Speciation in ninespine stickleback: reproductive isolation and phenotypic divergence among cryptic species of Japanese ninespine stickleback

Although similar patterns of phenotypic diversification are often observed in phylogenetically independent lineages, differences in the magnitude and direction of phenotypic divergence have been also observed among independent lineages, even when exposed to the same ecological gradients. The stickleback family is a good model with which to explore the ecological and genetic basis of parallel and nonparallel patterns of phenotypic evolution, because there are a variety of populations and species that are locally adapted to divergent environments. Although the patterns of phenotypic divergence as well as the genetic and ecological mechanisms have been well characterized in threespine sticklebacks, Gasterosteus aculeatus, we know little about the patterns of phenotypic diversification in other stickleback lineages. In eastern Hokkaido, Japan, there are three species of ninespine sticklebacks, Pungitius tymensis and the freshwater type and the brackish‐water type of the P. pungitius–P. sinensis species complex. They utilize divergent habitats along coast–stream gradients of rivers. Here, we investigated genetic, ecological and phenotypic divergence among three species of Japanese ninespine sticklebacks. Divergence in trophic morphology and salinity tolerance occurred in the direction predicted by the patterns observed in threespine sticklebacks. However, the patterns of divergence in armour plate were different from those previously found in threespine sticklebacks. Furthermore, the genetic basis of plate variation may differ from that in threespine sticklebacks. Because threespine sticklebacks are well‐established model for evolutionary research, the sympatric trio of ninespine sticklebacks will be an invaluable resource for ecological and genetic studies on both common and lineage‐specific patterns of phenotypic diversification.     

Comparison of the community structure of the marine molluscs of the “Banco D. João de Castro” seamount (Azores,Portugal) with that of typical inshore habitats on the Azores archipelago

D. João de Castro Bank (DJC) is a shallow seamount with hydrothermal activity located between the islands of Terceira and São Miguel, Azores (Portugal). A survey of the molluscan fauna was conducted in this peculiar habitat. We found a smaller number of molluscan taxa and a different community structure compared to shore environments on the Azores. This coincides with impoverished environmental settings at this location. Possible reasons such as the degree of isolation (inshore vs. offshore locations), geological age, and special ecological conditions related to seamounts and hydrothermal vents are discussed.     

Effect of habitat quality and phenotypic variation on abundance- and trait-based early warning signals of population collapses

Loss of resilience in population numbers in response to environmental perturbations may be predicted with statistical metrics called early warning signals (EWS) that are derived from abundance time series. These signals, however, have been shown to have limited success, leading to the development of trait-based EWS that are based on information collected from phenotypic traits such as body size. Experimental work assessing the efficacy of EWS under varying ecological and environmental factors are rare. In addition, disentangling how such warning signals are affected under varying ecological and environmental factors is key to their application in biological conservation. Here, we experimentally test how different rates of environmental forcing (i.e. warming) and varying ecological factors (i.e. habitat quality and phenotypic diversity) affected population stability and predictive power of early warning signals of population collapse. We analyzed population density and body size time series data from three phenotypically different populations of a protozoan ciliate Askenasia volvox in two levels of habitat quality subjected to three different treatments of warming (i.e. no warming, fast warming and slow warming). We then evaluated how well abundance- and trait-based EWS predicted population collapses under different levels of phenotypic diversity, habitat quality and warming treatments. Our results suggest that habitat quality and warming treatments had more profound effects than phenotypic diversity had on both population stability and on the performance of abundance-based signals of population collapse. In addition, trait-based EWS generally performed well, were reliable and more robust in forecasting population collapse than abundance-based EWS, regardless of variation in environmental and ecological factors. Our study points towards the development of a predictive framework that includes information from phenotypic traits such as body size as an indicator of loss of resilience of ecological systems in response to environmental perturbations.     

