Showing papers in "Annual Review of Ecology, Evolution, and Systematics in 2008"
TL;DR: Understanding differential competitive potentials among co-occurring species mediated by shade tolerance is critical to predict ecosystem responses to global change drivers such as elevated CO2, climate change and the spread of invasive species.
Abstract: Light gradients are ubiquitous in nature, so all plants are exposed to some degree of shade during their lifetime. The minimum light required for survival, shade tolerance, is a crucial life-history trait that plays a major role in plant community dynamics. There is consensus on the suites of traits that influence shade tolerance, but debate over the relative importance of traits maximizing photosynthetic carbon gain in low light versus those minimizing losses. Shade tolerance is influenced by plant ontogeny and by numerous biotic and abiotic factors. Although phenotypic plasticity tends to be low in shade-tolerant species (e.g., scant elongation in low light), plasticity for certain traits, particularly for morphological features optimizing light capture, can be high. Understanding differential competitive potentials among co-occurring species mediated by shade tolerance is critical to predict ecosystem responses to global change drivers such as elevated CO2, climate change and the spread of invasive spe...
1,167 citations
TL;DR: The essential components of trait-based approaches to phytoplankton ecology are summarized and mathematical techniques for integrating traits into measures of growth and fitness and predicting how community structure varies along environmental gradients are described.
Abstract: Trait-based approaches are increasingly used in ecology. Phytoplankton communities, with a rich history as model systems in community ecology, are ideally suited for applying and further developing these concepts. Here we summarize the essential components of trait-based approaches and review their historical and potential application to illuminating phytoplankton community ecology. Major ecological axes relevant to phytoplankton include light and nutrient acquisition and use, natural enemy interactions, morphological variation, temperature sensitivity, and modes of reproduction. Tradeoffs between these traits play key roles in determining community structure. Freshwater and marine environments may select for a different suite of traits owing to their different physical and chemical properties. We describe mathematical techniques for integrating traits into measures of growth and fitness and predicting how community structure varies along environmental gradients. Finally, we outline challenges and future directions for the application of trait-based approaches to phytoplankton ecology.
977 citations
TL;DR: The extent of this climate mismatch has been revealed by physiologically based global vegetation simulations and by large empirical data sets, and the implication is that ecosystem structure and function depend on demographic transitions.
Abstract: Though the distribution of global vegetation can generally be predicted from climate, grasslands are an exception. C4 grassy biomes cover vast areas that are warm enough and wet enough to support closed forests. The extent of this climate mismatch has been revealed by physiologically based global vegetation simulations and by large empirical data sets. Reasons for the existence of grassy biomes have long been debated, polarized into bottom-up (resources) or top-down (fire, herbivory) arguments. Recent studies indicate that both are important, especially in suppressing woody recruits. Grasses are formidable competitors belowground, create highly flammable fuels, and can support large herbivore densities. The net effect on trees is rare and episodic recruitment of adults in tree-fall gaps. The implication is that ecosystem structure and function depend on demographic transitions. Tree cover is increasing and grass/forest boundaries are changing. These changes can have large feedbacks to the earth-atmosphere...
857 citations
TL;DR: How development produces covariation between traits can have substantial implications for understanding genetic variation and the potential for evolutionary change, but research in this area has only begun and many questions remain unanswered.
Abstract: Biological systems, from molecular complexes to whole organisms and ecological interactions, tend to have a modular organization. Modules are sets of traits that are internally integrated by interactions among traits, but are relatively independent from other modules. The interactions within modules rely on different mechanisms, depending on the context of a study. For morphological traits, modularity occurs in developmental, genetic, functional, and evolutionary contexts. A range of methods for quantifying integration and modularity in morphological data is available, and a number of comparative and experimental designs can be used to compare the different contexts. How development produces covariation between traits can have substantial implications for understanding genetic variation and the potential for evolutionary change, but research in this area has only begun and many questions remain unanswered.
678 citations
TL;DR: This work has concluded that floral scent is a sexual signal and should be subject to the same selective pressures and modes of sig...
