The American Naturalist

Published by University of Chicago Press
Online ISSN: 1537-5323
Print ISSN: 0003-0147
Publications
Within large taxonomic assemblages, the number of species with adult body mass M is characterized by a broad but asymmetric distribution, with the largest mass being orders of magnitude larger than the typical mass. This canonical shape can be explained by cladogenetic diffusion that is bounded below by a hard limit on viable species mass and above by extinction risks that increase weakly with mass. Here we introduce and analytically solve a simplified cladogenetic diffusion model. When appropriately parameterized, the diffusion-reaction equation predicts mass distributions that are in good agreement with data on 4,002 terrestrial mammals from the late Quaternary and 8,617 extant bird species. Under this model, we show that a specific trade-off between the strength of within-lineage drift toward larger masses (Cope's rule) and the increased risk of extinction from increased mass is necessary to produce realistic mass distributions for both taxa. We then make several predictions about the evolution of avian species masses.
 
Model of tetraploid origins from diploid ancestors. The relationships of diploid gray tree frogs and Hyla avivoca are depicted in the tree at the bottom. Extinct diploids (2N), H. sp. A and H. sp. B, were inferred from tetraploid allele lineages. Tetraploid gray tree frogs, Hyla versicolor (4N), were formed multiple times from extinct diploid ancestors ( , , and ). Tetraploid gray tree frogs now share this gene pool. A # B A # C B# C netic analysis, which suggests gene flow among lineages of tetraploids. Multiple independent origins of reproductively compatible tetraploids from more than two diploid ancestors have not been reported, even in groups such as plants in which speciation by polyploidy is common (Grant 1981; Otto and Whitton 2000). Given that the tetraploid and diploid frogs are reproductively isolated (Littlejohn et al. 1960; Johnson 1963; Gerhardt et al. 1994), recognition and subsequent mating among the different tetraploid lineages seems counterintuitive. Premating reproductive isolation between diploids and tetraploids occurs because tetraploid pulse rates are approximately half those of the diploids, and females strongly discriminate against calls that differ by this order of magnitude from those of conspecific calls (Littlejohn et al. 1960; Johnson 1966; Gerhardt 1974a, 1994). All tetraploid gray tree frogs (regardless of origins) have a slower pulse rate than H. chrysoscelis, suggesting that a reduction in pulse rate may be a direct consequence of ploidy level (Keller and Gerhardt 2001), a phenomenon observed in some other tetraploid frog species (Martino and Sinsch 2002). Tetraploid cells have approximately twice the volume of diploid cells, even though the adult body size is indistinguishable (Cash and Bogart 1978). This suggests a possible mechanism for mate recognition 
Polyploidization is one of the few mechanisms that can produce instantaneous speciation. Multiple origins of tetraploid lineages from the same two diploid progenitors are common, but here we report the first known instance of a single tetraploid species that originated repeatedly from at least three diploid ancestors. Parallel evolution of advertisement calls in tetraploid lineages of gray tree frogs has allowed these lineages to interbreed, resulting in a single sexually interacting polyploid species despite the separate origins of polyploids from different diploids. Speciation by polyploidization in these frogs has been the source of considerable debate, but the various published hypotheses have assumed that polyploids arose through either autopolyploidy or allopolyploidy of extant diploid species. We utilized molecular markers and advertisement calls to infer the origins of tetraploid gray tree frogs. Previous hypotheses did not sufficiently account for the observed data. Instead, we found that tetraploids originated multiple times from extant diploid gray tree frogs and two other, apparently extinct, lineages of tree frogs. Tetraploid lineages then merged through interbreeding to result in a single species. Thus, polyploid species may have complex origins, especially in systems in which isolating mechanisms (such as advertisement calls) are affected directly through hybridization and polyploidy.
 
The immunocompetence handicap hypothesis (ICHH) provides a functional explanation for how sexual ornaments can provide honest signals of male quality. A key aspect of this hypothesis is that testosterone (T) has a bimodal effect: a higher T level enhances the expression of ornaments (increasing mating success and, ultimately, fitness); however, at the same time, it suppresses immune function. Tests of the latter assumption, which have focused mainly on aspects of adaptive immunity in birds, led to equivocal results. We performed a hormone-implant experiment in male three-spined sticklebacks (Gasterosteus aculeatus) to test the key assumptions of the ICHH in a fish, where the dominant circulating androgen is 11-ketotestosterone (11kT) rather than T. Males were implanted with 11-ketoandrostenedione, which is a natural precursor of 11kT. Each individual's circulating 11kT level, ornamentation, and immunocompetence were measured 2 weeks later. In addition, we quantified oxidative tissue damage because the ICHH has been hypothesized to work via oxidative stress. We found that the males' 11kT levels correlated positively with ornamentation but negatively with immunocompetence, in particular, measures of innate immunity. Moreover, there was a trend for fish with high 11kT levels to suffer more from oxidative stress. Thus, our data provide support for the ICHH.
 
Although the evolutionary consequences of within-host competition among pathogens have been examined extensively, there exists a critical gap in our understanding of factors determining the prevalence of multiple infections. Here we examine the effects of relatedness among strains of the anther-smut pathogen Microbotryum violaceum on the probability of multiple infection in its host, Silene latifolia, after sequential inoculations. We found a significantly higher probability of multiple infection when interacting strains were more closely related, suggesting mechanisms of competitive exclusion that are conditional on genotypic characteristics of the strains involved. Pathogen relatedness therefore determines the prevalence of multiple infection in addition to its outcome, with important consequences for our understanding of virulence evolution and pathogen population structure and diversity.
 
Protista without contemporary identity
The discipline of evolutionary protistology has emerged in the past 30 yr. There is as yet no agreed view of how protists are interrelated or how they should be classified. The foundations of a stable taxonomic superstructure for the protists and other eukaryotes lie in cataloging the diversity of the major monophyletic lineages of these organisms. The use of common patterns of cell organization (ultrastructural identity) seems to provide us with the most robust hypotheses of such lineages. These lineages are placed in 71 groups without identifiable sister taxa. These groups are here referred to as "major building blocks." For the first time, the compositions, ultrastructural identities, synapomorphies (where available), and subgroups of the major building blocks are summarized. More than 200 further lineages without clear identities are listed. This catalog includes all known major elements of the comprehensive evolutionary tree of protists and eukaryotes. Different approaches among protistologists to issues of nomenclature, ranking, and definitions of these groups are discussed, with particular reference to two groups-the stramenopiles and the Archezoa. The concept of "extended in-group" is introduced to refer to in-groups and the most proximate sister group and to assist in identifying the hierarchical location of taxa.
 
Major types of canalization 
Numerical calculation of the equilibrium genetic load in a 
There has been a recent revival of interest in how genetic interactions evolve, spurred on by an increase in our knowledge of genetic interactions at the molecular level. Empirical work on genetic networks has revealed a surprising amount of robustness to perturbations, suggesting that robustness is an evolved feature of genetic networks. Here, we derive a general model for the evolution of canalization that can incorporate any form of perturbation. We establish an upper bound to the strength of selection on canalization that is approximately equal to the fitness load in the system. This method makes it possible to compare different forms of perturbation, including genetic, developmental, and environmental effects. In general, load that arises from mutational processes is low because the mutation rate is itself low. Mutation load can create selection for canalization in a small network that can be achieved through dominance evolution or gene duplication, and in each case selection for canalization is weak at best. In larger genetic networks, selection on genetic canalization can be reasonably strong because larger networks have higher mutational load. Because load induced through migration, segregation, developmental noise, and environmental variance is not mutation limited, each can cause strong selection for canalization.
 
