Population Regulation and Density-Dependent Demography in the Trinidadian Guppy

AbstractClassic theory for density-dependent selection for delayed maturation requires that a population be regulated through some combination of adult fecundity and/or juvenile survival. We tested whether those demographic conditions were met in four experimental populations of Trinidadian guppies in which delayed maturation of males evolved when the densities of those populations became high. We used monthly mark-recapture data to examine population dynamics and demography in these populations. Three of the four populations displayed clear evidence of regulation. In all four populations, monthly adult survival rates were independent of biomass density or actually increased with increased biomass density. Juvenile recruitment, which is a combination of adult fecundity and juvenile survival, decreased as biomass density increased in all four populations. Demography showed marked seasonality, with greater survival and higher recruitment in the dry season than the wet season. Population regulation via juvenile recruitment supports the hypothesis that density-dependent selection was responsible for the evolution of delayed maturity in males. This body of work represents one of the few complete tests of density-dependent selection theory.

Plastic maternal effects of social density on reproduction and fitness in the least killifish, Heterandria formosa

Environmental parental effects, also known as transgenerational plasticity, are widespread in plants and animals. Less well known is whether those effects contribute to maternal fitness in the same manner in different populations. We carried out a multigenerational laboratory experiment with females drawn from two populations of the least killifish, Heterandria formosa, to assess transgenerational plasticity in reproductive traits in response to differences in social density and its effects on maternal fitness. In the first and second generations, increased density decreased reproductive rate and increased offspring size in females from both populations. There were complicated patterns of transgenerational plasticity on maternal fitness that differed between females from different populations. Females from a population with historically low densities whose mothers experienced lower density had higher fitness than females whose mothers experienced higher density, regardless of their own density. The opposite pattern emerged in females from the population with historically high densities: Females whose mothers experienced higher density had higher fitness than females whose mothers experienced lower density. This transgenerational plasticity is not anticipatory but might be considered adaptive in both populations if providing those "silver spoons" enhances offspring fitness in all environments.

Female preference for rare males is maintained by indirect selection in Trinidadian guppies

When females prefer mates with rare phenotypes, sexual selection can maintain rather than deplete genetic variation. However, there is no consensus on why this widespread and frequently observed preference might evolve and persist. We examine the fitness consequences of female preference for rare male color patterns in a natural population of Trinidadian guppies, using a pedigree that spans 10 generations. We demonstrate (i) a rare male reproductive advantage, (ii) that females that mate with rare males gain an indirect fitness advantage through the mating success of their sons, and (iii) the fitness benefit that females accrue through their "sexy sons" evaporates for their grandsons as their phenotype becomes common. Counter to prevailing theory, we show that female preference can be maintained through indirect selection.

Does the evolution of ontogenetic niche shifts favour species coexistence? An empirical test in Trinidadian streams

A major question in ecology is how often competing species evolve to reduce competitive interactions and facilitate coexistence. One untested route for a reduction in competitive interactions is through ontogenetic changes in the trophic niche of one or more of the interacting species. In such cases, theory predicts that two species can coexist if the weaker competitor changes its resource niche to a greater degree with increased body size than the superior competitor. We tested this prediction using stable isotopes that yield information about the trophic position (δ¹⁵ N) and carbon source (δ¹³ C) of two coexisting fish species: Trinidadian guppies Poecilia reticulata and killifish Rivulus hartii. We examined fish from locations representing three natural community types: (1) where killifish and guppies live with predators, (2) where killifish and guppies live without predators and (3) where killifish are the only fish species. We also examined killifish from communities in which we had introduced guppies, providing a temporal sequence of the community changes following the transition from a killifish only to a killifish-guppy community. We found that killifish, which are the weaker competitor, had a much larger ontogenetic niche shift in trophic position than guppies in the community where competition is most intense (killifish-guppy only). This result is consistent with theory for size-structured populations, which predicts that these results should lead to stable coexistence of the two species. Comparisons with other communities containing guppies, killifish and predators and ones where killifish live by themselves revealed that these results are caused primarily by a loss of ontogenetic niche changes in guppies, even though they are the stronger competitor. Comparisons of these natural communities with communities in which guppies were translocated into sites containing only killifish showed that the experimental communities were intermediate between the natural killifish-guppy community and the killifish-guppy-predator community, suggesting contemporary evolution in these ontogenetic trophic differences. These results provide comparative evidence for ontogenetic niche shifts in contributing to species coexistence and comparative and experimental evidence for evolutionary or plastic changes in ontogenetic niche shifts following the formation of new communities.