Abstract: Floral scent constitutes an ancient and important channel of communication between flowering plants, their pollinators, and enemies. Fragrance is a highly complex component of floral phenotype, with dynamic patterns of emission and chemical composition. The information content of specific volatile compounds is highly context dependent, and scent can function in direct and indirect ways from landscape to intrafloral scales. Floral scent promotes specialization in plant–pollinator relationships through private channels of unusual compounds, unique ratios of more widespread compounds, or through multicomponent floral filters. Floral scent also promotes outcrossing and reproductive isolation through floral constancy, via appetitive conditioning and discrimination on the basis of diverse mechanisms, including pheromone mimicry, odor intensity, complexity, composition, and synergy with visual stimuli. Finally, floral scent is a sexual signal and should be subject to the same selective pressures and modes of sig...
677 citations
TL;DR: A large and rapidly expanding literature bears on these issues, but it is highly fragmented, principally comprises particular case studies, and employs a diverse array of approaches as mentioned in this paper, and the major problems that remain unresolved.
Abstract: Protected areas are a cornerstone of local, regional, and global strategies for the conservation of biodiversity. However, the ecological performance of these areas, both in terms of the representation and the maintenance of key biodiversity features, remains poorly understood. A large and rapidly expanding literature bears on these issues, but it is highly fragmented, principally comprises particular case studies, and employs a diverse array of approaches. Here we provide a synthetic review of this work, discriminating between issues of performance of inventory and condition at the scale of individual protected areas, portfolios, and networks of protected areas. We emphasize the insights that follow and the links between the different issues, as well as highlight the major problems that remain unresolved.
609 citations
TL;DR: There is a growing appreciation that chromosome inversions affect rates of adaptation, speciation, and the evolution of sex chromosomes, but few genes within inversions responsible for fitness effects or speciation have been identified.
Abstract: There is a growing appreciation that chromosome inversions affect rates of adaptation, speciation, and the evolution of sex chromosomes. Comparative genomic studies have identified many new paracentric inversion polymorphisms. Population models suggest that inversions can spread by reducing recombination between alleles that independently increase fitness, without epistasis or coadaptation. Areas of linkage disequilibrium extend across large inversions but may be interspersed by areas with little disequilibrium. Genes located within inversions are associated with a variety of traits including those involved in climatic adaptation. Inversion polymorphisms may contribute to speciation by generating underdominance owing to inviable gametes, but an alternative view gaining support is that inversions facilitate speciation by reducing recombination, protecting genomic regions from introgression. Likewise, inversions may facilitate the evolution of sex chromosomes by reducing recombination between sex determining alleles and alleles with sex-specific effects. However, few genes within inversions responsible for fitness effects or speciation have been identified.
573 citations
TL;DR: The potential for male competition to drive rapid divergence in weapon morphology remains one of the most exciting and understudied topics in sexual selection research today.
Abstract: Males in many species invest substantially in structures that are used in combat with rivals over access to females. These weapons can attain extreme proportions and have diversified in form repeatedly. I review empirical literature on the function and evolution of sexually selected weapons to clarify important unanswered questions for future research. Despite their many shapes and sizes, and the multitude of habitats within which they function, animal weapons share many properties: They evolve when males are able to defend spatially restricted critical resources, they are typically the most variable morphological structures of these species, and this variation honestly reflects among-individual differences in body size or quality. What is not clear is how, or why, these weapons diverge in form. The potential for male competition to drive rapid divergence in weapon morphology remains one of the most exciting and understudied topics in sexual selection research today.
558 citations
TL;DR: The ability to adapt to marginal habitats, in which survival and reproduction are initially poor, plays a crucial role in the evolution of ecological niches and species ranges as mentioned in this paper, but adaptation to marginal habitat may be limited by genetic, developmental, and functional constraints, but also by consequences of demographic characteristics of marginal populations, which makes them demographically and genetically dependent on core habitats and prone to gene flow counteracting local selection.
Abstract: The ability to adapt to marginal habitats, in which survival and reproduction are initially poor, plays a crucial role in the evolution of ecological niches and species ranges. Adaptation to marginal habitats may be limited by genetic, developmental, and functional constraints, but also by consequences of demographic characteristics of marginal populations. Marginal populations are often sparse, fragmented, prone to local extinctions, or are demographic sinks subject to high immigration from high-quality core habitats. This makes them demographically and genetically dependent on core habitats and prone to gene flow counteracting local selection. Theoretical and empirical research in the past decade has advanced our understanding of conditions that favor adaptation to marginal habitats despite those limitations. This review is an attempt at synthesis of those developments and of the emerging conceptual framework.
