Collecting eco‐evolutionary data in the dark: Impediments to subterranean research and how to overcome them

1. Caves and other subterranean habitats fulfill the requirements of experimental model systems to address general questions in ecology and evolution. Yet, the harsh working conditions of these environments and the uniqueness of the subterranean organisms have challenged most attempts to pursuit standardized research.
2. Two main obstacles have synergistically hampered previous attempts. First, there is a habitat impediment related to the objective difficulties of exploring subterranean habitats and our inability to access the network of fissures that represents the elective habitat for the so‐called “cave species.” Second, there is a biological impediment illustrated by the rarity of most subterranean species and their low physiological tolerance, often limiting sample size and complicating laboratory experiments.
3. We explore the advantages and disadvantages of four general experimental setups (in situ, quasi in situ, ex situ, and in silico) in the light of habitat and biological impediments. We also discuss the potential of indirect approaches to research. Furthermore, using bibliometric data, we provide a quantitative overview of the model organisms that scientists have exploited in the study of subterranean life.
4. Our over‐arching goal is to promote caves as model systems where one can perform standardized scientific research. This is important not only to achieve an in‐depth understanding of the functioning of subterranean ecosystems but also to fully exploit their long‐discussed potential in addressing general scientific questions with implications beyond the boundaries of this discipline.

     

A modified niche model for generating food webs with stage‐structured consumers: The stabilizing effects of life‐history stages on complex food webs

1. Almost all organisms grow in size during their lifetime and switch diets, trophic positions, and interacting partners as they grow. Such ontogenetic development introduces life‐history stages and flows of biomass between the stages through growth and reproduction. However, current research on complex food webs rarely considers life‐history stages. The few previously proposed methods do not take full advantage of the existing food web structural models that can produce realistic food web topologies.
2. We extended the niche model developed by Williams and Martinez (Nature, 2000, 404, 180–183) to generate food webs that included trophic species with a life‐history stage structure. Our method aggregated trophic species based on niche overlap to form a life‐history structured population; therefore, it largely preserved the topological structure of food webs generated by the niche model. We applied the theory of allometric predator–prey body mass ratio and parameterized an allometric bioenergetic model augmented with biomass flow between stages via growth and reproduction to study the effects of a stage structure on the stability of food webs.
3. When life‐history stages were linked via growth and reproduction, more food webs persisted, and persisting food webs tended to retain more trophic species. Topological differences between persisting linked and unlinked food webs were small to modest. The slopes of biomass spectra were lower, and weak interaction links were more prevalent in the linked food webs than the unlinked ones, suggesting that a life‐history stage structure promotes characteristics that can enhance stability of complex food webs.
4. Our results suggest a positive relationship between the complexity and stability of complex food webs. A life‐history stage structure in food webs may play important roles in dynamics of and diversity in food webs.

     

Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels,Dreissena rostriformis bugensis in flowing water

1. The early detection of invasive non‐native species (INNS) is important for informing management actions. Established monitoring methods require the collection or observation of specimens, which is unlikely at the beginning of an invasion when densities are likely to be low. Environmental DNA (eDNA) analysis is a highly promising technique for the detection of INNS—particularly during the early stages of an invasion.
2. Here, we compared the use of traditional kick‐net sampling with two eDNA approaches (targeted detection using both conventional and quantitative PCR and passive detection via metabarcoding with conserved primers) for detection of quagga mussel, Dreissena rostriformis bugensis, a high priority INNS, along a density gradient on the River Wraysbury, UK.
3. All three molecular tools outperformed traditional sampling in terms of detection. Conventional PCR and qPCR both had 100% detection rate in all samples and outperformed metabarcoding when the target species was at low densities. Additionally, quagga mussel DNA copy number (qPCR) and relative read count (metabarcoding) were significantly influenced by both mussel density and distance from source population, with distance being the most significant predictor.
4. Synthesis and application. All three molecular approaches were more sensitive than traditional kick‐net sampling for the detection of the quagga mussel in flowing water, and both qPCR and metabarcoding enabled estimates of relative abundance. Targeted approaches were more sensitive than metabarcoding, but metabarcoding has the advantage of providing information on the wider community and consequently the impacts of INNS.

