad in shallow water flowing through rainforest. Depending upon the orientation of the pair, the female sees the male displays against gravel or other stream bed substrates or against the spacelight—the roughly uniform light coming from the water column away from the bank. We observed courting pairs in two adjacent natural streams and noted the directions of each male display. We found that the female sees the male more often against spacelight than against gravel when females either faced the spacelight from the opposite bank or from downstream, or both. Visual modelling using natural substrate reflectances and field light measurements showed higher chromatic contrast of males against spacelight than against substrates independent of the two ambient light environments used during displays, but achromatic contrast depended upon the ambient light habitat. This suggests that courtship involves both chromatic and achromatic contrast. We conclude that the orientation of courting pairs and the ambient light spectrum should be accounted for in studies of mate choice, because the visual background and light affect visibility, and these differ with orientation.

Sexual Selection May Not Often Reduce Gene Flow Between Locally Adapted Populations. A Review of Some Evidence, and Suggestions for Better Tests

Sexually selected traits often depend on an individual’s physical condition, or otherwise indirectly reflect the ecological performance of individuals. When individuals disperse between populations that are locally adapted to different environments, their ecological performance may decline. This in turn may result in more poorly expressed sexual traits, and therefore in a lower reproductive success. Hence, sexual selection may reduce the effective gene flow between populations, and thereby maintain or even enhance population divergence. This hypothesis was published in a highly visible journal (van Doorn et al., 2009, Science). Here I review the subsequently published empirical tests of this hypothesis. I downloaded all metadata (incl. abstracts) of papers citing van Doorn et al. (2009) and read those papers that undertook relevant tests. To my surprise, only very few papers provided explicit tests of the hypothesis, this never involved plants, and only one study found support for it. While sexual selection may therefore not often reduce gene flow between locally adapted populations, some improvements to experimental design and choice of study system are noted. I therefore also provide a detailed list of suggestions for high quality tests of this hypothesis. This hopefully acts as a catalyst for more and better studies to test whether sexual and natural selection can work in synergy to reduce effective dispersal, and thereby protect and promote adaptive population divergence.

Habitat-linked genetic variation supports microgeographic adaptive divergence in an island-endemic bird species

We investigated the potential mechanisms driving habitat-linked genetic divergence within a bird species endemic to a single 250 km² island. The island scrub-jay (Aphelocoma insularis) exhibits microgeographic divergence in bill morphology across pine-oak ecotones on Santa Cruz Island, California (USA) similar to adaptive differences described in mainland congeners over much larger geographic scales. To test whether individuals exhibit genetic differentiation related to habitat type and divergence in bill length, we genotyped over 3,000 single nucleotide polymorphisms (SNPs) in 123 adult island scrub-jay males from across Santa Cruz Island using restriction site-associated DNA sequencing (RADseq). Neutral landscape genomic analyses revealed that genome-wide genetic differentiation was primarily related to geographic distance and differences in habitat composition. We also found 168 putatively adaptive loci associated with habitat type using multivariate redundancy analysis (RDA) while controlling for spatial effects. Finally, two genome-wide association analyses revealed a polygenic basis to variation in bill length with multiple loci detected in or near genes known to affect bill morphology in other birds. Our findings support the hypothesis that divergent selection at microgeographic scales can cause adaptive divergence in the presence of ongoing gene flow.