553 citations
TL;DR: Evidence suggests that top predators may function as structuring agents and biodiversity indicators in some ecosystems but not others, and that they perform poorly as umbrella species; more consensus exists for their efficacy as sentinel and flagship species.
Abstract: We review the ecological rationale behind the potential compatibility between top predators and biodiversity conservation, and examine their effectiveness as surrogate species. Evidence suggests that top predators promote species richness or are spatio-temporally associated with it for six causative or noncausative reasons: resource facilitation, trophic cascades, dependence on ecosystem productivity, sensitivity to dysfunctions, selection of heterogeneous sites and links to multiple ecosystem components. Therefore, predator-centered conservation may deliver certain biodiversity goals. To this aim, predators have been employed in conservation as keystone, umbrella, sentinel, flagship, and indicator species. However, quantitative tests of their surrogate-efficacy have been astonishingly few. Evidence suggests they may function as structuring agents and biodiversity indicators in some ecosystems but not others, and that they perform poorly as umbrella species; more consensus exists for their efficacy as sentinel and flagship species. Conservation biologists need to use apex predators more cautiously, as part of wider, context-dependent mixed strategies.
521 citations
TL;DR: After a 12-million-year process, the Central American Isthmus was completed 2.8 My ago and launched marine organisms of the two oceans into independent evolutionary trajectories and those that did not go extinct have diverged.
Abstract: After a 12-million-year (My) process, the Central American Isthmus was completed 2.8 My ago. Its emergence affected current flow, salinity, temperature, and primary productivity of the Pacific and the Atlantic and launched marine organisms of the two oceans into independent evolutionary trajectories. Those that did not go extinct have diverged. As no vicariant event is better dated than the isthmus, molecular divergence between species pairs on its two coasts is of interest. A total of 38 regions of DNA have been sequenced in 9 clades of echinoids, 38 of crustaceans, 42 of fishes, and 26 of molluscs with amphi-isthmian subclades. Of these, 34 are likely to have been separated at the final stages of Isthmus completion, 73 split earlier and 8 maintained post-closure genetic contact. Reproductive isolation has developed between several isolates, but is complete in only the sea urchin Diadema. Adaptive divergence can be seen in life history parameters. Lower primary productivity in the Caribbean has led to th...
TL;DR: It is found for whole plants as well as for different tissues that nitrogen concentrations increase slower than phosphorus concentrations and a lack of data prevents the establishment of relations between nitrogen and other elements.
Abstract: Stoichiometric relations in plants, with emphasis on C:N:P, are reviewed. Both theoretically and empirically it is found for whole plants as well as for different tissues that nitrogen concentrations increase slower than phosphorus concentrations. A lack of data prevents the establishment of relations between nitrogen and other elements. Optimal element ratios where elements are simultaneously limiting growth can be established. There is a considerable variability around these optimal ratios in observed values. Conclusions about the ecological significance of stoichiometric relations based on these observations may therefore be biased. The significance of this variability remains to be established.
TL;DR: Gambusia affinis and G. holbrooki, introduced worldwide from eastern North America, are collectively the most abundant, widespread freshwater fish in the world, which is not surprising because they tolerate, and sometimes thrive under, an exceptional range of environmental conditions and have high reproductive potential.
Abstract: Gambusia affinis and G. holbrooki, introduced worldwide from eastern North America, are collectively the most abundant, widespread freshwater fish in the world, which is not surprising because they tolerate, and sometimes thrive under, an exceptional range of environmental conditions and have high reproductive potential. Some know them as mosquitofish because of a legendary ability to control mosquitoes, and diseases they carry, while others doubt this ability or argue that indigenous fish are equally or more effective. However, rigorous evidence to support these views remains scant, so the legend persists. Some know them as plague minnow because of negative impacts on many native animal species, and abundant evidence exists to support this view. Despite such polarized attitudes toward them, their high abundance and wide distribution, and a large scientific literature devoted to them, many important aspects of their biology remain poorly known.
TL;DR: The potential for quantitative genetic analyses in wild populations to address fundamental evolutionary questions about the maintenance of genetic diversity and to reveal hidden genetic conflicts or constraints not apparent at the phenotypic level is illustrated.