Pathways to global-change effects on biodiversity: new opportunities for dynamically forecasting demography and species interactions

In structured populations, persistence under environmental change may be particularly threatened when abiotic factors simultaneously negatively affect survival and reproduction of several life cycle stages, as opposed to a single stage. Such effects can then be exacerbated when species interactions generate reciprocal feedbacks between the demographic rates of the different species. Despite the importance of such demographic feedbacks, forecasts that account for them are limited as individual-based data on interacting species are perceived to be essential for such mechanistic forecasting-but are rarely available. Here, we first review the current shortcomings in assessing demographic feedbacks in population and community dynamics. We then present an overview of advances in statistical tools that provide an opportunity to leverage population-level data on abundances of multiple species to infer stage-specific demography. Lastly, we showcase a state-of-the-art Bayesian method to infer and project stage-specific survival and reproduction for several interacting species in a Mediterranean shrub community. This case study shows that climate change threatens populations most strongly by changing the interaction effects of conspecific and heterospecific neighbours on both juvenile and adult survival. Thus, the repurposing of multi-species abundance data for mechanistic forecasting can substantially improve our understanding of emerging threats on biodiversity.

Phenotypic Plasticity

Phenotypic plasticity is the capacity of a single genotype to produce a variety of phenotypes under different environmental conditions. The response of a genotype to a particular environmental factor is called its “norm of reaction.” Some norms of reaction reflect unavoidable consequences of adverse situations, like the progressive stunting of fish when developing at progressively higher densities. Others reflect the influence of physical or chemical factors in an organism’s environment, like the slowing of development in ectothermic animals as temperatures decrease. Many responses to an environmental stimulus enhance fitness, like the production of toxic chemicals in the leaves of some plants when attacked by herbivores. Plasticity takes many forms. Some plasticity is reversible, like the remodeling of muscle and bone in vertebrates in response to physical stress or the ability of an animal to learn and, in some cases, unlearn. Irreversible plasticity is reflected in developmental transitions like the response of flowering time to temperature in plants. For over a century, biologists have devoted enormous effort to understanding plasticity. Some of the earliest studies focused on how much phenotypic variation among populations might be due to plasticity. The widespread prevalence of plasticity led to asking whether observed norms of reaction, characteristic of particular populations, were the signature of natural selection in a variable environment. A classic case study was the demonstration that water fleas produce a thicker carapace, often with long projections, when they develop in the presence of a predator, the larvae of the phantom midge. The thickened carapace and its projections protect the water flea from predation by midges. In the absence of midges, the water fleas do not develop the thickened carapace. The theory for how norms of reaction could evolve through natural selection and the tests of these theories in a staggering array of organisms has produced an enormous literature. In recent years, ecologists have examined the role of plasticity in helping organisms survive and persist in stressful conditions and how it facilitates the establishment and expansion of populations in novel environments. Evolutionary biologists have asked when plasticity will promote or preclude further evolutionary change. The recognition that norms of reaction could reach across generations via maternal effects opened an enormous opportunity for new research. The search for the mechanistic bases of norms of reaction—that is, their genetic control—has led to the integration of epigenetics into ecology and evolutionary biology.

Size-dependent intraguild predation, cannibalism, and resource allocation determine the outcome of species coexistence

AbstractIntraguild predation (IGP), a system in which species compete for resources and prey on each other, is more common than existing theory predicts. In theory, an IG predator and its prey can coexist if the IG predator is a weaker competitor for a shared resource and the predator directly benefits from consuming the prey. However, many species that are IG predators also consume members of their own species (cannibalism). Here, we ask whether cannibalism can help resolve the paradox of IGP systems. Our approach differs from previous work on IGP and cannibalism by explicitly considering the size dependence of predatory interactions and how the benefits of predation are allocated to survival, growth, and fecundity of the predator or cannibal. Our results show that cannibalism facilitates coexistence under conditions that are opposite of those predicted by standard IGP theory: species can coexist when the cannibal is a better competitor on the shared resources, directly benefits little from consuming conspecifics, and allocates resources from predation more toward growth and fecundity over survival. Because the effects of IGP and cannibalism are opposite, when an IGP predator is also a cannibal, coexistence between the IGP predator and its prey is not possible and instead depends on the operation of other coexistence mechanisms (e.g., resource partitioning). These results point to the importance of understanding the relative rates of IGP and cannibalism as well as the resource allocation strategy of the IG predator in determining the likelihood of species coexistence.