Lichens and animal camouflage: some observations from central Asian ecoregions

Camouflage is a fitness-relevant trait that supports survival and fosters evolutionary adaptation by which animals match their body pattern to a background setting. Lichens are among the most common of these backgrounds that several animal species use for camouflage. Lichens are omnipresent and grow in wide arrays of colorations and compositions. Their composition and phenotypic diversity might facilitate cryptic coloration and habitat matching by various animal species. Here, we describe the role of lichens in providing camouflage to various animal species in central Asian and Caucasus mountain ecoregions, which are categorized as global biodiversity hotspots. Despite multiple ecological studies, no information is available on the role of this regions‘ lichen diversity in providing animal camouflage. Casual field observations of lichen camouflage are reported for four (one mammal and three reptile) species: the Persian Leopard’s Panthera pardus saxicolor body coat seems to closely match the colors and patterns of saxicolous lichens (Acarospora sp. and Circinaria sp.) in their habitat.  A similar background matching pattern was observed in both morphs of the Caucasian Rock Agama Paralaudakia caucasia upon crustose lichens: Caloplaca spp., Circinaria spp., and the Radde’s Rock Lizard Darevskia raddei to the crustose lichens Acarospora sp. and Caloplaca sp. Likewise, the Horny-scaled Agama’s Trapelus ruderatus grey matches with the color of multiple lichens (Lecanora spp., Circinaria spp., Protoparmeliopsis spp., Rinodina spp., and Anaptychia spp.). Our observations preliminarily suggest that lichens play an important role for species of different trophic levels, ensuring adaptation and survival through camouflage. We call for more field-based empirical and experimental studies in various terrestrial ecosystems in other parts of the world to test the role of lichens in local adaption and evolutionary plasticity of regional species.

The Role of Directed Dispersal in Driving Genetic and Morphological Structure in Invasive Smallmouth Bass

Dispersal is an essential life-history trait crucial to species persistence and diversification. This is particularly important in spatiotemporal fluctuating environments such as freshwater habitats, where species movement is confined to the dendritic network and wetted boundaries. To persist in such fluctuating environments, a species can modify, adaptively and plastically, its phenotypic variation to better match the environment or escape via directed dispersal to a more suitable habitat (i.e., matching habitat choice). We use the invasive smallmouth bass, Micropterus dolomieu, sampled at 10 km intervals, to assess the effect of directed dispersal on the fine scale genetic and phenotypic variation in populations of M. dolomieu along a river course. Gene flow was used as a proxy for dispersal. By comparing population genetic structure, morphological variation (of linear traits and geometric landmarks), and environmental heterogeneity, we discovered a clear correlation between environmental variation and morphological traits. Although isolation by distance seemed to have shaped the overall genetic pattern detected among the populations, the strong genetic structuring observed within the Ratel tributary appeared to be non-random. These results provide novel insights into the potential mechanisms promoting the spread and establishment of invasive species and the possible influence multiple introductions may have on fine scale genetic structuring.

OUP accepted manuscript

Organisms interact with their environments in various ways. We present a conceptual framework that distinguishes three mechanisms of organism–environment interaction. We call these NC³ mechanisms: niche construction, in which individuals make changes to the environment; niche choice, in which individuals select an environment; and niche conformance, in which individuals adjust their phenotypes in response to the environment. Each of these individual-level mechanisms affects an individual's phenotype–environment match, its fitness, and its individualized niche, defined in terms of the environmental conditions under which the individual can survive and reproduce. Our framework identifies how individuals alter the selective regimes that they and other organisms experience. It also places clear emphasis on individual differences and construes niche construction and other processes as evolved mechanisms. The NC³ mechanism framework therefore helps to integrate population-level and individual-level research.

Habitat choice promotes and constrains phenotypic plasticity

Habitat choice can either speed up or slow rates of phenotypic evolution, depending on which trait is measured. We suggest that habitat choice plays an analogous, and generally overlooked, role in shaping patterns of phenotypic plasticity. Using our work with an amphibious fish, we discuss two case studies that demonstrate how habitat choice can both promote and constrain expression of plasticity. First, habitat choice during the dry season accentuates adaptive metabolic plasticity and minimizes maladaptive changes to muscle, ultimately increasing survival time out of water. Second, a trade-off between water- and air-breathing drives matching habitat choice, resulting in positive feedback that reinforces respiratory specialization and environmental preference. Overall, these case studies demonstrate that we must consider the interactions between plasticity and habitat choice to fully understand how animals survive in the face of environmental change. Without considering both processes simultaneously, the performance of animals in challenging conditions can be either under- or over-estimated. Finally, because habitat choice shapes the frequency and predictability of environmental changes that animals experience, feedback between habitat choice and expressions of phenotypic plasticity may be an important factor that influences how plasticity evolves.