     

Age‐specific habitat preference,carrying capacity,and landscape structure determine the response of population spatial variability to fishing‐driven age truncation

1. Understanding the mechanisms underlying spatial variability of exploited fish is critical for the sustainable management of fish stocks. Empirical studies suggest that size‐selective fishing can elevate fish population spatial variability (i.e., more heterogeneous distribution) through age truncation, making the population less resilient to changing environment. However, species differ in how their spatial variability responds to age truncation and the underlying mechanisms remain unclear.
2. We hypothesize that age‐specific habitat preference, together with environmental carrying capacity and landscape structure, determines the response of population spatial variability to fishing‐induced age truncation. To test these hypotheses, we design an individual‐based model of an age‐structured fish population on a two‐dimensional landscape under size‐selective fishing. Individual fish reproduces and survives, and moves between habitats according to age‐specific habitat preference and density‐dependent habitat selection.
3. Population spatial variability elevates with increasing age truncation, and the response is stronger for populations with stronger age‐specific habitat preference. On a gradient landscape, reducing carrying capacity elevates the relative importance of density dependence in habitat selection, which weakens the response of spatial variability to age truncation for populations with strong age‐specific habitat preference. On a fragmented landscape, both populations with strong and weak age‐specific habitat preferences are restricted at local optimal habitats, and reducing carrying capacity weakens the responses of spatial variability to age truncation for both populations.
4. Synthesis and applications. We demonstrate that to track and predict the changes in population spatial variability under exploitation, it is essential to consider the interactive effects of age‐specific habitat preference, carrying capacity, and landscape structure. To improve spatial management in fisheries, it is crucial to enhance empirical and theoretical developments in the methodology to quantify age‐specific habitat preference of marine fish, and to understand how climatic change influences carrying capacity and landscape continuity.

     

Population dynamics of little brown bats (Myotis lucifugus) at summer roosts: Apparent survival,fidelity, abundance,and the influence of winter conditions

1. White‐nose syndrome (WNS) has caused the death of millions of bats, but the impacts have been more difficult to identify in western North America. Understanding how WNS, or other threats, impacts western bats may require monitoring other roosts, such as maternity roosts and night roosts, where bats aggregate in large numbers.
2. Little brown bats (Myotis lucifugus) are experiencing some of the greatest declines from WNS. Estimating survival and understanding population dynamics can provide valuable data for assessing population declines and informing conservation efforts.
3. We conducted a 5‐year mark–recapture study of two M. lucifugus roosts in Colorado. We used the robust design model to estimate apparent survival, fidelity, and abundance to understand population dynamics, and environmental covariates to understand how summer and winter weather conditions impact adult female survival. We compared the fidelity and capture probability of M. lucifugus between colonies to understand how bats use such roosts.
4. Overwinter survival increased with the number of days with temperatures below freezing (β > 0.100, SE = 0.003) and decreased with the number of days with snow cover (β < −0.40, SE < 0.13). Adult female fidelity was higher at one maternity roost than the other. Overwinter and oversummer adult female survival was high (>0.90), and based on survival estimates and fungal‐swabbing results, we believe these populations have yet to experience WNS.
5. Recapture of M. lucifugus using antennas that continuously read passive integrated transponder tags allows rigorous estimation of bat population parameters that can elucidate trends in abundance and changes in survival. Monitoring populations at summer roosts can provide unique population ecology data that monitoring hibernacula alone may not. Because few adult males are captured at maternity colonies, and juvenile males have low fidelity, additional effort should focus on understanding male M. lucifugus population dynamics.

     

Current and time‐lagged effects of climate on innate immunity in two sympatric snake species

1. Changing environments result in alterations at all levels of biological organization, from genetics to physiology to demography. The increasing frequency of droughts worldwide is associated with higher temperatures and reduced precipitation that can impact population persistence via effects on individual immune function and survival.
2. We examined the effects of annual climate variation on immunity in two sympatric species of garter snakes from four populations in California over a seven‐year period that included the record‐breaking drought.
3. We examined three indices of innate immunity: bactericidal competence (BC), natural antibodies (NABs), and complement‐mediated lysis (CL).
4. Precipitation was the only climatic variable explaining variation in immune function: spring precipitation of the current year was positively correlated to Thamnophis sirtalis BC and NABs, whereas spring precipitation of the previous year was positively correlated to T. elegans BC and NABs. This suggests that T. elegans experiences a physiological time‐lag in response to reduced precipitation, which may reflect lack of capital for investment in immunity in the year following a dry year.
5. In general, our findings demonstrate compelling evidence that climate can influence wild populations through effects on physiological processes, suggesting that physiological indices such as these may offer valuable opportunities for monitoring the effects of climate.