Fishes show one of the widest ranges of sperm competition intensity of any animal group. Here we present a comparative study whose aim is to investigate the effect of relative intensity of sperm competition on investment in spermatogenesis and the number and size of sperm produced. We find that both the gonadosomatic index (GSI = [gonad weight/body weight] x 100) and sperm numbers increase with intensity of sperm competition across species but that sperm length decreases. These new findings are consistent with a raffle-based mode of sperm competition in fishes. Most of these results (positive correlation of the GSI and sperm number with sperm competition intensity) concur with the predictions of current sperm competition theory. However, we also find that sperm longevity decreases with sperm length across species. Current models for continuous fertilization suggest that if length increases a sperm's speed but decreases its longevity, sperm length should increase with sperm competition intensity, whereas models for instant fertilization suggest that sperm length should remain constant. The negative relationship found between sperm competition and sperm length therefore does not fit predictions of either model.
 
hypothesis that adaptive divergence leads to speciation and to the evolution of traits and behaviors that influence the prospects for species coexistence. A key issue here is the role of character displacement in the origin and mainte- nance of diversity. Pfennig and Pfennig find substantial evidence that character displacement plays an important role in the evolution of species interactions and identify a number of additional areas that Darwin had not con- sidered, including sexual selection and phenotypic plas- ticity. Their paper clearly illustrates how Darwin's original observations continue to shape our thinking on the in- terface between ecology, behavior, and evolution. Of the many insightful observations presented in The Origin, perhaps none is more remarkable than Darwin's discussion of the evolution of hybrid sterility. He under- stood that sterility could not have evolved as an adaptation of individual species and that interactions in the hybrids stemming from the contributions of each parent caused incompatibilities, but without today's specific knowledge of genetics, he was unable to reach a satisfactory expla- nation. Presgraves (2010) reviews this topic in detail, in- cluding an historical perspective on the contributions by Darwin, Muller, and Dobzhansky to the problem. He also provides an overview of the recent advances in our un- derstanding of the genetic mechanisms that contribute to the evolution of hybrid incompatibilities. This includes evidence that genetic conflict, and not adaptive divergence, may be a primary cause of hybrid sterility and inviability. Darwin considered multiple sources of evidence to gain support for his theory of natural selection, including the evolution of both living and extinct organisms. Hunt (2010) describes Darwin's attempts to use the fossil record to test the hypothesis that evolution by natural selection is a gradual process. Darwin argued at the time that the record was too incomplete to provide an adequate test. Hunt reviews the current paleontological record and con- cludes that over short periods, rates of morphological evo- lution are sometimes considerably faster than Darwin had proposed. Sticklebacks provide a particularly illustrative case, where a nearly continuous record extending over the last 10 million years shows that most phenotypic evolution occurred over a brief period of approximately 1,000 gen- erations. Moreover, for a wide variety of organisms and
 
We present a new simple model for the evolution of premating reproductive isolation. Using this model we first analyze the level of genetic variability maintained by mutation in a large stable population. Then we consider the plausibility of the evolution of strong premating reproductive isolation after a founder event. We demonstrate that after a founder event a new adaptive combination of genes may rise to high frequencies in the presence of an old combination of genes. We compare the probabilities of speciation after a founder event with those in a stable population and with those when reproductive isolation is due to viability selection against hybrids. We argue that premating reproductive isolation is more efficient than postmating reproductive isolation in maintaining the integrity of sympatric species. This might have contributed to the pattern of stronger premating isolation than postmating isolation between closely related pairs of sympatric species.
 
Resolving the order of events that occurred during the transition from prokaryotic to eukaryotic cells remains one of the greatest problems in cell evolution. One view, the Archezoa hypothesis, proposes that the endosymbiotic origin of mitochondria occurred relatively late in eukaryotic evolution and that several mitochondrion-lacking protist groups diverged before the establishment of the organelle. Phylogenies based on small subunit ribosomal RNA and several protein-coding genes supported this proposal, placing amitochondriate protists such as diplomonads, parabasalids, and Microsporidia as the earliest diverging eukaryotic lineages. However, trees of other molecules, such as tubulins, heat shock protein 70, TATA box-binding protein, and the largest subunit of RNA polymerase II, indicate that Microsporidia are not deeply branching eukaryotes but instead are close relatives of the Fungi. Furthermore, recent discoveries of mitochondrion-derived genes in the nuclear genomes of entamoebae, Microsporidia, parabasalids, and diplomonads suggest that these organisms likely descend from mitochondrion-bearing ancestors. Although several protist lineages formally remain as candidates for Archezoa, most evidence suggests that the mitochondrial endosymbiosis took place prior to the divergence of all extant eukaryotes. In addition, discoveries of proteobacterial-like nuclear genes coding for cytoplasmic proteins indicate that the mitochondrial symbiont may have contributed more to the eukaryotic lineage than previously thought. As genome sequence data from parabasalids and diplomonads accumulate, it is becoming clear that the last common ancestor of these protist taxa and other extant eukaryotic groups already possessed many of the complex features found in most eukaryotes but lacking in prokaryotes. However, our confidence in the deeply branching position of diplomonads and parabasalids among eukaryotes is weakened by conflicting phylogenies and potential sources of artifact. Our current picture of early eukaryotic evolution is in a state of flux.
 
The observation that traits closely related to fitness ("fitness traits") have lower heritabilities than traits more distantly associated with fitness has traditionally been framed in terms of Fisher's fundamental theorem of natural selection-fitness traits are expected to have low levels of additive genetic variance due to rapid fixation of alleles conferring highest fitness. Subsequent treatments have challenged this view by pointing out that high environmental and nonadditive genetic contributions to phenotypic variation may also explain the low heritability of fitness traits. Analysis of a large data set from the collared flycatcher Ficedula albicollis confirmed a previous finding that traits closely associated with fitness tend to have lower heritability. However, analysis of coefficients of additive genetic variation (CVA) revealed that traits closely associated with fitness had higher levels of additive genetic variation (VA) than traits more distantly associated with fitness. Hence, the negative relationship between a trait's association with fitness and its heritability was not due to lower levels of VA in fitness traits but was due to their higher residual variance. However, whether the high residual variance was mainly due to higher levels of environmental variance or due to higher levels of nonadditive genetic variance remains a challenge to be addressed by further studies. Our results are consistent with earlier suggestions that fitness-related traits may have more complex genetic architecture than traits more distantly associated with fitness.
 
The divergence of premating behavior and morphology plays a primary role in speciation, and an understanding of the genetic architectures of these phenotypes is essential for the evaluation of models of the speciation process. However, our empirical knowledge of the genetics underlying speciation-related traits remains limited. In this article, we argue that a dissection of specific aspects of the genetic architecture of such traits in a comparative context can allow us to rule out some mechanisms of divergence. We discuss these ideas with reference to our investigation of intersexual communication behaviors involved in mate recognition in the Hawaiian cricket genus Laupala. Different species of Laupala sing distinctively and show species-specific acoustic preferences. We focus on the sister species Laupala paranigra and Laupala kohalensis, characterized by differences in these classic courtship phenotypes. We discuss our preliminary results on the directionality of effect of substituted alleles underlying these species differences. We then discuss these results in the context of historical inference, a necessary perspective for testing the genomic predictions made by theories of speciation that focus on evolution of mate recognition systems.
 