Phenotypic variation in urban environments: mechanisms and implications

In the past decade, numerous studies have explored how urbanisation affects the mean phenotypes of populations, but it remains unknown how urbanisation impacts phenotypic variation, a key target of selection that shapes, and is shaped by, eco-evolutionary processes. Our review suggests that urbanisation may often increase intraspecific phenotypic variation through several processes; a conclusion aligned with results from our illustrative analysis on tit morphology across 13 European city/forest population pairs. Urban-driven changes in phenotypic variation will have immense implications for urban populations and communities, particularly through urbanisation's effects on individual fitness, species interactions, and conservation. We call here for studies that incorporate phenotypic variation in urban eco-evolutionary research alongside advances in theory.

Social competition as a driver of phenotype-environment correlations: implications for ecology and evolution

While it is universally recognised that environmental factors can cause phenotypic trait variation via phenotypic plasticity, the extent to which causal processes operate in the reverse direction has received less consideration. In fact individuals are often active agents in determining the environments, and hence the selective regimes, they experience. There are several important mechanisms by which this can occur, including habitat selection and niche construction, that are expected to result in phenotype–environment correlations (i.e. non‐random assortment of phenotypes across heterogeneous environments). Here we highlight an additional mechanism – intraspecific competition for preferred environments – that may be widespread, and has implications for phenotypic evolution that are currently underappreciated. Under this mechanism, variation among individuals in traits determining their competitive ability leads to phenotype–environment correlation; more competitive phenotypes are able to acquire better patches. Based on a concise review of the empirical evidence we argue that competition‐induced phenotype–environment correlations are likely to be common in natural populations before highlighting the major implications of this for studies of natural selection and microevolution. We focus particularly on two central issues. First, competition‐induced phenotype–environment correlation leads to the expectation that positive feedback loops will amplify phenotypic and fitness variation among competing individuals. As a result of being able to acquire a better environment, winners gain more resources and even better phenotypes – at the expense of losers. The distinction between individual quality and environmental quality that is commonly made by researchers in evolutionary ecology thus becomes untenable. Second, if differences among individuals in competitive ability are underpinned by heritable traits, competition results in both genotype–environment correlations and an expectation of indirect genetic effects (IGEs) on resource‐dependent life‐history traits. Theory tells us that these IGEs will act as (partial) constraints, reducing the amount of genetic variance available to facilitate evolutionary adaptation. Failure to recognise this will lead to systematic overestimation of the adaptive potential of populations. To understand the importance of these issues for ecological and evolutionary processes in natural populations we therefore need to identify and quantify competition‐induced phenotype–environment correlations in our study systems. We conclude that both fundamental and applied research will benefit from an improved understanding of when and how social competition causes non‐random distribution of phenotypes, and genotypes, across heterogeneous environments.

Urban specialization reduces habitat connectivity by a highly mobile wading bird

BACKGROUND

Mobile animals transport nutrients and propagules across habitats, and are crucial for the functioning of food webs and for ecosystem services. Human activities such as urbanization can alter animal movement behavior, including site fidelity and resource use. Because many urban areas are adjacent to natural sites, mobile animals might connect natural and urban habitats. More generally, understanding animal movement patterns in urban areas can help predict how urban expansion will affect the roles of highly mobile animals in ecological processes.

METHODS

Here, we examined movements by a seasonally nomadic wading bird, the American white ibis (Eudocimus albus), in South Florida, USA. White ibis are colonial wading birds that forage on aquatic prey; in recent years, some ibis have shifted their behavior to forage in urban parks, where they are fed by people. We used a spatial network approach to investigate how individual movement patterns influence connectivity between urban and non-urban sites. We built a network of habitat connectivity using GPS tracking data from ibis during their non-breeding season and compared this network to simulated networks that assumed individuals moved indiscriminately with respect to habitat type.

RESULTS

We found that the observed network was less connected than the simulated networks, that urban-urban and natural-natural connections were strong, and that individuals using urban sites had the least-variable habitat use. Importantly, the few ibis that used both urban and natural habitats contributed the most to connectivity.

CONCLUSIONS

Habitat specialization in urban-acclimated wildlife could reduce the exchange of propagules and nutrients between urban and natural areas, which has consequences both for beneficial effects of connectivity such as gene flow and for detrimental effects such as the spread of contaminants or pathogens.