Polyphenisms and polymorphisms: Genetic variation in plasticity and color variation within and among bluefin killifish populations

The presence of stable color polymorphisms within populations begs the question of how genetic variation is maintained. Consistent variation among populations in coloration, especially when correlated with environmental variation, raises questions about whether environmental conditions affect either the fulcrum of those balanced polymorphisms, the plastic expression of coloration, or both. Color patterns in male bluefin killifish provoke both types of questions. Red and yellow morphs are common in all populations. Blue males are more common in tannin-stained swamps relative to clear springs. Here, we combined crosses with a manipulation of light to explore how genetic variation and phenotypic plasticity shape these patterns. We found that the variation in coloration is attributable mainly to two axes of variation: (1) a red-yellow axis with yellow being dominant to red, and (2) a blue axis that can override red-yellow and is controlled by genetics, phenotypic plasticity, and genetic variation for phenotypic plasticity. The variation among populations in plasticity suggests it is adaptive in some populations but not others. The variation among sires in plasticity within the swamp population suggests balancing selection may be acting not only on the red-yellow polymorphism but also on plasticity for blue coloration.

Life histories as mosaics: plastic and genetic components differ among traits that underpin life-history strategies

Life‐history phenotypes emerge from clusters of traits that are the product of genes and phenotypic plasticity. If the impact of the environment differs substantially between traits, then life histories might not evolve as a cohesive whole. We quantified the sensitivity of components of the life history to food availability, a key environmental difference in the habitat occupied by contrasting ecotypes, for 36 traits in fast‐ and slow‐reproducing Trinidadian guppies. Our dataset included six putatively independent origins of the slow‐reproducing, derived ecotype. Traits varied substantially in plastic and genetic control. Twelve traits were influenced only by food availability (body lengths, body weights), five only by genetic differentiation (interbirth intervals, offspring sizes), 10 by both (litter sizes, reproductive timing), and nine by neither (fat contents, reproductive allotment). Ecotype‐by‐food interactions were negligible. The response to low food was aligned with the genetic difference between high‐ and low‐food environments, suggesting that plasticity was adaptive. The heterogeneity among traits in environmental sensitivity and genetic differentiation reveals that the components of the life history may not evolve in concert. Ecotypes may instead represent mosaics of trait groups that differ in their rate of evolution.

The evolution of size-dependent competitive interactions promotes species coexistence

Theory indicates that competing species coexist in a community when intraspecific competition is stronger than interspecific competition. When body size determines the outcome of competitive interactions between individuals, coexistence depends also on how resource use and the ability to compete for these resources change with body size. Testing coexistence theory in size-structured communities, therefore, requires disentangling the effects of size-dependent competitive abilities and niche shifts. Here, we tested the hypothesis that the evolution of species- and size-dependent competitive asymmetries increased the likelihood of coexistence between interacting species. We experimentally estimated the effects of size-dependent competitive interactions on somatic growth rates of two interacting fish species, Trinidadian guppies Poecilia reticulata and killifish Rivulus hartii. We controlled for the effects of size-dependent changes in the niche at two competitive settings representing the early (allopatric) and late (sympatric) evolutionary stages of a killifish-guppy community. We fitted the growth data to a model that incorporates species- and size-dependent competitive asymmetries to test whether changes in the competitive interactions across sizes increased the likelihood of species coexistence from allopatry to sympatry. We found that guppies are competitively superior to killifish but were less so in sympatric populations. The decrease in the effects of interspecific competition on the fitness of killifish and increase in the interspecific effect on guppies' fitness increased the likelihood that sympatric guppies and killifish will coexist. However, while the competitive asymmetries between the species changed consistently between allopatry and sympatry between drainages, the magnitude of the size-dependent competitive asymmetries varied between drainages. These results demonstrate the importance of integrating evolution and trait-based interactions into the research on how species coexist.

Ancestral ecological regime shapes reaction to food limitation in the Least Killifish, Heterandria formosa

Populations with different densities often show genetically based differences in life histories. The divergent life histories could be driven by several agents of selection, one of which is variation in per-capita food levels. Its relationship with population density is complex, as it depends on overall food availability, individual metabolic demand, and food-independent factors potentially affecting density, such as predation intensity. Here, we present a case study of two populations of a small live-bearing freshwater fish, one characterized by high density, low predation risk, low overall food availability, and presumably low per-capita food levels, and the other by low density, high predation risk, high overall food availability, and presumably high per-capita food levels. Using a laboratory experiment, we examined whether fish from these populations respond differently to food limitation, and whether size at birth, a key trait with respect to density variation in this species, is associated with any such differential responses. While at the lower food level growth was slower, body size smaller, maturation delayed, and survival reduced in both populations, these fitness costs were smaller in fish from the high-density population. At low food, only 15% of high-density fish died, compared to 75% of low-density fish. This difference was much smaller at high food (0% vs. 15% mortality). The increased survival of high-density fish may, at least partly, be due to their larger size at birth. Moreover, being larger at birth enabled fish to mature relatively early even at the lower food level. We demonstrate that sensitivities to food limitation differ between study populations, consistent with selection for a greater ability to tolerate low per-capita food availability in the high-density population. While we cannot preclude other agents of selection from operating in these populations simultaneously, our results suggest that variation in per-capita food levels is one of those agents.