     

Context‐dependent outcomes in a reproductive mutualism between two freshwater fish species

1. The development of encompassing general models of ecology is precluded by underrepresentation of certain taxa and systems. Models predicting context‐dependent outcomes of biotic interactions have been tested using plants and bacteria, but their applicability to higher taxa is largely unknown.
2. We examined context dependency in a reproductive mutualism between two stream fish species: mound nest‐building bluehead chub Nocomis leptocephalus and mountain redbelly dace Chrosomus oreas, which often uses N. leptocephalus nests for spawning. We hypothesized that increased predator density and decreased substrate availability would increase the propensity of C. oreas to associate with N. leptocephalus and decrease reproductive success of both species.
3. In a large‐scale in situ experiment, we manipulated egg predator density and presence of both symbionts (biotic context), and replicated the experiment in habitats containing high‐ and low‐quality spawning substrate (abiotic context).
4. Contradictory to our first hypothesis, we observed that C. oreas did not spawn without its host. The interaction outcome switched from commensalistic to mutualistic with changing abiotic and biotic contexts, although the net outcome was mutualistic.
5. The results of this study yielded novel insight into how context dependency operates in vertebrate mutualisms. Although the dilution effect provided by C. oreas positively influenced reproductive success of N. leptocephalus, it was not enough to overcome both egg predation and poor spawning habitat quality. Outcomes of the interaction may be ultimately determined by associate density. Studies of context dependency in vertebrate systems require detailed knowledge of species life‐history traits.

     

Weather variation affects the dispersal of grasshoppers beyond their elevational ranges

1. Understanding how abiotic conditions influence dispersal patterns of organisms is important for understanding the degree to which species can track and persist in the face of changing climate.
2. The goal of this study was to understand how weather conditions influence the dispersal pattern of multiple nonmigratory grasshopper species from lower elevation grassland habitats in which they complete their life‐cycles to higher elevations that extend beyond their range limits.
3. Using over a decade of weekly spring to late‐summer field survey data along an elevational gradient, we explored how abundance and richness of dispersing grasshoppers were influenced by temperature, precipitation, and wind speed and direction. We also examined how changes in population sizes at lower elevations might influence these patterns.
4. We observed that the abundance of dispersing grasshoppers along the gradient declined 4‐fold from the foothills to the subalpine and increased with warmer conditions and when wind flow patterns were mild or in the downslope direction. Thirty‐eight unique grasshopper species from lowland sites were detected as dispersers across the survey years, and warmer years and weak upslope wind conditions also increased the richness of these grasshoppers. The pattern of grasshoppers along the gradient was not sex biased. The positive effect of temperature on dispersal rates was likely explained by an increase in dispersal propensity rather than by an increase in the density of grasshoppers at low elevation sites.
5. The results of this study support the hypothesis that the dispersal patterns of organisms are influenced by changing climatic conditions themselves and as such, that this context‐dependent dispersal response should be considered when modeling and forecasting the ability of species to respond to climate change.

     

pyResearchInsights—An open‐source Python package for scientific text analysis

1. With an increasing number of scientific articles published each year, there is a need to synthesize and obtain insights across ever‐growing volumes of literature. Here, we present pyResearchInsights, a novel open‐source automated content analysis package that can be used to analyze scientific abstracts within a natural language processing framework.
2. The package collects abstracts from scientific repositories, identifies topics of research discussed in these abstracts, and presents interactive concept maps to visualize these research topics. To showcase the utilities of this package, we present two examples, specific to the field of ecology and conservation biology.
3. First, we demonstrate the end‐to‐end functionality of the package by presenting topics of research discussed in 1,131 abstracts pertaining to birds of the Tropical Andes. Our results suggest that a large proportion of avian research in this biodiversity hotspot pertains to species distributions, climate change, and plant ecology.
4. Second, we retrieved and analyzed 22,561 abstracts across eight journals in the field of conservation biology to identify twelve global topics of conservation research. Our analysis shows that conservation policy and landscape ecology are focal topics of research. We further examined how these conservation‐associated research topics varied across five biodiversity hotspots.
5. Lastly, we compared the utilities of this package with existing tools that carry out automated content analysis, and we show that our open‐source package has wider functionality and provides end‐to‐end utilities that seldom exist across other tools.