Root architecture,plant size and soil nutrient variation in natural populations of <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Phenotypic variation in ecologically important traits may vary at large and small geographic scales, and may be shaped by natural selection. Here our explicit aim is to evaluate phenotypic differentiation among local populations and examine its relationship with ecological edaphic and climatic features that could lead to local adaptation. We characterized six populations of the model plant Arabidopsis thaliana over 3 years in the field in its native range. At each site, we measured edaphic conditions and aboveground and belowground phenotypes. In addition, we grew plants from the six characterized populations in a common greenhouse along with an additional fifteen populations from the Iberian Peninsula to examine evolutionary and ecological differentiation among populations, and relationships between geographic and ecological distance to phenotypic differences among populations. Significant differences in aboveground and belowground traits, population density, and micro- and macro-nutrient soil concentrations were found among the field populations. In particular, root architectural traits differed significantly among field populations. Complex patterns of ecological differences among population and plant phenotypes emerged when examining edaphic conditions in the Extremadura region, and geographic and climate variables at a broader scale of the Iberian Peninsula. We report levels of phenotypic variation at the local scale comparable to those found at broad geographic scales and report that local edaphic conditions contribute to population-level phenotypic variation in root and shoot traits. To our knowledge, these are the first reports of among population root architectural variation from natural field populations for this model organism. We demonstrate how ecological features, such as soil nutrients, can be associated with the phenotypic variation of A. thaliana measured in natural populations and may contribute to adaptive differentiation at a local scale.     

Ecology of Children’s Growth: An Example from Transitional Populations of the Brazilian Amazon

The intense environmental and social changes taking place in Amazonia make this a key area for health studies of populations transitioning to a cosmopolitan lifestyle and market economy. Caboclos are among those populations. They comprise the majority of rural Brazilian Amazon peoples. At present there is limited information about their patterns of growth and health. In this paper, anthropometric data on Caboclo children from three groups living in different environments are presented and discussed within a bioanthropological framework. Caxiuanã, Aracampina, and Santana have a combined population of 1,069 people. Caxiuanã relies more on subsistence activities for survival and Santana more on commerce, while Aracampina uses both subsistence strategies. Compared to US children, Caboclo are generally shorter and lighter in all age groups. However, their weight-for-height is above the 50th percentile. In relation to skinfolds, age groups 0–2, 6–8, and 9–11 years present statistically significant differences among the three communities. Caxiuanã children have the smallest and Aracampina children have the largest skinfolds. While seasonal and environmental differences may account for some of the observed variation in growth and fatness patterns, socioeconomic factors also play a key role in the trends observed. Thus, an ecological model provides the best framework for explaining these findings. Caxiuanã children are small and thin as a result of their combined poor environment and limited access to cash, western goods, and health care. Aracampina and Santana’s fuller access to such socioeconomic influences and richer ecology results in taller and fatter children. Understanding similar interactions between ecology and social factors will be fundamental to developing sustainable health initiatives among rural Amazonian populations.     

Phenotypic plasticity opposes species invasions by altering fitness surface

Understanding species invasion is a central problem in ecology because invasions of exotic species severely impact ecosystems, and because invasions underlie fundamental ecological processes. However, the influence on invasions of phenotypic plasticity, a key component of many species interactions, is unknown. We present a model in which phenotypic plasticity of a resident species increases its ability to oppose invaders, and plasticity of an invader increases its ability to displace residents. Whereas these effects are expected due to increased fitness associated with phenotypic plasticity, the model additionally reveals a new and unforeseen mechanism by which plasticity affects invasions: phenotypic plasticity increases the steepness of the fitness surface, thereby making invasion more difficult, even by phenotypically plastic invaders. Our results should apply to phenotypically plastic responses to any fluctuating environmental factors including predation risk, and to other factors that affect the fitness surface such as the generalism of predators. We extend the results to competition, and argue that phenotypic plasticity's effect on the fitness surface will destabilize coexistence at local scales, but stabilize coexistence at regional scales. Our study emphasizes the need to incorporate variable interaction strengths due to phenotypic plasticity into invasion biology and ecological theory on competition and coexistence in fragmented landscapes.     

Measuring the contribution of evolution to community trait structure in freshwater zooplankton

There are currently few predictions about when evolutionary processes are likely to play an important role in structuring community features. Determining predictors that indicate when evolution is expected to impact ecological processes in natural landscapes can help researchers identify eco-evolutionary ‘hotspots', where eco-evolutionary interactions are more likely to occur. Using data collected from a survey in freshwater cladoceran communities, landscape population genetic data and phenotypic trait data measured in a common garden, we applied a Bayesian linear model to assess whether the impact of local trait evolution in the keystone species Daphnia magna on cladoceran community trait values could be predicted by population genetic properties (within-population genetic diversity, genetic distance among populations), ecological properties (Simpson's diversity, phenotypic divergence) or environmental divergence. We found that the impact of local trait evolution varied among communities. Moreover, community diversity and phenotypic divergence were found to be better predictors of the contribution of evolution to community trait values than environmental features or genetic properties of the evolving species. Our results thus indicate the importance of ecological context for the impact of evolution on community features. Our study also demonstrates one way to detect signatures of eco-evolutionary interactions in communities inhabiting heterogeneous landscapes using survey data of contemporary ecological and evolutionary structure.     