Reproductive Mode and Conflict Shape the Evolution of Male Attributes and Rate of Speciation in the Fish Family Poeciliidae

Sexual conflict is caused by differences between the sexes in how fitness is maximized. These differences are shaped by the discrepancy in the investment in gametes, how mates are chosen and how embryos and young are provided for. Fish in the family Poeciliidae vary from completely provisioning eggs before they are fertilized to providing virtually all resources after fertilization via the functional equivalent of a mammalian placenta. This shift in when females provision their young relative to when an egg is fertilized is predicted to cause a fundamental change in when and how sexual conflict is manifested. If eggs are provisioned before fertilization, there should be strong selection for females to choose with whom they mate. Maternal provisioning after fertilization should promote a shift to post-copulatory mate choice. The evolution of maternal provisioning may in turn have cascading effects on the evolution of diverse features of the biology of these fish because of this shift in when mates are chosen. Here we summarize what these consequences are and show that the evolution of maternal provisioning is indeed associated with and appears to govern the evolution of male traits associated with sexual selection. The evolution of placentas and associated conflict does not cause accelerated speciation, contrary to predictions. Accelerated speciation rate is instead correlated with the evolution of male traits associated with sexual selection, which implies a more prominent role of pre-copulatory reproductive isolation in causing speciation in this family.

Can You Trust Who You See? The Evolution of Socially Cued Anticipatory Plasticity

AbstractThe social environment can affect development and fitness. However, we do not know how selection acts on individuals that cue developmental pathways using features of the social environment. Socially cued anticipatory plasticity (SCAP) is a hypothetical strategy whereby juveniles use social cues to alter development to match their adult phenotype to the social environment that they expect to encounter. While intuitively appealing, the evolution of such plasticity is a puzzle, because the cue changes when individuals use it. Can socially cued plasticity evolve when such a feedback occurs? We use individual-based simulations to model evolution of SCAP in an environment that fluctuates between favoring each of two discrete phenotypes. We found that socially cued plasticity evolved, but only when strong selection acted on survival rather than on fecundity differences between adult phenotypes. In this case, the social cue reliably predicted which phenotype would be favored on maturation. Surprisingly, costs to plasticity increased the range of conditions under which it was adaptive. In the absence of costs, evolution led to a state where SCAP individuals could not effectively respond to environmental changes. Costs to plasticity lowered the proportion of the population that used SCAP, which in turn increased the reliability of the social cue and allowed individuals that used socially cued plasticity to switch between the favored phenotypes more consistently. Our results suggest that the evolution of adaptive plasticity in response to social cues may represent a larger class of problems in which evolution is hard to predict because of feedbacks among critical processes.

The experimental range extension of guppies (Poecilia reticulata) influences the metabolic activity of tropical streams

The ecological consequences of biological range extensions reflect the interplay between the functional characteristics of the newly arrived species and their recipient ecosystems. Teasing apart the relative contribution of each component is difficult because most colonization events are studied retrospectively, i.e., after a species became established and its consequences apparent. We conducted a prospective experiment to study the ecosystem consequences of a consumer introduction, using whole-stream metabolism as our integrator of ecosystem activity. In four Trinidadian streams, we extended the range of a native fish, the guppy (Poecilia reticulata), by introducing it over barrier waterfalls that historically excluded it from these upper reaches. To assess the context dependence of these range extensions, we thinned the riparian forest canopy on two of these streams to increase benthic algal biomass and productivity. Guppy's range extension into upper stream reaches significantly impacted stream metabolism but the effects depended upon the specific stream into which they had been introduced. Generally, increases in guppy biomass caused an increase in gross primary production (GPP) and community respiration (CR). The effects guppies had on GPP were similar to those induced by increased light level and were larger in strength than the effects stream stage had on CR. These results, combined with results from prior experiments, contribute to our growing understanding of how consumers impact stream ecosystem function when they expand their range into novel habitats. Further study will reveal whether local adaptation, known to occur rapidly in these guppy populations, modifies the ecological consequences of this species introduction.