     

Spatial capture–recapture with random thinning for unidentified encounters

1. Spatial capture–recapture (SCR) models have increasingly been used as a basis for combining capture–recapture data types with variable levels of individual identity information to estimate population density and other demographic parameters. Recent examples are the unmarked SCR (or spatial count model), where no individual identities are available and spatial mark–resight (SMR) where individual identities are available for only a marked subset of the population. Currently lacking, though, is a model that allows unidentified samples to be combined with identified samples when there are no separate classes of “marked” and “unmarked” individuals and when the two sample types cannot be considered as arising from two independent observation models. This is a common scenario when using noninvasive sampling methods, for example, when analyzing data on identified and unidentified photographs or scats from the same sites.
2. Here we describe a “random thinning” SCR model that utilizes encounters of both known and unknown identity samples using a natural mechanistic dependence between samples arising from a single observation model. Our model was fitted in a Bayesian framework using NIMBLE.
3. We investigate the improvement in parameter estimates by including the unknown identity samples, which was notable (up to 79% more precise) in low‐density populations with a low rate of identified encounters. We then applied the random thinning SCR model to a noninvasive genetic sampling study of brown bear (Ursus arctos) density in Oriental Cantabrian Mountains (North Spain).
4. Our model can improve density estimation for noninvasive sampling studies for low‐density populations with low rates of individual identification, by making use of available data that might otherwise be discarded.

     

Growth patterns of the pan‐European freshwater mussel,Anodonta anatina (Linnaeus, 1758) (Bivalvia: Unionidae), vary with sex and mortality in populations

1. Post‐maturation growth leading to indeterminate growth patterns is widespread in nature. However, its adaptive value is unclear. Life history theory suggests this allocation strategy may be favored by temporal pulses in the intensity of mortality and/or the capacity to produce new tissues.
2. Addressing the origin of indeterminate growth and the variability of growth patterns, we studied the growth of duck mussels, Anodonta anatina, a pan‐European unionid, in 18 Polish lakes. For each population, the sex, size, and age of collected mussels were measured to estimate Bertalanffy''s growth curve parameters. We integrated information on A. anatina mortality rates, lake trophy, biofouling by zebra mussels, Dreissena polymorpha, and the prevalence of parasitic trematode larvae to identify selective conditions in lakes.
3. We found two sources of mortality in A. anatina populations, pertaining to adverse effects of zebra mussel biofouling and trophy state on mussel survival. Additionally, populations with heavier biofouling presented a smaller abundance of parasites, indicative of a relationship between filtering intensity and contraction of water‐borne trematode larvae by filtering A. anatina.
4. Consistently for each sex, populations with a greater trophy‐related mortality were characterized in A. anatina by a smaller asymptotic size L_max, indicative of a life history response to mortality risk involving early maturation at a smaller body size. In all populations, females featured higher mortality and larger asymptotic size versus males.
5. Our findings support a theoretical view that adaptive responses to selection involve adjustments in the lifetime resource allocation patterns. These adjustments should be considered drivers of the origin of indeterminate growth strategy in species taking parental care by offspring brooding in body cavities.

     

Age‐ and sex‐related dietary specialization facilitate seasonal resource partitioning in a migratory shorebird

1. Dietary specialization is common in animals and has important implications for individual fitness, inter‐ and intraspecific competition, and the adaptive potential of a species. Diet composition can be influenced by age‐ and sex‐related factors including an individual''s morphology, social status, and acquired skills; however, specialization may only be necessary when competition is intensified by high population densities or increased energetic demands.
2. To better understand the role of age‐ and sex‐related dietary specialization in facilitating seasonal resource partitioning, we inferred the contribution of biofilm, microphytobenthos, and benthic invertebrates to the diets of western sandpipers (Calidris mauri) from different demographic groups during mid‐winter (January/February) and at the onset of the breeding migration (April) using stable isotope mixing models. Western sandpipers are sexually dimorphic with females having significantly greater body mass and bill length than males.
3. Diet composition differed between seasons and among demographic groups. In winter, prey consumption was similar among demographic groups, but, in spring, diet composition differed with bill length and body mass explaining 31% of the total variation in diet composition. Epifaunal invertebrates made up a greater proportion of the diet in males which had lesser mass and shorter bills than females. Consumption of Polychaeta increased with increasing bill length and was greatest in adult females. In contrast, consumption of microphytobenthos, thought to be an important food source for migrating sandpipers, increased with decreasing bill length and was greatest in juvenile males.
4. Our results provide the first evidence that age‐ and sex‐related dietary specialization in western sandpipers facilitate seasonal resource partitioning that could reduce competition during spring at the onset of the breeding migration.
5. Our study underscores the importance of examining resource partitioning throughout the annual cycle to inform fitness and demographic models and facilitate conservation efforts.