Abstract: Recent years have seen a rapid expansion in the scope of quantitative genetic analyses undertaken in wild populations. We illustrate here the potential for such studies to address fundamental evolutionary questions about the maintenance of genetic diversity and to reveal hidden genetic conflicts or constraints not apparent at the phenotypic level. Trade-offs between different components of fitness, sexually-antagonistic genetic effects, maternal effects, genotype-by-environment interactions, genotype-by-age interactions, and variation between different regions of the genome in localized genetic correlations may all prevent the erosion of genetic variance. We consider ways in which complex interactions between ecological conditions and the expression of genetic variation can be elucidated, and emphasize the benefits of conducting selection analyses within a quantitative genetic framework. We also review potential developments associated with rapid advances in genomic technology, in particular the increased availability of extensive marker information. Our conclusions highlight the complexity of processes contributing to the maintenance of genetic diversity in wild populations, and underline the value of a quantitative genetic approach in parameterizing models of life-history evolution.
TL;DR: A general formalization of these processes remains challenging, but approaches drawing on hierarchical covariance models appear promising, and analyses integrating paleontological and neontological data for a single set of clades would be especially powerful.
Abstract: Species selection in the broad sense—also termed species sorting—shapes evolutionary patterns through differences in speciation and extinction rates (and their net outcome, often termed the emergent fitness of clades) that arise by interaction of intrinsic biological traits with the environment. Effectmacroevolution occurs when those biotic traits, such as body size or fecundity, reside at the organismic level. Strict-sense species selection occurs when those traits are emergent at the species level, such as geographic range or population size. The fields of paleontology, comparative phylogenetic analysis, macroecology, and conservation biology are rich in examples of species sorting, but relatively few instances have been well documented, so the extent and efficacy of the specific processes remain poorly known. A general formalization of these processes remains challenging, but approaches drawing on hierarchical covariance models appear promising. Analyses integrating paleontological and neontological data for a single set of clades would be especially powerful.
TL;DR: This work addresses several key issues in evolutionary ecology, including evolution of breeding systems (shifts between monoecy and dioecy), factors that promote the stability of mutualisms, precision of adaptation, and trajectories of community assembly and coevolution in systems with multiple interacting partners.
Abstract: Over the past decade a proliferation of research has enriched and dramatically altered our understanding of the biology of figs, their pollinator wasps, and the myriad of other organisms that depend on them. Ecologically, this work underscores the crucial role that fig fruits play in sustaining and shaping tropical frugivore communities. More generally, this work addresses several key issues in evolutionary ecology, including evolution of breeding systems (shifts between monoecy and dioecy), factors that promote the stability of mutualisms, precision of adaptation, and trajectories of community assembly and coevolution in systems with multiple interacting partners. Moreover, both the pollinating and nonpollinating wasps associated with figs provide unparalleled opportunities for examining how different population structures can differentially affect sex allocation, kin selection, the evolution of parasite virulence, and many fundamental parameters of population genetics (e.g., levels of genetic variation and rates of silent and nonsilent base substitutions).
TL;DR: It is suggested that despite sanctions, less-effective symbionts still persist and is suggested this is because of mixed infection at spatial scales that limit the effects of sanctions.
Abstract: There are both costs and benefits for host plants that associate with microbes in the rhizosphere. Typically, an individual plant associates with multiple microbial genotypes varying in mutualistic benefit. This creates a potential tragedy of the commons where less-mutualistic strains potentially share in the collective benefits, while paying less of the costs. Therefore, maintaining cooperation over the course of evolution requires specific mechanisms that reduce the fitness benefits from “cheating.” Sanctions that discriminate among partners based on actual symbiotic performance are a key mechanism in rhizobia and may exist in many rhizosphere mutualisms, including rhizobia, mycorrhizal fungi, root endophytes, and perhaps free-living rhizosphere microbes. Where they exist, sanctions may take different forms depending on the system. Despite sanctions, less-effective symbionts still persist. We suggest this is because of mixed infection at spatial scales that limit the effects of sanctions, variation amon...
TL;DR: A number of endogenous and exogenous factors that may contribute to the successful establishment and spread of peregrine species are identified and quantification of these factors may help to determine why certain species become invasive while others do not.
Abstract: Introduced exotic earthworms now occur in every biogeographic region in all but the driest or coldest habitat types on Earth. The global distribution of a few species (e.g., Pontoscolex corethrurus) was noted by early natural- ists, but now approximately 120 such peregrine species are recognized to be widespread from regional to global scales, mainly via human activities. Species adapted to human transport and to colonization of disturbed habi- tats are most widespread and are the principal invasive species. We identify a number of endogenous and exogenous factors that may contribute to the successful establishment and spread of peregrine species. Quantification of these factors may help to determine why certain species become invasive while others do not. Recent advances in theory and modeling of biological invasions and in molecular techniques should prove fruitful in improving our understanding of invasive earthworms, as well as in predicting their impacts on ecosystems.