Sex differences in the plasticity of life history in response to social environment

Predicting how social environment affects life history variation is critical to understanding if, and when, selection favors alternative life history development, especially in systems in which social interactions change over time or space. Although sexual selection theory predicts that males and females should respond differently to variation in the social environment, few studies have examined the responses of both male and female phenotypes to the same gradient of social environment. In this study, we used a livebearing fish to determine how males and females altered their life histories in response to variation in the social environment during development. We found that both males and females delayed maturity and attained larger sizes when their social environment included adults, in contrast to developing in juvenile-only environments. The magnitude of this effect differed substantially between the sexes. The common pattern of response in the sexes suggested that life history trade-offs, rather than sexual selection, is responsible for these changes in life history expression. These effects make the relationship between genotype and phenotype depend strongly on the environment experienced by each individual. These results indicate that social environment is an important driver of life history variation in sailfin mollies and can be at least as important as abiotic effects.

Towards a more precise - and accurate - view of eco-evolution

Over the past 15 years, the number of papers focused on 'eco-evo dynamics' has increased exponentially (Figure 1). This pattern suggests the rapid growth of a new, integrative discipline. We argue this overstates the case. First, the terms 'eco-evo dynamics' and 'eco-evo interactions' are used too imprecisely. As a result, many studies that claim to describe eco-evo dynamics are actually describing basic ecological or evolutionary processes. Second, these terms are often used as if the study of how ecological and evolutionary processes are intertwined is novel when, in fact, it is not. The result is confusion over what the term 'eco-evolution' and its derivatives describe. We advocate a more precise definition of eco-evolution that is more useful in efforts to understand and characterise the diversity of ecological and evolutionary processes and that focuses attention on the subset of those processes that occur only when ecological and evolutionary timescales are comparable. [Figure: see text].

Environmental Change, If Unaccounted, Prevents Detection of Cryptic Evolution in a Wild Population

AbstractDetecting contemporary evolution requires demonstrating that genetic change has occurred. Mixed effects models allow estimation of quantitative genetic parameters and are widely used to study evolution in wild populations. However, predictions of evolution based on these parameters frequently fail to match observations. Here, we applied three commonly used quantitative genetic approaches to predict the evolution of size at maturity in a wild population of Trinidadian guppies. Crucially, we tested our predictions against evolutionary change observed in common-garden experiments performed on samples from the same population. We show that standard quantitative genetic models underestimated or failed to detect the cryptic evolution of this trait as demonstrated by the common-garden experiments. The models failed because (1) size at maturity and fitness both decreased with increases in population density, (2) offspring experienced higher population densities than their parents, and (3) selection on size was strongest at high densities. When we accounted for environmental change, predictions better matched observations in the common-garden experiments, although substantial uncertainty remained. Our results demonstrate that predictions of evolution are unreliable if environmental change is not appropriately captured in models.

Mate availability determines use of alternative reproductive phenotypes in hermaphrodites

In many species, individuals can employ alternative reproductive phenotypes, with profound consequences for individual fitness and population dynamics. This is particularly relevant for self-compatible hermaphrodites, which have exceptionally many reproductive options. Here we investigated the occurrence of reproductive phenotypes in the simultaneously hermaphroditic freshwater snail Radix balthica under experimentally simulated conditions of low versus moderate population density. We captured all mating behavior on camera and measured individual female lifetime reproductive success. We found every possible reproductive phenotype: (1) both male and female (i.e., truly hermaphroditic) reproduction, (2) purely female and (3) purely male reproduction, (4) male reproduction combined with self-fertilization and (5) female mating activity, (6) pure self-fertilization without mating and (7–8) two types of reproductive failure. Variation in alternative reproductive phenotypes was explained by mate availability (10.8%) and individual condition, approximated by a snail’s mean daily growth rate (17.5%). Increased mate availability resulted in a lower diversity of reproductive phenotypes, in particular increasing the frequency of true hermaphrodites. However, it lowered phenotype-specific fecundities and hence reduced the population growth rate. Snails in better condition were more likely to reproduce as true hermaphrodites or pure females, whereas low-condition snails tended to suffer reproductive failure. Overall, we show substantial variation in alternative reproductive phenotypes in a hermaphrodite, which is possibly in part maintained by fluctuations in population density and thus mate availability, and by variation in individual condition. We also provide evidence of an almost 2-fold increase in clutch size that can be ascribed specifically to mating as a female.

The microbiome of diabetic foot ulcers: a comparison of swab and tissue biopsy wound sampling techniques using 16S rRNA gene sequencing

Background

Health-care professionals need to collect wound samples to identify potential pathogens that contribute to wound infection. Obtaining appropriate samples from diabetic foot ulcers (DFUs) where there is a suspicion of infection is of high importance. Paired swabs and tissue biopsies were collected from DFUs and both sampling techniques were compared using 16S rRNA gene sequencing.