     

Spatial structure of reproductive success infers mechanisms of ungulate invasion in Nearctic boreal landscapes

1. Landscape change is a key driver of biodiversity declines due to habitat loss and fragmentation, but spatially shifting resources can also facilitate range expansion and invasion. Invasive populations are reproductively successful, and landscape change may buoy this success.
2. We show how modeling the spatial structure of reproductive success can elucidate the mechanisms of range shifts and sustained invasions for mammalian species with attendant young. We use an example of white‐tailed deer (deer; Odocoileus virginianus) expansion in the Nearctic boreal forest, a North American phenomenon implicated in severe declines of threatened woodland caribou (Rangifer tarandus).
3. We hypothesized that deer reproductive success is linked to forage subsidies provided by extensive landscape change via resource extraction. We measured deer occurrence using data from 62 camera traps in northern Alberta, Canada, over three years. We weighed support for multiple competing hypotheses about deer reproductive success using multistate occupancy models and generalized linear models in an AIC‐based model selection framework.
4. Spatial patterns of reproductive success were best explained by features associated with petroleum exploration and extraction, which offer early‐seral vegetation resource subsidies. Effect sizes of anthropogenic features eclipsed natural heterogeneity by two orders of magnitude. We conclude that anthropogenic early‐seral forage subsidies support high springtime reproductive success, mitigating or exceeding winter losses, maintaining populations.
5. Synthesis and Applications. Modeling spatial structuring in reproductive success can become a key goal of remote camera‐based global networks, yielding ecological insights into mechanisms of invasion and range shifts to inform effective decision‐making for global biodiversity conservation.

     

A community context for aggression? Multi‐species audience effects on territorial aggression in two species of Paridae

1. Territorial aggression in birds is widely observed and is commonly linked to sex, age, body size, physiology, seasonal cues, food resource, urbanization, and a variety of social contexts including conspecific audience effects. However, little is known about the heterospecific audience effects on territorial aggression.
2. Here, we address an emerging idea that heterospecific audience effects may be pervasive influences in the social lives of free‐living birds. We tested the hypothesis that the composition, number, and relative body size of heterospecific audiences observing an aggressive contest will influence the response probability and intensity of aggression displayed.
3. We subjected two Paridae species, tufted titmouse (TUTI, Baeolophus bicolor) and Carolina chickadee (CACH, Poecile carolinensis), to playbacks of aggressive calls during a breeding season in north‐central Florida. At widely spaced playback sites (N = 134) in woodland habitats, we characterized the makeup of heterospecific audiences, aggression type (intra vs. interspecific territoriality), local population density, and various environmental factors (tree density, wind speed, and noise level) that are likely to influence territorial aggression.
4. We found that the presence of heterospecific audiences increased TUTI aggression levels and that both parids were more likely to respond to playback stimuli when their audiences had higher heterospecific diversity (more heterospecific individuals and species). We also found TUTI were more likely to respond when CACH were present but not vice versa.
5. In conclusion, we found evidence that heterospecific audiences significantly influenced the metrics of territorial aggression of free‐living animals and we suggest that the definition of audience effects on the behavior of free‐living animals be expanded to incorporate heterospecific audiences.

     

Nutrient trade‐offs mediated by ectomycorrhizal strategies in plants: Evidence from an Abies species in subalpine forests

1. Ectomycorrhizal (ECM) symbiosis is an evolutionary biological trait of higher plants for effective nutrient uptakes. However, little is known that how the formation and morphological differentiations of ECM roots mediate the nutrients of below‐ and aboveground plant tissues and the balance among nutrient elements across environmental gradients. Here, we investigated the effects of ECM foraging strategies on root and foliar N and P concentrations and N:P ratio Abies faxoniana under variations of climate and soil conditions.
2. The ECM symbionts preferentially mediated P uptake under both N and P limitations. The uptake efficiency of N and P was primarily associated with the ECM root traits, for example, ECM root tip density, superficial area of ECM root tips, and the ratio of living to dead root tips, and was affected by the ECM proliferations and morphological differentiations. The tissue N and P concentrations were positively associated with the abundance of the contact exploration type and negatively with that of the short‐distance exploration type.
3. Our findings indicate that the nutritional status of both below‐ and aboveground plant tissues can be strongly affected by ECM symbiosis in natural environments. Variations in the ECM strategies in response to varying environmental conditions significantly influence plant nutrient uptakes and trade‐offs.