Ecological interactions and the natural selection they cause play a prominent causal role in biological diversification and speciation. As a discipline, ecological genetics integrates the two components of adaptive evolution (natural selection and genetic variability) to study the mechanisms of evolution. Ecological genetics is a fruitful approach to the study of how reproductive isolation can evolve under natural selection. The essence of this way of thinking and the ways in which it can be used to address persistent open questions in speciation are discussed.
 
Summary of components of color distinguishing Aq- uilegia formosa and Aquilegia pubescens A. formosa mean (SD, range) A. pubescens mean (SD, range) DSD 
Floral characters measured in this study. Left, line drawing of a flower of an F 2 plant from a cross between Aquilegia formosa and Aquilegia pubescens. The orientation of the flower is measured as the angle of the flower axis relative to gravity. Right, line drawing of a single petal; the four measurements made are indicated.
Summary of floral characters differentiating Aquilegia formosa and Aquilegia pubescens and their F 2 hybrids Character A. formosa mean (SD) A. pubescens mean (SD) DSD F 2 mean (SD) Repeatability, F 
Reproductive isolation between Aquilegia formosa and Aquilegia pubescens is influenced by differences in their flowers through their effects on pollinator visitation and pollen transfer. Here, we investigate the genetic basis of floral characters differentiating these species. We found that in addition to the effects of flower orientation and the length of nectar spurs previously described, other characters such as flower color or odor affect hawkmoth visitation. Repeatability of measurements in an F2 population ranged from 0.53 to 0.83 among five floral traits, indicating that using the means of multiple measures per plant will substantially increase the power of a quantitative trait locus (QTL) analysis. Integration of floral traits was indicated by significant correlations among traits in an F2 population. In a separate F2 population we found that QTL for different floral traits were often closely associated, indicating that linkage or pleiotropy cause at least some of this integration. In addition, we found QTL for all floral traits examined. Because Aquilegia species are largely interfertile and vary extensively in both floral morphology and ecology, they offer the opportunity for QTL studies of a wide range of characters affecting reproductive isolation.
 
A large number of mathematical models have been developed that show how natural and sexual selection can cause prezygotic isolation to evolve. This article attempts to unify this literature by identifying five major elements that determine the outcome of speciation caused by selection: a form of disruptive selection, a form of isolating mechanism (assortment or a mating preference), a way to transmit the force of disruptive selection to the isolating mechanism (direct selection or indirect selection), a genetic basis for increased isolation (a one- or two-allele mechanism), and an initial condition (high or low initial divergence). We show that the geographical context of speciation (allopatry vs. sympatry) can be viewed as a form of assortative mating. These five elements appear to operate largely independently of each other and can be used to make generalizations about when speciation is most likely to happen. This provides a framework for interpreting results from laboratory experiments, which are found to agree generally with theoretical predictions about conditions that are favorable to the evolution of prezygotic isolation.
 
Parameter values used in the simulation model 
Hybridization in flowering plants is determined in part by the rate at which animal pollinators move between species and by the effectiveness of such movements in transferring pollen. Pollinator behavior can also influence hybrid fitness by determining receipt and export of pollen. We incorporated information on pollinator effectiveness and visitation behavior into a simulation model that predicts pollen transfer between Ipomopsis aggregata, Ipomopsis tenuituba, and hybrids. These predictions were compared with estimates of pollen transfer derived from movement of fluorescent dyes in experimental plant arrays. Interspecific pollen transfer was relatively uncommon in these arrays, whereas transfer between hybrids and the parental species was at least as common as conspecific transfer. Backcrossing was asymmetrical; I. aggregata flowers frequently received mixed loads of hybrid and conspecific pollen. The simulation suggests that these patterns of pollen transfer are largely explained by the visitation sequences of hummingbird and insect pollinators, with little contribution from mechanical isolation. Pollen receipt by hybrids exceeded that of both parental species in a year when pollinators preferred to visit F(1) and F(2) hybrids and was intermediate in another year when they preferred to visit I. aggregata. This suggests that natural variation in pollination may produce spatiotemporal variation in hybridization and hybrid fitness.
 
We describe a model for the evolutionary consequences of plasticity in an environmentally heterogeneous metapopulation in which specialists for each of two alternative environments and one plastic type are initially present. The model is similar to that proposed by Moran (1992) but extends her work to two sites. We show that with migration between sites the plastic type is favored over local specialists across a broad range of parameter space. The plastic type may dominate or be fixed even in an environmentally uniform site, and even if the plasticity has imperfect accuracy or bears some cost such that a local specialist has higher fitness in that site, as long as there is some migration between sites with different distributions of environmental states. These results suggest that differences among taxa in dispersal and hence realized migration rates may play a heretofore unrecognized role in their patterns of adaptive population differentiation. Migration relaxes the thresholds for both environmental heterogeneity and accuracy of plastic response above which plasticity is favored. Furthermore, small changes in response accuracy can dramatically and abruptly alter the evolutionary outcome in the metapopulation. A fitness cost to plasticity will substantially reduce the range of conditions in which the plastic type will prevail only if the cost is both large and global rather than environment specific.
 
ANOVA of haplotype, treatment, haplotype by treatment interaction, growth chamber, and shelf effects 
Correlations among character grand means and plasticities calculated using haplotype means Leaves Rosette Bolting Stem length Basal stems Seed set Main fruits Basal fruits 
Matrix correlation relating differences between populations in their means and plasticities in response to foliar shade for the same trait 
In this article, we compare the reaction norms to foliage shade (changes in light quality, spatially fine-grained environmental variation) and photoperiod (day length, spatially coarse-grained environmental variation) in several haplotypes of Arabidopsis thaliana from Scandinavia. We found that both across-environment means and phenotypic plasticities evolved continuously and very rapidly within this group. Both character means and trait plasticities were highly integrated, in part as predicted by the adaptive plasticity hypothesis for response to foliage shade (the so-called shade-avoidance syndrome). We found that a significant but small fraction of the variance in across-treatment trait means and plasticities in response to one environmental factor is explained by variation of the same traits in response to the other factor. Genetic relatedness based on chloroplast DNA sequence variation among haplotypes was not associated with variation in across-treatment character means or their plasticities, suggesting that evolution of these characters has occurred on a local geographic scale via reticulation (outcrossing) among maternal lines rather than by the differential survival of selfing lineages.
 