Results

Mean bacterial abundance determined using quantitative polymerase chain reaction (qPCR) was significantly lower in tissue biopsies (p = 0.03). The mean number of reads across all samples was significantly higher in wound swabs \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \Big(\overline{X} $$\end{document}(X¯ = 32,014) compared to tissue (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \overline{X} $$\end{document}X¯ = 15,256, p = 0.001). Tissue biopsies exhibited greater overall diversity of bacteria relative to swabs (Shannon’s H diversity p = 0.009). However, based on a presence/absence analysis of all paired samples, the frequency of occurrence of bacteria from genera of known and potential pathogens was generally higher in wound swabs than tissue biopsies. Multivariate analysis identified significantly different bacterial communities in swabs compared to tissue (p = 0.001). There was minimal correlation between paired wound swabs and tissue biopsies in the number and types of microorganisms. RELATE analysis revealed low concordance between paired DFU swab and tissue biopsy samples (Rho = 0.043, p = 0.34).

Conclusions

Using 16S rRNA gene sequencing this study identifies the potential for using less invasive swabs to recover high relative abundances of known and potential pathogen genera from DFUs when compared to the gold standard collection method of tissue biopsy.

Are you more than the sum of your parents' genes? Phenotypic plasticity in a clonal vertebrate and F1 hybrids of its parental species

All known vertebrate clones have originated from hybridization events and some have produced distinct evolutionary lineages via hybrid speciation. Amazon mollies (Poecilia formosa) present an excellent study system to investigate how clonal species have adapted to heterogeneous environments because they are the product of a single hybridization event between male sailfin mollies (Poecilia latipinna) and female Atlantic mollies (Poecilia mexicana). Here, we ask whether the hybrid species differs from the combination of its parental species' genes in its plastic response to different environments. Using a three-way factorial design, we exposed neonates produced by Amazon mollies and reciprocal F1 hybrid crosses to different thermal (24°C and 29°C) and salinity (0/2, 12, and 20 ppt) regimes. We measured various ontogenetic and life history characteristics across the life span of females. Our major results were as follows: (1) Reaction norms of growth and maturation to temperature and salinity are quite similar between the two hybrid crosses; (2) Amazon molly reaction norms were qualitatively different than the P. latipinna male and P. mexicana female (L×M) hybrids for the ontogenetic variables; (3) Amazon molly reaction norms in reproductive traits were also quite different from L×M hybrids; and (4) The reaction norms of net fertility were very different between Amazon mollies and L×M hybrids. We conclude that best locale for Amazon mollies is not the best locale for hybrids, which suggests that Amazon mollies are not just an unmodified mix of parental genes but instead have adapted to the variable environments in which they are found. Hybridization resulting in asexuality may represent an underappreciated mechanism of speciation because the unlikely events required to produce such hybrids rarely occur and is dependent upon the genetic distance between parental species.

Where Is Natural History in Ecological, Evolutionary, and Behavioral Science?

Natural history is the careful observation of nature, wherever nature is. Ultimately, it is what ecological, evolutionary, and behavioral science are supposed to explain. It is difficult to use natural history alone to test hypotheses in these fields because of the complex paths between process and pattern. Few patterns are predicted by one and only one hypothesis, so experiments are almost always necessary. However, the robustness of experimental results depends on how well experimental conditions reflect the integration of natural history. Natural history also plays a vital role in how well we can apply Krogh's principle to our work. Krogh's principle is that scientists begin with an important hypothesis and find a system (organism, habitat, species interaction) with which to test it. However, natural history is essential for knowing whether the question applies to the system or whether we are forcing the question on the system. There is value in beginning one's research not by identifying an interesting question and searching for the right system but by identifying an interesting system in which to ask the right question. This approach carries the danger of parochialism, which can be avoided only by having a command of theory as well as natural history. A command of both areas allows nature to tell us which question to ask instead of demanding that nature answer the question we find most interesting.

Experimental Studies of Evolution and Eco-Evo Dynamics in Guppies (Poecilia reticulata)

Guppies in Trinidad range across aquatic environments with fish communities that vary in risk of predation. These communities are often discrete, separated by waterfalls, with high-predation communities downstream and low-predation communities upstream. This gradient is repeated in many rivers; in each one, we see the same divergence between guppy populations in life history, behavior, morphology, and physiology. We have shown that the agent of selection on the life history, behavior, and physiology in low-predation communities is high population density and the cascade of ecological effects that stems from it. In effect, guppy populations modify their ecosystem and, in so doing, impose selection on themselves and shape their own evolution, which further changes the ecosystem. Evolution unfolds rapidly in this system, which has enabled us to study the dynamics of the process, not just its end points. Those studies enable us to answer some very general questions in ecology and evolutionary biology.