Adaptive processes drive ecomorphological convergent evolution in antwrens (Thamnophilidae)

Phylogenetic niche conservatism (PNC) and convergence are contrasting evolutionary patterns that describe phenotypic similarity across independent lineages. Assessing whether and how adaptive processes give origin to these patterns represent a fundamental step toward understanding phenotypic evolution. Phylogenetic model‐based approaches offer the opportunity not only to distinguish between PNC and convergence, but also to determine the extent that adaptive processes explain phenotypic similarity. The Myrmotherula complex in the Neotropical family Thamnophilidae is a polyphyletic group of sexually dimorphic small insectivorous forest birds that are relatively homogeneous in size and shape. Here, we integrate a comprehensive species‐level molecular phylogeny of the Myrmotherula complex with morphometric and ecological data within a comparative framework to test whether phenotypic similarity is described by a pattern of PNC or convergence, and to identify evolutionary mechanisms underlying body size and shape evolution. We show that antwrens in the Myrmotherula complex represent distantly related clades that exhibit adaptive convergent evolution in body size and divergent evolution in body shape. Phenotypic similarity in the group is primarily driven by their tendency to converge toward smaller body sizes. Differences in body size and shape across lineages are associated to ecological and behavioral factors.     

Applicability of borrowed diatom-based water quality assessment indices in streams around São Carlos-SP,Brazil

Diatom-based indices are increasingly becoming important tools for the assessment of ecological conditions in lotic systems. The applicability of regional and foreign diatom-based water quality assessment indices to streams around São Carlos-SP, Brazil, is discussed. The relationship between measured water quality variables and diatom index scores was assessed. The indices, when compared to chemical analyses, proved useful in providing an indication of the quality of the investigated waters. Though all borrowed indices were applicable to the study area because many widely distributed diatom species have similar environmental tolerances to those recorded for these species elsewhere, ecological requirements of some diatom species from Brazil need to be clarified and incorporated in a diatom-based water quality assessment protocol unique to the region.     

Conceptual problems and scale limitations of defining ecological communities: a critique of the CI concept (Community of Individuals)

Recently, Looijen & van Andel (1999) proposed a new definition of an ecological community by using two criteria: (1) restricting membership by taxonomic relatedness, and (2) defining boundaries by the intersection of the area of population range boundaries. I analyze the implications of their definition and explore the limitations of the approach. Overall, I show this definition to be highly scale-limited, to not encompass many ecological concepts developed for the community level, and to have hidden assumptions that are not met in natural systems. An alternative model of the ecological community is proposed as a contrast, a model based on the community of an individual, in which individuals and interactions are used to develop the larger entity of an ecological community. This alternative model illustrates that the principal problems Looijen & van Andel (1999) discussed about previous community concepts with respect to application to vegetation classification are not ‘problems’ but are characteristics of ecological communities. Any definition of an ecological community must be able to incorporate these characteristics as well as current ecological concepts used at the community level.     

Interface of biotechnology and ecology for environmental risk assessments of transgenic fish

Genetically engineered fish with enhanced phenotypic traits have yet to be implemented into commercial applications. This is partly because of the difficulties in reliably predicting the ecological risk of transgenic fish should they escape into the wild. The ecological consequences of the phenotypic differences between transgenic and wild-type fish, as determined in the laboratory, can be uncertain because of genotype-by-environment effects (GXE). Additionally, we are limited in our ability to extrapolate simple phenotypes to the complex ecological interactions that occur in nature. Genetic background can also shape the phenotypic effects of transgenes, which, over time and among different wild populations, can make risk assessments a continuously evolving target. These uncertainties suggest that assessments of transgenic fish in contained facilities need to be conducted under as wide a range of conditions as possible, and that efficacious physical and biological containment strategies remain as crucial approaches to ensure the safe application of transgenic fish technology.     