A conceptual model depicting 14 scenarios representing different pathways or mechanisms by which species invasions and extinctions can drive biotic homogenization (increased
Patterns of community similarity change under the 14 invasion-extinction scenarios for three levels of initial community similarity ( , 0.50, and 0.75). Results are for all combinations of numbers of winners and losers (averaged over all levels of species richness [see J p 0.25 initial fig. 2]). Square symbol is the median, boxes represent interquartile ranges, and whiskers represent the minimum and maximum values. Dashed line demarcates homogenization (positive community similarity) from differentiation (negative community similarity).  
(continued)  
The widespread replacement of native species with cosmopolitan, nonnative species is homogenizing the global fauna and flora. While the empirical study of biotic homogenization is substantial and growing, theoretical aspects have yet to be explored. Consequently, the breadth of possible ecological mechanisms that can shape current and future patterns and rates of homogenization remain largely unknown. Here, we develop a conceptual model that describes 14 potential scenarios by which species invasions and/or extinctions can lead to various trajectories of biotic homogenization (increased community similarity) or differentiation (decreased community similarity); we then use a simulation approach to explore the model's predictions. We found changes in community similarity to vary with the type and number of nonnative and native species, the historical degree of similarity among the communities, and, to a lesser degree, the richness of the recipient communities. Homogenization is greatest when similar species invade communities, causing either no extinction or differential extinction of native species. The model predictions are consistent with current empirical data for fish, bird, and plant communities and therefore may represent the dominant mechanisms of contemporary homogenization. We present a unifying model illustrating how the balance between invading and extinct species dictates the outcome of biotic homogenization. We conclude by discussing a number of critical but largely unrecognized issues that bear on the empirical study of biotic homogenization, including the importance of spatial scale, temporal scale, and data resolution. We argue that the study of biotic homogenization needs to be placed in a more mechanistic and predictive framework in order for studies to provide adequate guidance in conservation efforts to maintain regional distinctness of the global biota.
 
Few studies have shown both reciprocal selection and reciprocal adaptations for a coevolving system in the wild. The goal of our study was to determine whether the patterns of selection on Rocky Mountain lodgepole pine (Pinus contorta spp. latifolia) and red crossbills (Loxia curvirostra complex) were concordant with earlier published evidence of reciprocal adaptations in lodgepole pine and crossbills on isolated mountain ranges in the absence of red squirrels (Tamiasciurus hudsonicus). We found that selection (directional) by crossbills on lodgepole pine where Tamiasciurus are absent was divergent from the selection (directional) exerted by Tamiasciurus on lodgepole pine. This resulted in divergent selection between areas with and without Tamiasciurus that was congruent with the geographic patterns of cone variation. In the South Hills, Idaho, where Tamiasciurus are absent and red crossbills are thought to be coevolving with lodgepole pine, crossbills experienced stabilizing selection on bill size, with cone structure as the agent of selection. These results show that crossbills and lodgepole pine exhibit reciprocal adaptations in response to reciprocal selection, and they provide insight into the traits mediating and responding to selection in a coevolutionary arms race.
 
A notable and consistent ecological observation known for a long time is that spatial variance in the abundance of a species increases with its mean abundance and that this relationship typically conforms well to a simple power law (Taylor 1961). Indeed, such models can be used at a spectrum of spatial scales to describe spatial variance in the abundance of a single species at different times or in different regions and of different species across the same set of areas (Taylor et al. 1978; Taylor and Woiwod 1982).
 
Stepwise multiple regressions of the logarithm of land bird species richness on several attributes of islands in the Lesser Antilles 
Species-area relationships for three historically distinguished groups of birds in the Lesser Antilles. The slopes are calculated for simple logarithmic regressions of species on area. 
We examined the species-area relationship for three historically distinct subsets of Lesser Antillean birds identified by molecular phylogenetic analysis of island and continental populations. The groups comprised recent colonists from continental or Greater Antillean source populations, old taxa having recently expanded distributions within the Lesser Antilles, and old endemic taxa lacking evidence of recent dispersal between islands. The number of young taxa was primarily related to distance from the source of colonists in South America. In a multiple regression, the logarithmic slope of the species-area relationship for this group was shallow (0.066+/-0.016). Old endemic taxa were restricted to islands with high elevation, and within this subset, species richness was related primarily to island area, with a steep slope (0.719+/-0.110). The number of recently spread endemic taxa was related primarily to island elevation, apparently reflecting the persistence of such populations on islands with large areas of forested and montane habitats. Historical analysis of the Lesser Antillean avifauna supports the dynamic concept of island biogeography of MacArthur and Wilson, rather than the more static view of David Lack, in that colonists exhibit dispersal limitation and extinction plays a role in shaping patterns of diversity. However, the avifauna of the Lesser Antilles is probably not in equilibrium at present, and the overall species-area relationship might reflect changing proportions of historically distinguishable subsets of species.
 
Hormonal mechanisms underlie many life-history traits and their interactions. We studied the role of ecdysteroids with regard to wing pattern and development time of the polyphenic butterfly Bicyclus anynana. Ecdysteroid titers and sensitivity to ecdysone injection were assayed for two-trait selected lines (ventral eyespot size and development time concurrently). These two traits are genetically and phenotypically coupled, having a common endocrinal basis. Two-trait selection had been applied both antagonistically (opposite the correlation) and synergistically (in the same direction as the correlation). Although selected lines had diverged most in eyespot size, the widest differences in timing of ecdysteroid titers were observed between the development time selection regimes; fast selected lines had an earlier hormonal increase after pupation than slow selected lines (even when corrected for differential pupal times). This endocrine peak was also earlier for females than for males. Furthermore, sensitivity to ecdysone injection as measured by a subsequent decrease in pupal time was significantly lower for slow selected lines than for fast or unselected lines. We conclude that the observed response in eyespot size to artificial selection must have been achieved via alteration of, or selection on, other developmental mechanisms, because the dynamics of the alternative, hormonal, pathway were dictated by development time selection. The developmental system is flexible enough to allow evolution in directions opposing the correlation between wing pattern and developmental time, and responses to selection are not constrained by a shared hormonal system.
 
On the basis of physiological and ecological costs of defense allocation, most plant defense theories predict the occurrence of trade-offs between resource investment in different types of antiherbivore defenses. To test this prediction, we conducted a meta-analysis of 31 studies published in 1976-2002 that provided data on covariation of different defensive traits in plant genotypes. We found no overall negative association between different defensive traits in plants; instead, the relationship between defensive traits varied from positive to negative depending on the types of co-occurring defenses. Evidence of trade-off was found only between constitutive and induced defenses. Therefore, to a large extent, plants appear to be jacks-of-all-trades, masters of all and may successfully produce several types of defense without paying considerable trade-offs. Our survey thus provides little evidence that genetic trade-offs between defensive traits significantly constrain the evolution of multiple defenses in plants.
 
Twenty-one Empirical Studies of the Mid-Domain Effect a 
If species' ranges are randomly shuffled within a bounded geographical domain free of environmental gradients, ranges overlap increasingly toward the center of the domain, creating a "mid-domain" peak of species richness. This "mid-domain effect" (MDE) has been controversial both in concept and in application. Empirical studies assess the degree to which the evolutionary, ecological, and historical processes that undeniably act on individual species and clades produce geographical patterns that resemble those produced by MDE models. MDE models that resample empirical range size frequency distributions (RSFDs) balance the risk of underestimating and overestimating the role of MDE, whereas theoretical RSFDs are generally biased toward underestimating MDE. We discuss the inclusion of nonendemic species in MDE models, rationales for setting domain limits, and the validity of one- and two-dimensional MDE models. MDE models, though null models, are not null hypotheses to be simplistically rejected or accepted. They are a means of estimating the expected effect of geometric constraints within the context of multiple causality. We call for assessment of MDE on an equal statistical footing with other candidate explanations for richness gradients. Although some critics have categorically dismissed MDE, an overview of the 21 MDE studies published to date reveals a substantial signature of MDE in natural patterns and justifies continued work.
 