The genome of the live-bearing fish Heterandria formosa implicates a role of conserved vertebrate genes in the evolution of placental fish

Background

The evolution of complex organs is thought to occur via a stepwise process, each subsequent step increasing the organ’s complexity by a tiny amount. This evolutionary process can be studied by comparing closely related species that vary in the presence or absence of their organs. This is the case for the placenta in the live-bearing fish family Poeciliidae, as members of this family vary markedly in their ability to supply nutrients to their offspring via a placenta. Here, we investigate the genomic basis underlying this phenotypic variation in Heterandria formosa, a poeciliid fish with a highly complex placenta. We compare this genome to three published reference genomes of non-placental poeciliid fish to gain insight in which genes may have played a role in the evolution of the placenta in the Poeciliidae.

Results

We sequenced the genome of H. formosa, providing the first whole genome sequence for a placental poeciliid. We looked for signatures of adaptive evolution by comparing its gene sequences to those of three non-placental live-bearing relatives. Using comparative evolutionary analyses, we found 17 genes that were positively selected exclusively in H. formosa, as well as five gene duplications exclusive to H. formosa. Eight of the genes evolving under positive selection in H. formosa have a placental function in mammals, most notably endometrial tissue remodelling or endometrial cell proliferation.

Conclusions

Our results show that a substantial portion of positively selected genes have a function that correlates well with the morphological changes that form the placenta of H. formosa, compared to the corresponding tissue in non-placental poeciliids. These functions are mainly endometrial tissue remodelling and endometrial cell proliferation. Therefore, we hypothesize that natural selection acting on genes involved in these functions plays a key role in the evolution of the placenta in H. formosa.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1484-2) contains supplementary material, which is available to authorized users.

Widespread Biases in Ecological and Evolutionary Studies

There has been widespread discussion of biases in the sciences. The extent of most forms of bias has scarcely been confronted with rigorous data. In the present article, we evaluated the potential for geographic, taxonomic, and citation biases in publications between temperate and tropical systems for nine broad topics in ecology and evolutionary biology. Across 1,800 papers sampled from 60,000 peer-reviewed, empirical studies, we found consistent patterns of bias in the form of increased numbers of studies in temperate systems. Tropical studies were nearly absent from some topics. Furthermore, there were strong taxonomic biases across topics and geographic regions, as well as evidence for citation biases in many topics. Our results indicate a strong geographic imbalance in publishing patterns and among different taxonomic groups across a wide range of topics. The task ahead is to address what these biases mean and how they influence the state of our knowledge in ecology and evolution.

Landscape patterns in top-down control of decomposition: omnivory disrupts a tropical detrital-based trophic cascade

Detrital-based trophic cascades are often considered weak or absent in tropical stream ecosystems because of the prevalence of omnivorous macroconsumers and the dearth of leaf-shredding insects. In this study, we isolate top-down effects of three macroconsumer species on detrital processing in headwater streams draining Trinidad's northern mountains. We separated effects of different macroconsumers by experimentally manipulating their temporal access to isolated benthic habitat over the diel cycle. We found no evidence that omnivorous macroconsumers, including a freshwater crab (Eudaniela garmani) and guppy (Poecilia reticulata), increased leaf decomposition via consumption. By contrast, above a waterfall excluding guppies, the insectivorous killifish, Anablepsoides hartii, reduced the biomass of the leaf-shredding insect Phylloicus hansoni 4-fold, which consequently reduced leaf decomposition rates 1.6-fold. This detrital cascade did not occur below the barrier waterfall, where omnivorous guppies join the assemblage and reduce killifish densities; here killifish had no significant effects on Phylloicus or decomposition rates. These patterns of detrital processing were also observed in upstream-downstream comparisons in a landscape study across paired reaches of six streams. Above waterfalls, where killifish were present, but guppies absent, leaf decomposition rates and Phylloicus biomass were 2.5- and ~35-fold lower, respectively, compared to measurements below waterfalls. Moreover, the strength of top-down control by killifish is reflected by the 20- and 5-fold reductions in variability (±SE) surrounding mean Phylloicus biomass and leaf decomposition rates in upstream relative to downstream reaches where no top-down control was detected. Findings show a clear, detrital-based trophic cascade among killifish, a leaf-shredding insect, and leaf decomposition rates. Results also show how omnivorous guppies disrupt this cascade by depressing killifish densities, thereby releasing invertebrate shredders from predation, and significantly increasing decomposition rates. Moreover, this combination of direct and indirect trophic interactions drives patterns in decomposition rates in stream networks at a landscape scale, resulting in significantly lower rates of decomposition above vs. below barrier waterfalls. Our findings reveal that omnivory can result in significant indirect effects on a key ecosystem process, illustrating the importance of these hidden trophic pathways in detrital-based systems and suggesting that resource control in tropical systems may be even more complex than previously envisioned.