     

Differential spatial responses of rodents to masting on forest sites with differing disturbance history

Mast seeding, the synchronized interannual variation in seed production of trees, is a well‐known bottom‐up driver for population densities of granivorous forest rodents. Such demographic effects also affect habitat preferences of the animals: After large seed production events, reduced habitat selectivity can lead to spillover from forest patches into adjacent alpine meadows or clear‐cuts, as has been reported for human‐impacted forests. In unmanaged, primeval forests, however, gaps created by natural disturbances are typical elements, yet it is unclear whether the same spillover dynamics occur under natural conditions. To determine whether annual variation in seed production drives spillover effects in naturally formed gaps, we used 14 years of small mammal trapping data combined with seed trap data to estimate population densities of Apodemus spp. mice and bank voles (Myodes glareolus) on 5 forest sites with differing disturbance history. The study sites, located in a forest dominated by European beech (Fagus sylvatica), Norway spruce (Picea abies), and silver fir (Abies alba), consisted of two primeval forest sites with small canopy gaps, two sites with larger gaps (after an avalanche event and a windthrow event), and a managed forest stand with closed canopy as a control. Hierarchical Bayesian N‐mixture models revealed a strong influence of seed rain on small rodent abundance, which were site‐specific for M. glareolus but not for Apodemus spp. Following years of moderate or low seed crop, M. glareolus avoided open habitat patches but colonized those habitats in large numbers after full mast events, suggesting that spillover events also occur in unmanaged forests, but not in all small rodents. The species‐ and site‐specific characteristics of local density responding to food availability have potentially long‐lasting effects on forest gap regeneration dynamics and should be addressed in future studies.     

PhenoSpace: A Shiny application to visualize trait data in the phenotypic space of the global spectrum of plant form and function

1. A recent analysis of variation in six major traits conducted on a large worldwide sample of vascular plant species showed that three‐quarters of trait variation was captured by a two‐dimensional global spectrum of plant form and function (“global spectrum” hereafter). We developed the PhenoSpace application, whose aim is to visualize and export the position of any individual/population/species in the phenotypic space of the global spectrum.
2. PhenoSpace is a Shiny application that helps users to manipulate and visualize data pertaining to the global spectrum of plant form and function. It is freely accessible at the following URL: https://shiny.cefe.cnrs.fr/PhenoSpace/.
3. PhenoSpace has three main functionalities. First, it allows users to visualize the phenotypic space of the global spectrum using different combinations of traits and growth forms. Second, trait data from any new user‐defined dataset can be projected onto the phenotypic space of the global spectrum, provided that at least two of the six traits are available. Finally, figures produced and loadings of the imported data on the PCA axes can be downloaded, allowing users to conduct further analyses.
4. PhenoSpace fulfills the practical goal of positioning plants in the phenotypic space of the global spectrum, making it possible to compare trait variation at any level of organization against the worldwide background. This serves a major aim of comparative plant ecology, which is to put specific sets of individuals, populations or species into a broader context, facilitating comparison and synthesis of results across different continents and environments using relevant indicators of plant design and function.

     

Differences in dietary composition and preference maintained despite gene flow across a woodrat hybrid zone