Recent experiments on plant defenses against pathogens or herbivores have shown various patterns of the association between resistance, which reduces the probability of being infected or attacked, and tolerance, which reduces the loss of fitness caused by the infection or attack. Our study describes the simultaneous evolution of these two strategies of defense in a population of hosts submitted to a pathogen. We extended previous approaches by assuming that the two traits are independent (e.g., determined by two unlinked genes), by modeling different shapes of the costs of defenses, and by taking into account the demographic and epidemiological dynamics of the system. We provide novel predictions on the variability and the evolution of defenses. First, resistance and tolerance do not necessarily exclude each other; second, they should respond in different ways to changes in parameters that affect the epidemiology or the relative costs and benefits of defenses; and third, when comparing investments in defenses among different environments, the apparent associations among resistance, tolerance, and fecundity in the absence of parasites can lead to the false conclusion that only one defense trait is costly. The latter result emphasizes the problems of estimating trade-offs and costs among natural populations without knowledge of the underlying mechanisms.
 
Relationship between aspergillosis and recruitment. On six of seven reefs, recruitment declined with disease prevalence. Data were combined for the Keys-wide analysis. Reef abbreviations as in figure 1.  
Changes in size class structure of sea fans between August 1997 and August 2003. Note the general decline in larger sea fans. Data were combined for the Keys-wide analysis. Reef abbreviations as in figure 1.  
Drivers of disease cycles are poorly understood in marine ecosystems in spite of increasing outbreaks. We monitored a newly emerged fungal epizootic (aspergillosis) affecting sea fan corals (Gorgonia ventalina L.) in the Florida Keys to evaluate causes of its rise and fall over 6 years. Since August 1997, aspergillosis has nearly eradicated large sea fans at some sites. However, sea fan densities have remained relatively constant due to episodic recruitment replacing large fans with small. Recruitment itself was affected by infection and occurred only when prevalence of disease was low. This impact on recruitment occurred because the largest, potentially most fecund colonies had the highest prevalence of disease, and the pathogen significantly suppressed reproduction of infected fans. Moreover, high mortality among adults resulted in a demographic shift to smaller colonies. The most dramatic impact of aspergillosis was the Keys-wide loss of >50% of sea fan tissue from complete and partial mortality. Aspergillosis prevalence has declined steadily over the last 6 years, and we consider the following hypotheses for decline of the epizootic: change in environment, change in pathogen input, and increase in host resistance. We conclude that increasing host resistance is the most likely driver of the decline. However, a change in any of a number of factors, for example, recruitment of naive hosts, rate of pathogen input, or environmental conditions (water quality and temperature), is likely to promote reemergence of the epizootic.
 
When selection on males and females differs, the sexes may diverge in phenotype. Hormones serve as a proximate regulator of sex differences by mediating sex-biased trait expression. To integrate these perspectives, we consider how suites of traits mediated by the same hormone in both sexes might respond to selection. In male birds, plasma testosterone (T) varies seasonally and among species according to mating system. When elevated experimentally, it is known to enhance some components of fitness and to decrease others. We report that female T also varies seasonally and co-varies with male T. Female T is higher in relation to male T in sexually monomorphic species and is higher absolutely in females of species with socially monogamous mating systems, which suggests adaptation. We also consider the effect of experimentally elevated T on females and whether traits are sensitive to altered T. We hypothesize that sensitive traits could become subject to selection after a natural change in T and that traits with opposing fitness consequences in males and females could constrain dimorphism. Results from birds, including the dark-eyed junco (Junco hyemalis), reveal many sensitive traits, some of which appear costly and may help to account for observed levels of sexual dimorphism.
 
Means (SE) of traits for the different selection lines in the last generation of both selection programs for males and females and results of the one-way ANOVAs 
In dioecious plants, females typically invest more biomass in reproduction than males and consequently experience stronger life-history trade-offs. Sexual dimorphism in life history runs counter to this pattern in Silene latifolia: females acquire less carbon and invest more biomass in reproduction, but males pay a higher cost of reproduction. The species is sexually dimorphic for many traits, especially flower number, with males producing many, small flowers compared to females. We tested whether the cost of reproduction is higher in males because flower number, which we presume to be under sexual selection in males, is genetically correlated with traits that would affect life-history trade-offs. We performed artificial selection to reduce the sexual dimorphism in flower size and looked at correlated responses in ecophysiological traits. We found significant correlated responses in total vegetative mass, leaf mass, leaf thickness, and measures of CO(2) exchange. Individuals in the many-and-small-flowered selection lines did not grow as large or invest as much biomass in leaves, and their leaves exhibited an up-regulated physiology that shortened leaf life span. Our results are consistent with the hypothesis that genetic correlations between floral display and ecophysiological traits lead to a higher cost of reproduction for males.
 
Diagram of the metabolism of a mixotroph. The shaded box encloses the organism, the lighter part of which denotes its membranes
Vertical profiles and adaptive landscape for the monomorphic population (solid lines) and those for the dimorphic population after evolutionary branching has taken place (dotted and dashed lines). The former consists of mixotrophs that have reached the singular strategy; the latter population consists of separate heterotrophs (dashed line h) and almost pure autotrophs (dashed line a) that have reached an evolutionarily stable coexistence. A–E show the densities of dissolved inorganic carbon ( ), X C dissolved inorganic nitrogen ( ), detritus ( ), biomass ( ), and the light X X X N D V intensity gradient ( ), plotted against the depth . The adaptive landscapes J L L,F z in F plot invasion fitness against a range of mutant strategies s (r ) r mut res ; the dashed line shows the adaptive landscape with two resident stratr mut egies after branching, and the dotted line shows the (almost flat) adaptive landscape at the singular strategy for a homogeneous system.  
In recent years, the population dynamics of plankton in light- or nutrient-limited environments have been studied extensively. Their evolutionary dynamics, however, have received much less attention. Here, we used a modeling approach to study the evolutionary behavior of a population of plankton living in a mixed water column. Initially, the organisms are mixotrophic and thus have both autotrophic and heterotrophic abilities. Through evolution of their trophic preferences, however, they can specialize into separate autotrophs and heterotrophs. It was found that the light intensity gradient enables evolutionary branching and thus may result in the ecological specialization of the mixotrophs. By affecting the gradient, other environmental properties also acquire influence on this evolutionary process. Intermediate mixing intensities, large mixing depths, and high nutrient densities were found to facilitate evolutionary branching and thus specialization. Later results may explain why mixotrophs are often more dominant in oligotrophic systems while specialist strategies are associated with eutrophic systems.
 
Seed dispersal is a critical but poorly understood life-history stage of plants. Here we use a genetic approach to describe seed dispersal patterns accurately in a natural population of the Neotropical tree species Jacaranda copaia (Bignoniaceae). We used microsatellite genotypes from maternally derived tissue on the diaspore to identify which individual of all possible adult trees in the population was the true source of a given seed collected after it dispersed. Wind-dispersed seeds were captured in two different years in a large array of seed traps in an 84-ha mapped area of tropical forest on Barro Colorado Island, Panama. We were particularly interested in the proportion of seeds that traveled long distances and whether there was evidence for direct dispersal into gaps, which are required for successful recruitment of this pioneer tree species. Maximum likelihood procedures were used to fit single- and multiple-component dispersal kernels to the distance data. Mixture models, with separate distributions near and far, best fit the observed dispersal distances, albeit with considerable uncertainty in the tail. We discuss the results in light of different mechanisms responsible for separate distributions near the adult source and in the tail of the curve.
 