What Role Should Government Regulation Play in Ecological Restoration? Ongoing Debate in São Paulo State,Brazil

Around the world, there is growing desire and momentum for ecological restoration to happen faster, with better quality, and in more extensive areas. The question we ask is how can laws and governmental regulations best contribute to effective, successful, and broad‐scale restoration? In the state of São Paulo, Brazil, there is a legal instrument (SMA 08‐2008) whose aim is to increase the effectiveness of tropical forest restoration projects in particular. It establishes, among other things, requirements regarding the minimum number of native tree species to be reached within a given period of time in restoration projects and the precise proportion of functional groups or threatened species to be included when reforestation with native species is used as a restoration technique. There are, however, two differing perspectives among Brazilian restoration ecologists on the appropriateness of such detailed legal rules. For some, the rules help increase the chances that mandatory projects of ecological restoration will succeed. For the other group, there is no single way to achieve effective ecosystem restoration, and the existing science and know‐how are far from sufficient to establish standardized technical and methodological norms or to justify that such norms be imposed. Both points of view are discussed here, aiming to help those developing new legislation and improving existing laws about ecological restoration. The precedents established in São Paulo, and at the federal level in Brazil, and the ongoing debate about those laws are worth considering and possibly applying elsewhere.     

How fast is fast? Eco‐evolutionary dynamics and rates of change in populations and phenotypes

It is increasingly recognized that evolution may occur in ecological time. It is not clear, however, how fast evolution – or phenotypic change more generally – may be in comparison with the associated ecology, or whether systems with fast ecological dynamics generally have relatively fast rates of phenotypic change. We developed a new dataset on standardized rates of change in population size and phenotypic traits for a wide range of species and taxonomic groups. We show that rates of change in phenotypes are generally no more than 2/3, and on average about 1/4, the concurrent rates of change in population size. There was no relationship between rates of population change and rates of phenotypic change across systems. We also found that the variance of both phenotypic and ecological rates increased with the mean across studies following a power law with an exponent of two, while temporal variation in phenotypic rates was lower than in ecological rates. Our results are consistent with the view that ecology and evolution may occur at similar time scales, but clarify that only rarely do populations change as fast in traits as they do in abundance.     

Parallel selective pressures drive convergent diversification of phenotypes in pythons and boas

Pythons and boas are globally distributed and distantly related radiations with remarkable phenotypic and ecological diversity. We tested whether pythons, boas and their relatives have evolved convergent phenotypes when they display similar ecology. We collected geometric morphometric data on head shape for 1073 specimens representing over 80% of species. We show that these two groups display strong and widespread convergence when they occupy equivalent ecological niches and that the history of phenotypic evolution strongly matches the history of ecological diversification, suggesting that both processes are strongly coupled. These results are consistent with replicated adaptive radiation in both groups. We argue that strong selective pressures related to habitat‐use have driven this convergence. Pythons and boas provide a new model system for the study of macro‐evolutionary patterns of morphological and ecological evolution and they do so at a deeper level of divergence and global scale than any well‐established adaptive radiation model systems.     

Ecomorphological diversification following continental colonization in muroid rodents (Rodentia: Muroidea)

The emergence of exceptionally diverse clades is often attributed to ecological opportunity. For example, the exceptional diversity in the most diverse superfamily of mammals, muroid rodents, has been explained in terms of multiple independent adaptive radiations. If multiple ecological opportunity events are responsible for generating muroid diversity, we expect to find evidence of these lineages ecologically diversifying following dispersal into new biogeographical areas. In the present study, we tested the trait‐based predictions of ecological opportunity using data on body size, appendages, and elevation in combination with previously published data on biogeographical transitions and a time‐calibrated molecular phylogeny. We identified weak to no support of early ecological diversification following the initial colonizations of all continental regions, based on multiple tests, including node height tests, disparity through time plots, evolutionary model comparison, and Bayesian analysis of macroevolutionary mixtures. Clades identified with increased diversification rates, not associated with geographical transitions, also did not show patterns of phenotypic divergence predicted by ecological opportunity, which suggests that phylogenetic diversity and phenotypic disparity may be decoupled in muroids. These results indicate that shifts in diversification rates and biogeographically‐mediated ecological opportunity are poor predictors of phenotypic diversity patterns in muroids.     