1. Ecotones, characterized by adjacent yet distinct biotic communities, provide natural laboratories in which to investigate how environmental selection influences the ecology and evolution of organisms. For wild herbivores, differential plant availability across sharp ecotones may be an important source of dietary‐based selection.
2. We studied small herbivore diet composition across a sharp ecotone where two species of woodrat, Neotoma bryanti and N. lepida, come into secondary contact with one another and hybridize. We quantified woodrat dietary preference through trnL metabarcoding of field‐collected fecal pellets and experimental choice trials. Despite gene flow, parental N. bryanti and N. lepida maintain distinct diets across this fine spatial scale, and across temporal scales that span both wet and dry conditions.
3. Neotoma bryanti maintained a more diverse diet, with Frangula californica (California coffeeberry) making up a large portion of its diet. Neotoma lepida maintains a less diverse diet, with Prunus fasciculata (desert almond) comprising more than half of its diet. Both F. californica and P. fasciculata are known to produce potentially toxic plant secondary compounds (PSCs), which should deter herbivory, yet these plants have relatively high nutritional value as measured by crude protein content.
4. Neotoma bryanti and N. lepida consumed F. californica and P. fasciculata, respectively, in greater abundance than these plants are available on the landscape—indicating dietary selection. Finally, experimental preference trials revealed that N. bryanti exhibited a preference for F. californica, while N. lepida exhibited a relatively stronger preference for P. fasciculata. We find that N. bryanti exhibit a generalist herbivore strategy relative to N. lepida, which exhibit a more specialized feeding strategy in this study system.
5. Our results suggest that woodrats respond to fine‐scale environmental differences in plant availability that may require different metabolic strategies in order to balance nutrient acquisition while minimizing exposure to potentially toxic PSCs.

     

Looking for the needle in a downsized haystack: Whole‐exome sequencing unravels genomic signals of climatic adaptation in Douglas‐fir (Pseudotsuga menziesii)

1. Conifers often occur along steep gradients of diverse climates throughout their natural ranges, which is expected to result in spatially varying selection to local climate conditions. However, signals of climatic adaptation can often be confounded, because unraveled clines covary with signals caused by neutral evolutionary processes such as gene flow and genetic drift. Consequently, our understanding of how selection and gene flow have shaped phenotypic and genotypic differentiation in trees is still limited.
2. A 40‐year‐old common garden experiment comprising 16 Douglas‐fir (Pseudotsuga menziesii) provenances from a north‐to‐south gradient of approx. 1,000 km was analyzed, and genomic information was obtained from exome capture, which resulted in an initial genomic dataset of >90,000 single nucleotide polymorphisms. We used a restrictive and conservative filtering approach, which permitted us to include only SNPs and individuals in environmental association analysis (EAA) that were free of potentially confounding effects (LD, relatedness among trees, heterozygosity deficiency, and deviations from Hardy–Weinberg proportions). We used four conceptually different genome scan methods based on F_ST outlier detection and gene–environment association in order to disentangle truly adaptive SNPs from neutral SNPs.
3. We found that a relatively small proportion of the exome showed a truly adaptive signal (0.01%–0.17%) when population substructuring and multiple testing was accounted for. Nevertheless, the unraveled SNP candidates showed significant relationships with climate at provenance origins, which strongly suggests that they have featured adaptation in Douglas‐fir along a climatic gradient. Two SNPs were independently found by three of the employed algorithms, and one of them is in close proximity to an annotated gene involved in circadian clock control and photoperiodism as was similarly found in Populus balsamifera.

Synthesis. We conclude that despite neutral evolutionary processes, phenotypic and genomic signals of adaptation to climate are responsible for differentiation, which in particular explain disparity between the well‐known coastal and interior varieties of Douglas‐fir.     

Ecological adaptation drives wood frog population divergence in life history traits

Phenotypic variation among populations is thought to be generated from spatial heterogeneity in environments that exert selection pressures that overcome the effects of gene flow and genetic drift. Here, we tested for evidence of isolation by distance or by ecology (i.e., ecological adaptation) to generate variation in early life history traits and phenotypic plasticity among 13 wood frog populations spanning 1200 km and 7° latitude. We conducted a common garden experiment and related trait variation to an ecological gradient derived from an ecological niche model (ENM) validated to account for population density variation. Shorter larval periods, smaller body weight, and relative leg lengths were exhibited by populations with colder mean annual temperatures, greater precipitation, and less seasonality in precipitation and higher population density (high-suitability ENM values). After accounting for neutral genetic variation, the Q_ST–F_ST analysis supported ecological selection as the key process generating population divergence. Further, the relationship between ecology and traits was dependent upon larval density. Specifically, high-suitability/high-density populations in the northern part of the range were better at coping with greater conspecific competition, evidenced by greater postmetamorphic survival and no difference in body weight when reared under stressful conditions of high larval density. Our results support that both climate and competition selection pressures drive clinal variation in larval and metamorphic traits in this species. Range-wide studies like this one are essential for accurate predictions of population’s responses to ongoing ecological change.Subject terms: Biogeography, Ecological modelling, Evolutionary ecology, Evolution