A cornerstone of evolutionary ecology is that population density affects adaptation: r and K selection is the obvious example. The reverse is also appreciated: adaptation impacts population density. Yet, empirically demonstrating a direct connection between population density and adaptation is challenging. Here, we address both evolution and ecology of population density in models of viral (bacteriophage) chemostats. Chemostats supply nutrients for host cell growth, and the hosts are prey for viral reproduction. Two different chemostat designs have profoundly different consequences for viral evolution. If host and virus are confined to the same chamber, as in a predator-prey system, viral regulation of hosts feeds back to maintain low viral density (measured as infections per cell). Viral adaptation impacts host density but has a small effect on equilibrium viral density. More interesting are chemostats that supply the viral population with hosts from a virus-free refuge. Here, a type of evolutionary succession operates: adaptation at low viral density leads to higher density, but high density then favors competitive ability. Experiments support these models with both phenotypic and molecular data. Parallels to these designs exist in many natural systems, so these experimental systems may yield insights to the evolution and regulation of natural populations.
 
Source populations for Helianthus plant material used in the common gardens and in production of the experimental backcross (BC 1 ) populations 
Incidence of herbivore damage in the four experimental populations 
Trait values (mean SE) for four Helianthus taxa in common gardens in two central Texas sites 
MANOVAs for two sets of traits measured on four Helianthus taxa in common gardens in two central Texas sites 
Selection differentials (s ) and selection gradients (b) for resistance and damage traits in two Helianthus annuus annuus # Helianthus debilis BC 1 populations in central Texas 
The role of hybridization in adaptive evolution is contentious. While many cases of adaptive trait introgression have been proposed, the relevant traits have rarely been identified, resulting in a lack of clear examples of this process. Here, we examine a purported case of adaptive introgression in which the annual sunflower Helianthus annuus annuus has captured alleles from a congener (Helianthus debilis) to form a stabilized hybrid, Helianthus annuus texanus. We tested the hypotheses that herbivore resistance traits have introgressed from H. debilis to H. annuus and have increased adaptation in the latter. In two common gardens, fitness (estimated by seed production) was on average 55% higher in H. a. texanus than in H. a. annuus. For H. a. texanus, three damage traits (of seven tested) differed significantly from the H. a. annuus parent in one or both sites and were shifted in the direction of the more resistant H. debilis. Natural selection favored H. a. annuusxH. debilis BC(1) hybrids (synthesized to mimic the ancestors of H. a. texanus) with H. debilis-like resistance to seed midges Neolasioptera helianthis and to receptacle/seed feeding Lepidoptera at one or both sites. Assuming similar herbivore pressures in the past, these results suggest that introgression of biotic resistance traits was important in the adaptation of H. annuus to central and southern Texas.
 
We developed a theoretical framework based on phylogenetic comparative methods to integrate phylogeny into three measures of biodiversity: species variability, richness, and evenness. These metrics can be used in conjunction with permutation procedures to test for phylogenetic community structure. As an illustration, we analyzed data on the composition of 58 lake fish communities in Wisconsin. The fish communities showed phylogenetic underdispersion, with communities more likely to contain closely related species. Using information about differences in environmental characteristics among lakes, we demonstrated that phylogenetic underdispersion in fish communities was associated with environmental factors. For example, lakes with low pH were more likely to contain species in the same clade of acid-tolerant species. Our metrics differ from existing metrics used to calculate phylogenetic community structure, such as net relatedness index and Faith's phylogenetic diversity. Our metrics have the advantage of providing an integrated and easy-to-understand package of phylogenetic measures of species variability, richness, and evenness with well-defined statistical properties. Furthermore, they allow the easy evaluation of contributions of individual species to different aspects of the phylogenetic organization of communities. Therefore, these metrics should aid with the incorporation of phylogenetic information into strategies for understanding biodiversity and its conservation.
 
Phenotypic plasticity and related processes (learning, developmental noise) have been proposed to both accelerate and slow down genetically based evolutionary change. While both views have been supported by various mathematical models and simulations, no general predictions have been offered as to when these alternative outcomes should occur. Here we propose a general framework to study the effects of plasticity on the rate of evolution under directional selection. It is formulated in terms of the fitness gain gradient, which measures the effect of a marginal change in the degree of plasticity on the slope of the relationship between the genotypic value of the focal trait and log fitness. If the gain gradient has the same sign as the direction of selection, an increase in plasticity will magnify the response to selection; if the two signs are opposite, greater plasticity will lead to slower response. We use this general result to derive conditions for the acceleration/deceleration under several simple forms of plasticity, including developmental noise. We also show that our approach explains the results of several specific models from the literature and thus provides a unifying framework.
 
Taxa co-occurring in communities often represent a nonrandom sample, in phenotypic or phylogenetic terms, of the regional species pool. While heuristic arguments have identified processes that create community phylogenetic patterns, further progress hinges on a more comprehensive understanding of the interactions between underlying ecological and evolutionary processes. We created a simulation framework to model trait evolution, assemble communities (via competition, habitat filtering, or neutral assembly), and test the phylogenetic pattern of the resulting communities. We found that phylogenetic community structure is greatest when traits are highly conserved and when multiple traits influence species membership in communities. Habitat filtering produces stronger phylogenetic structure when taxa with derived (as opposed to ancestral) traits are favored in the community. Nearest-relative tests have greater power to detect patterns due to competition, while total community relatedness tests perform better with habitat filtering. The size of the local community relative to the regional pool strongly influences statistical power; in general, power increases with larger pool sizes for communities created by filtering but decreases for communities created by competition. Our results deepen our understanding of processes that contribute to phylogenetic community structure and provide guidance for the design and interpretation of empirical research.
 
The study of culturally inherited traits has led to the suggestion that the evolution of helping behaviors is more likely with cultural transmission than without. Here we evaluate this idea through a comparative analysis of selection on helping under both genetic and cultural inheritance. We develop two simple models for the evolution of helping through cultural group selection: one in which selection on the trait depends solely on Darwinian fitness effects and one in which selection is driven by nonreproductive factors, specifically imitation of strategies achieving higher payoffs. We show that when cultural variants affect Darwinian fitness, the selection pressure on helping can be markedly increased relative to that under genetic transmission. By contrast, when variants are driven by nonreproductive factors, the selection pressure on helping may be reduced relative to that under genetic inheritance. This occurs because, unlike biological offspring, the spread of cultural variants from one group to another through imitation does not reduce the number of these variants in the source group. As a consequence, there is increased within-group competition associated with traits increasing group productivity, which reduces the benefits of helping. In these cases, selection for harming behavior (decreasing the payoff to neighbors) may occur rather than selection for helping.
 