Branching in Syagrus cocoides (Arecaceae) in Maranhão,northeastern Brazil

This paper reports the discovery of an unusual population of Syagrus cocoides Martius located in the municipality of Barra do Corda, state of Maranhão, northeastern Brazil. The most interesting characteristic of this population is the high number of individuals with branched stems. Sampling showed that 16.12% of the population consisted of bifurcate adult individuals and 14.17% were bifurcate seedlings. The branching phenomenon in palms is reviewed, anc competing hypotheses are discussed to explain the branching in Syagrus cocoides and its ecological and evolutionary significance. We conclude that the most likely type of branching is by dichotomy.     

Don'T fall off the adaptation cliff: when asymmetrical fitness selects for suboptimal traits

The cliff-edge hypothesis introduces the counterintuitive idea that the trait value associated with the maximum of an asymmetrical fitness function is not necessarily the value that is selected for if the trait shows variability in its phenotypic expression. We develop a model of population dynamics to show that, in such a system, the evolutionary stable strategy depends on both the shape of the fitness function around its maximum and the amount of phenotypic variance. The model provides quantitative predictions of the expected trait value distribution and provides an alternative quantity that should be maximized ("genotype fitness") instead of the classical fitness function ("phenotype fitness"). We test the model's predictions on three examples: (1) litter size in guinea pigs, (2) sexual selection in damselflies, and (3) the geometry of the human lung. In all three cases, the model's predictions give a closer match to empirical data than traditional optimization theory models. Our model can be extended to most ecological situations, and the evolutionary conditions for its application are expected to be common in nature.     

Genetic and developmental basis for parallel evolution and its significance for hominoid evolution

Greater understanding of ape comparative anatomy and evolutionary history has brought a general appreciation that the hominoid radiation is characterized by substantial homoplasy.^1–4 However, little consensus has been reached regarding which features result from repeated evolution. This has important implications for reconstructing ancestral states throughout hominoid evolution, including the nature of the Pan‐Homo last common ancestor (LCA). Advances from evolutionary developmental biology (evo‐devo) have expanded the diversity of model organisms available for uncovering the morphogenetic mechanisms underlying instances of repeated phenotypic change. Of particular relevance to hominoids are data from adaptive radiations of birds, fish, and even flies demonstrating that parallel phenotypic changes often use similar genetic and developmental mechanisms. The frequent reuse of a limited set of genes and pathways underlying phenotypic homoplasy suggests that the conserved nature of the genetic and developmental architecture of animals can influence evolutionary outcomes. Such biases are particularly likely to be shared by closely related taxa that reside in similar ecological niches and face common selective pressures. Consideration of these developmental and ecological factors provides a strong theoretical justification for the substantial homoplasy observed in the evolution of complex characters and the remarkable parallel similarities that can occur in closely related taxa. Thus, as in other branches of the hominoid radiation, repeated phenotypic evolution within African apes is also a distinct possibility. If so, the availability of complete genomes for each of the hominoid genera makes them another model to explore the genetic basis of repeated evolution.     

Reaction norms of Arabidopsis. V. Flowering time controls phenotypic architecture in response to nutrient stress

The evolutionary and environmental stability of character correlations has increasingly been the focus of ecological and quantitative genetic studies. Although the genetic stability of character correlations is a central assumption of quantitative genetic models of phenotypic evolution, theoretical considerations suggest that both the genetic and the phenotypic architecture should change in response to selection and to environmental heterogeneity. We investigate genetic (population) differences and plasticity to nutrient availability of the phenotypic architecture describing the whole-plant phenotype of Arabidopsis thaliana (Brassicaceae). We found significant genetic differences among early and late flowering ecotypes in the relationships between several traits, when a path-analytical model was used to estimate character correlations. Furthermore, we found significant plasticity of several path coefficients when nutrient levels were altered. A whole-plant analysis considering all paths in the model simultaneously confirmed that populations of A. thaliana are characterized by distinct phenotypic architectures, and that these are altered in different ways by environmental changes. We discuss the implications of these findings for our understanding of selective pressure on and response by multivariate phenotypes.     

Testing for different rates of continuous trait evolution using likelihood

Rates of phenotypic evolution have changed throughout the history of life, producing variation in levels of morphological, functional, and ecological diversity among groups. Testing for the presence of these rate shifts is a key component of evaluating hypotheses about what causes them. In this paper, general predictions regarding changes in phenotypic diversity as a function of evolutionary history and rates are developed, and tests are derived to evaluate rate changes. Simulations show that these tests are more powerful than existing tests using standardized contrasts. The new approaches are distributed in an application called Brownie and in r8s.