The effects of food level and social density on reproduction in the Least Killifish, Heterandria formosa

The feedbacks from population density to demographic parameters, which drive population regulation, are the accumulated results of several ecological processes. The compensatory feedback from increased population density to fertility includes at least two distinct factors, the effects of decreases in per capita food level and increases in the social density (the number of interacting individuals). Because these effects have been studied separately, their relative importance is unknown. It is also unclear whether food limitation and social density combine additively to influence fertility. We investigated these questions with two factorial experiments on reproduction in the Least Killifish, Heterandria formosa. In one experiment, we crossed two levels of density with two levels of a total food ration that was distributed to all individuals. In the other experiment, we crossed two levels of density with two levels of per capita food. Whereas the first experiment suggested that the effects of variation in food level and density were synergistic, the second experiment indicated that they were not. The apparent synergism-the statistical interaction of food and density levels-was the result of confounding per capita food with social density in that design. In the second experiment, the effects of social density on reproductive rate were stronger than the effects of food level, whereas the effects of food level were stronger on offspring size at parturition than those of social density. The results suggest that the social stresses that emerge at higher densities play an important role in the compensatory response of fertility to density, a role, that is, at least as important as that of decreased per capita food levels.

From low to high gear: there has been a paradigm shift in our understanding of evolution

Experimental studies of evolution performed in nature and the associated demonstration of rapid evolution, observable on a time scale of months to years, were an acclaimed novelty in the 1980-1990s. Contemporary evolution is now considered ordinary and is an integrated feature of many areas of research. This shift from extraordinary to ordinary reflects a change in the perception of evolution. It was formerly thought of as a historical process, perceived through the footprints left in the fossil record or living organisms. It is now seen as a contemporary process that acts in real time. Here we review how this shift occurred and its consequences for fields as diverse as wildlife management, conservation biology, and ecosystems ecology. Incorporating contemporary evolution in these fields has caused old questions to be recast, changed the answers, caused new and previously inconceivable questions to be addressed, and inspired the development of new subdisciplines. We argue further that the potential of contemporary evolution has yet to be fulfilled. Incorporating evolutionary dynamics in any research program can provide a better assessment of how and why organisms and communities came to be as they are than is attainable without an explicit treatment of these dynamics.

Unique maternal and environmental effects on the body morphology of the Least Killifish, Heterandria formosa

An important step in diagnosing local adaptation is the demonstration that phenotypic variation among populations is at least in part genetically based. To do this, many methods experimentally minimize the environmental effect on the phenotype to elucidate the genetic effect. Minimizing the environmental effect often includes reducing possible environmental maternal effects. However, maternal effects can be an important factor in patterns of local adaptation as well as adaptive plasticity. Here, we report the results of an experiment with males from two populations of the poeciliid fish, Heterandria formosa, designed to examine the relative influence of environmental maternal effects and environmental effects experienced during growth and development on body morphology, and, in addition, whether the balance among those effects is unique to each population. We used a factorial design that varied thermal environment and water chemistry experienced by mothers and thermal environment and water chemistry experienced by offspring. We found substantial differences between the two populations in their maternal and offspring norms of reaction of male body morphology to differences in thermal environment and water chemistry. We also found that the balance between maternal effects and postparturition environmental effects differed from one thermal regime to another and among traits. These results indicate that environmental maternal effects can be decidedly population-specific and, as a result, might either contribute to the appearance of or blur evidence for local adaptation. These results also suggest that local adaptation might also occur through the evolution of maternal norms of reaction to important, and varying, environmental factors.

Population variation in the trophic niche of the Trinidadian guppy from different predation regimes

Population variation in trophic niche is widespread among organisms and is of increasing interest given its role in both speciation and adaptation to changing environments. Trinidadian guppies (Poecilia reticulata) inhabiting stream reaches with different predation regimes have rapidly evolved divergent life history traits. Here, we investigated the effects of both predation and resource availability on guppy trophic niches by evaluating their gut contents, resource standing stocks, and δ15N and δ13C stable isotopes across five streams during the wet season. We found that guppies from low predation (LP) sites had a consistently higher trophic position and proportion of invertebrates in their guts and assimilate less epilithon than guppies from high predation (HP) sites. Higher trophic position was also associated with lower benthic invertebrate availability. Our results suggest that LP guppies could be more efficient invertebrate consumers, possibly as an evolutionary response to greater intraspecific competition for higher quality food. This may be intensified by seasonality, as wet season conditions can alter resource availability, feeding rates, and the intensity of intraspecific competition. Understanding how guppy diets vary among communities is critical to elucidating the role of niche shifts in mediating the link between environmental change and the evolution of life histories.