Power to detect hybridization under different parameters as determined by simulations. The population size parameter is in units of , where N E is the effective population size and m is the mutation rate; t 1 and t 2 are in units of , where T is the number of generations. v p 4N m t p Tm E  
Figure A1: Phylogram of one most parsimonious tree and parsimony statistics for the nrITS data set. Dotted lines indicate branches that collapse in the strict consensus tree.  
Figure A2: Phylogram of one most parsimonious tree and parsimony statistics for the J SA data set. Dotted lines indicate branches that collapse in the strict consensus tree.  
Figure A3: Posterior distributions obtained for branch lengths (t), population sizes (v), and locus rates (r) with the different priors used.
The extent and evolutionary significance of hybridization is difficult to evaluate because of the difficulty in distinguishing hybridization from incomplete lineage sorting. Here we present a novel parametric approach for statistically distinguishing hybridization from incomplete lineage sorting based on minimum genetic distances of a nonrecombining locus. It is based on the idea that the expected minimum genetic distance between sequences from two species is smaller for some hybridization events than for incomplete lineage sorting scenarios. When applied to empirical data sets, distributions can be generated for the minimum interspecies distances expected under incomplete lineage sorting using coalescent simulations. If the observed distance between sequences from two species is smaller than its predicted distribution, incomplete lineage sorting can be rejected and hybridization inferred. We demonstrate the power of the method using simulations and illustrate its application on New Zealand alpine buttercups (Ranunculus). The method is robust and complements existing approaches. Thus it should allow biologists to assess with greater accuracy the importance of hybridization in evolution.
 
Estimates of selection and epistasis 
Understanding the nature of selection against deleterious alleles is central to determining how populations are affected by the constant influx of new mutations. Important progress has been made in estimating basic attributes of the distribution of selection coefficients and gene interaction effects (epistasis). Although most aspects of selection are likely to be context dependent, little is known about the effect of stress on selection and epistasis at the level of individual genes, especially in multicellular organisms. Using Drosophila melanogaster, we measure how selection on 20 mutant alleles is affected by direct and indirect genetic factors across two environments. We find that environmental stress increases selection against individual mutations but reduces selection against combinations of mutations (i.e., epistasis becomes more positive). In addition, we find a high incidence of indirect genetic effects whereby the strength of selection against the alleles carried by offspring is dependent on the genotypes of their parents.
 
Canalization-the evolutionary loss of the capacity of organisms to develop different phenotypes in different environments-is an evolutionary phenomenon suspected to occur widely, although examples in natural populations are elusive. Because behavior is typically a highly flexible component of an individual's phenotype, it provides fertile ground for studying the evolution of canalization. Here we report how snail populations exposed for different lengths of time to a predatory crab introduced from Europe to America exhibit different degrees of canalization of an adaptive antipredator behavior: soft tissue withdrawal, measured as angular retraction depth. Where crab-snail contact is shortest (60 years), snails showed the highest behavioral flexibility. Where crabs invaded 110 years ago, snails showed significantly less behavioral flexibility, and where the interaction is ancient (Europe), snails exhibited highly canalized behavior. Selection therefore appears to have acted rapidly to increase canalization in wild snail populations, leading ultimately to the hard-wired behavior seen in European conspecifics.
 
Summary of univariate analyses (F statistic) of across-species cyt b divergences (HKY85 corrected) testing relationships with species- specific attributes and geographic distance 
Hierarchical AMOVA for cis-Andean population centers and results of polymorphism and historical demographic analyses for Inambari 
Despite the theoretical link between the ecology and the population genetics of species, little empirical evidence is available that corroborates the association. Here, we examined genetic variation in 40 codistributed species of lowland Neotropical rain forest birds that have populations isolated on either side of the Andes, the Amazon River, and the Madeira River. We found widely varying levels of genetic divergence among these taxa across the same biogeographic barriers. Our investigation of the extent to which ecological traits predicted the amount of cross-barrier divergence revealed a strongly significant relationship between the forest stratum at which a species forages and the level of cross-barrier genetic differentiation. Canopy species had statistically lower genetic divergence values across the Andes and the two Amazonian rivers than did understory birds. We hypothesize that the association reflects an effect of dispersal propensity, which is greater in canopy birds, on the movement of alleles among demes (i.e., migration) and, consequently, on the interdemic proportion of the genetic variance. Differences in dispersal propensity may also explain the observation that understory species contain a significantly greater number of subspecies than do canopy species. This result indicates that higher rates of diversification may occur in lineages with lower dispersal propensity.
 
Although divergent natural selection is common in nature, the extent to which genetic constraints bias evolutionary trajectories in its presence remains largely unknown. Here we develop a general framework to integrate estimates of divergent selection and genetic constraints to estimate their contributions to phenotypic divergence among natural populations. We apply these methods to estimates of phenotypic selection and genetic covariance from sexually selected traits that have undergone adaptive divergence among nine natural populations of the fly Drosophila serrata. Despite ongoing sexual selection within populations, differences in its direction among them, and genetic variance for all traits in all populations, divergent sexual selection only weakly resembled the observed pattern of divergence. Accounting for the influence of genetic covariance among the traits significantly improved the alignment between observed and predicted divergence. Our results suggest that the direction in which sexual selection generates divergence may depend on the pattern of genetic constraint in individual populations, ultimately restricting how sexually selected traits may diversify. More generally, we show how evolution is likely to proceed in the direction of major axes of genetic variance, rather than the direction of selection itself, when genetic variance-covariance matrices are ill conditioned and genetic variance is low in the direction of selection.
 
Number of plants with trichomes absent or present for each measurement set 
Insect herbivory is a major driving force of plant evolution. Phenotypic plasticity and developmental variation provide a means for plants to cope with variable herbivory. We characterized the genetics of developmental variation and phenotypic plasticity in trichome density, a putative defensive trait of Mimulus guttatus (yellow monkeyflower). Our results are evaluated in relation to the optimal defense theory, which provides testable predictions for plastic and developmental patterns in defense traits. We found that both developmental stage and simulated insect damage affected trichome production, but in different ways. Plants were more likely to produce at least some trichomes on later leaves than on earlier leaves, regardless of damage. Damage did not affect the average probability of producing trichomes, but it did increase the density of hairs on trichome-positive plants. We mapped trichome quantitative trait loci (QTL) by selectively genotyping a large panel of recombinant inbred lines derived from two highly divergent populations. Several highly pleiotropic QTL influenced multiple aspects of the trichome phenotype (constitutive, developmental, and/or plastic responses). Only one of the QTL influenced trichome induction following damage. In a result that is consistent with a central prediction of optimal defense theory, the high allele at this location was from the ancestral population with low constitutive trichome production.
 
Spearman rank correlations between metrics of phylo- genetic community dissimilarity (PCD) and the absolute values of differences in 16 environmental variables between lakes 
Power analysis of the ability of statistical tests based on PCD 
We derive a new metric of community similarity that takes into account the phylogenetic relatedness among species. This metric, phylogenetic community dissimilarity (PCD), can be partitioned into two components, a nonphylogenetic component that reflects shared species between communities (analogous to Sørensen' s similarity metric) and a phylogenetic component that reflects the evolutionary relationships among nonshared species. Therefore, even if a species is not shared between two communities, it will increase the similarity of the two communities if it is phylogenetically related to species in the other community. We illustrate PCD with data on fish and aquatic macrophyte communities from 59 temperate lakes. Dissimilarity between fish communities associated with environmental differences between lakes often has a phylogenetic component, whereas this is not the case for macrophyte communities. With simulations, we then compare PCD with two other metrics of phylogenetic community similarity, II(ST) and UniFrac. Of the three metrics, PCD was best at identifying environmental drivers of community dissimilarity, showing lower variability and greater statistical power. Thus, PCD is a statistically powerful metric that separates the effects of environmental drivers on compositional versus phylogenetic components of community structure.
 
We construct a model that combines extinction-colonization dynamics with the dynamics of local adaptation in a network of habitat patches of dissimilar qualities. We derive a deterministic approximation for the stochastic model that allows the calculation of patch-specific incidences of occupancy and levels of adaptation at steady state. Depending on (i) the strength of local selection, (ii) the amount of genetic variance, (iii) the demographic cost of maladaptation, (iv) the spatial scale of gene flow, and (v) the amount of habitat heterogeneity, the model predicts adaptation at different spatial scales. Local adaptation is predicted when there is much genetic variance and strong selection, while network-level adaptation occurs when the demographic cost of maladaptation is low. For little genetic variance and high cost of maladaptation, the model predicts network-level habitat specialization in species with long-range migration but an intermediate scale of adaptation (mosaic specialization) in species with short-range migration. In fragmented landscapes, the evolutionary dynamics of adaptation may both decrease and enhance metapopulation viability in comparison with no evolution. The model can be applied to real patch networks with given sizes, qualities, and spatial positions of habitat patches.
 
An overview of population genetic predictions under alternative models of range limits 
Abstract Theoretical models of species' geographic range limits have identified both demographic and evolutionary mechanisms that prevent range expansion. Stable range limits have been paradoxical for evolutionary biologists because they represent locations where populations chronically fail to respond to selection. Distinguishing among the proposed causes of species' range limits requires insight into both current and historical population dynamics. The tools of molecular population genetics provide a window into the stability of range limits, historical demography, and rates of gene flow. Here we evaluate alternative range limit models using a multilocus data set based on DNA sequences and microsatellites along with field demographic data from the annual plant Clarkia xantiana ssp. xantiana. Our data suggest that central and peripheral populations have very large historical and current effective population sizes and that there is little evidence for population size changes or bottlenecks associated with colonization in peripheral populations. Whereas range limit populations appear to have been stable, central populations exhibit a signature of population expansion and have contributed asymmetrically to the genetic diversity of peripheral populations via migration. Overall, our results discount strictly demographic models of range limits and more strongly support evolutionary genetic models of range limits, where adaptation is prevented by a lack of genetic variation or maladaptive gene flow.
 
Genetic demixing in experiments (A), on-lattice simulations (B), and off-lattice simulations (C). Different colors label different alleles, and the initial mixing ratio was 1:1. (A) The Petri dish was inoculated with a drop (bounded by the white circle) of a mixture of Pseudomonas aeruginosa cells labeled with two different fluorescent markers that do not affect the relative fitness of the cells. As the drop dries out and the colony starts to expand (shown with arrows), the population at the front of the expansion demixes (separates) into sectors of different colors. This genetic demixing is due to the loss of local genetic diversity during the expansion, see (Hallatschek et al., 2007; Hallatschek and Nelson, 2010; Korolev et al., 2010). This plate was incubated at 37 • C. (B) The habitat was a 1000 × 1000 array of islands arranged on a square lattice. Each island could harbor at most N = 30 individuals, consistent with the width of the layer of actively growing cells found in (Hallatschek et al., 2007). The simulation was started with a well-mixed population occupying a disk of radius R 0 = 80 lattice spacings in the center of the habitat. (C) The simulation was initiated with 1024 agents placed at random within a circular inoculant in the center of the habitat. The boxed region of the colony is shown in the inset at a higher magnification. We attribute the slightly square shape of the colony to the underlying square grid used to solve the nutrient reaction-diffusion equation.
It is widely accepted that population-genetics theory is the cornerstone of evolutionary analyses. Empirical tests of the theory, however, are challenging because of the complex relationships between space, dispersal, and evolution. Critically, we lack quantitative validation of the spatial models of population genetics. Here we combine analytics, on- and off-lattice simulations, and experiments with bacteria to perform quantitative tests of the theory. We study two bacterial species, the gut microbe Escherichia coli and the opportunistic pathogen Pseudomonas aeruginosa, and show that spatiogenetic patterns in colony biofilms of both species are accurately described by an extension of the one-dimensional stepping-stone model. We use one empirical measure, genetic diversity at the colony periphery, to parameterize our models and show that we can then accurately predict another key variable: the degree of short-range cell migration along an edge. Moreover, the model allows us to estimate other key parameters, including effective population size (density) at the expansion frontier. While our experimental system is a simplification of natural microbial community, we argue that it constitutes proof of principle that the spatial models of population genetics can quantitatively capture organismal evolution.
 
Personality differences can be found in a wide range of species across the animal kingdom, but why natural selection gave rise to such differences remains an open question. Frequency-dependent selection is a potent mechanism explaining variation; it does not explain, however, the other two key features associated with personalities, consistency and correlations. Using the hawk-dove game and a frequency-dependent foraging game as examples, we here show that this changes fundamentally whenever one takes into account the physiological architecture underlying behavior (e.g., metabolism). We find that the inclusion of physiology changes the evolutionary predictions concerning consistency and correlations: while selection gives rise to inconsistent individuals and stochastically fluctuating behavioral correlations in scenarios that neglect physiology, we find high levels of behavioral consistency and tight and stable trait correlations in scenarios that incorporate physiology. The coevolution of behavioral and physiological traits also gives rise to adaptive physiological differences that are systematically associated with behavioral differences. As well as providing a framework for understanding behavioral consistency and behavioral correlations, our work thus also provides an explanation for systematic physiological differences within populations, a phenomenon that appears to exist in a wide range of species but that, up to now, has been poorly understood.
 
Two independent evolutionary paths to tough leaves. Both lamina density and cellulose were positively correlated with lamina fracture toughness (A, B), but lamina density and cellulose were not correlated (C). Both positive and negative values of each phylogenetically independent contrast (PIC) are displayed, from which Pearson's correlation (r) was calculated. Scatterplots include the 95% probability density ellipse. The significance of correlations (P value) was evaluated by the nonparametric sign test.
Slow-growing juveniles of shade-tolerant plant species are predicted to have tough leaves because of the high cost of leaf replacement in shade relative to potential carbon gain. We assessed the degree of correlated evolution among eight traits associated with leaf toughness and the relationships of those traits with the growth and mortality rates of 197 tree and shrub species from the understory of the 50-ha forest dynamics plot on Barro Colorado Island, Panama. Path analysis with phylogenetically independent contrasts revealed that leaves attained material toughness (resistance to fracture per unit fracture area) through increases in tissue density, percent cellulose per unit dry mass, and vein fracture toughness. Lamina density and cellulose content evolved independently and thus represent different paths to material toughness. Structural toughness (resistance to fracture per unit fracture length) depended on material toughness and lamina thickness. Mortality rates of individuals 1-10 cm in stem diameter were negatively correlated with material toughness and lamina density but were independent of structural toughness and cell wall fiber contents. Leaf toughness traits were uncorrelated with relative growth rates. Results imply that material toughness enhances resistance to natural enemies, which increases survival and offsets the biomass allocation cost of producing tough leaves in the shaded understory.
 
Top-cited authors
H. Ronald Pulliam
  • University of Georgia
Robert P Freckleton
  • The University of Sheffield
Mark Pagel
  • University of Reading
Michel Loreau
  • French National Centre for Scientific Research
David Berrigan
  • National Institutes of Health