TL;DR: This article illustrates with examples some of the ways that considering the evolutionary relationships among species—phylogenies— has helped the study of both past and present species extinction.
Abstract: Species extinction is both a key process throughout the history of life and a pressing concern in the conservation of present-day biodiversity. These two facets have largely been studied by separate communities using different approaches. This article illustrates with examples some of the ways that considering the evolutionary relationships among species—phylogenies— has helped the study of both past and present species extinction. The focus is on three topics: extinction rates and severities, phylogenetic nonrandomness of extinction, and the testing of hypotheses relating extinction-proneness to attributes of organisms or species. Phylogenetic and taxic approaches to extinction have not fully fused, largely because of the difficulties of relating discrete taxa to the underlying continuity of phylogeny. Phylogeny must be considered in comparative tests of hypotheses about extinction, but care must be taken to avoid overcorrecting for phylogenetic nonindependence among taxa.
TL;DR: This review integrates factors to build a conceptual framework for looking at herbivore-mediated effects in ecosystems that systematically resolves how herbivores and carnivores directly and indirectly interact with plants to shape ecosystem functions.
Abstract: Herbivores not only consume resources, but they are resources for other consumers. Consequently, they have much potential to mediate effects that cascade up and down trophic chains in ecosystems. The way those effects are mediated depends on individual-scale properties of herbivores including constraints determining resource limitation, herbivore feeding mode, the adaptive trade-off to balance nutrient intake and predation risk avoidance, and the need to maintain homeostatic balance of elemental chemistry in the face of widely varying elemental composition of plant resources. These factors determine the rates of ecosystem functions such as production, decomposition and nutrient cycling. This review integrates those factors to build a conceptual framework for looking at herbivore-mediated effects in ecosystems. The framework systematically resolves how herbivores and carnivores directly and indirectly interact with plants to shape ecosystem functions. It can be used to motivate new field experimentation aimed at elucidating mechanisms of trophic control of ecosystem function.
TL;DR: In this paper, the authors synthesize existing knowledge into a framework that can both identify crucial gaps in the theory as well as facilitate empirical investigations, and highlight both invariant properties that are robust to increasing foodweb complexity and emergent properties that result from the interplay between foodweb dynamics and type of movement.
Abstract: Foodwebs are important units of biodiversity, and yet, our knowledge of their spatial dynamics is sketchy at best. Here I attempt to synthesize existing knowledge into a framework that can both identify crucial gaps in the theory as well as facilitate empirical investigations. The synthesis is based on two major axes, foodweb complexity and type of movement, and considers two types of spatial effects, foodweb persistence via a reduction in local extinction and foodweb diversity via an increase in species coexistence. It highlights both invariant properties that are robust to increasing foodweb complexity and emergent properties that result from the interplay between foodweb dynamics and type of movement. It underscores the need for a comparative theoretical framework that can yield testable predictions.
TL;DR: The intersection of life-history evolution, conflicts of interest, and frequency-dependent fitness provides much scope for theoretical exploration, and recent models indicate a complex range of evolutionary dynamics is possible, including consequences of CBP for population dynamics and conservation.
Abstract: Conspecific brood parasitism (CBP), whereby females lay eggs in the nests of other conspecifics, occurs in over 200 species of birds. As an alternative tactic to typical nesting, CBP expands and enriches the classic avian clutch size problem. It is an integral component of a flexible life-history strategy and, consequently, many intriguing aspects of this behavior—adaptive benefits to parasites, host-parasite interactions, population and evolutionary dynamics—can be understood best from a life-history perspective. Because parasite fitness depends on hosts, yet parasitism potentially reduces host fitness, CBP offers a novel opportunity to explore conflicts of interest within species. The intersection of life-history evolution, conflicts of interest, and frequency-dependent fitness provides much scope for theoretical exploration, and recent models indicate a complex range of evolutionary dynamics is possible, including consequences of CBP for population dynamics and conservation. CBP may also be a macroevolutionary stepping stone to diverse breeding systems.
TL;DR: In this article, the authors review the global effects of fisheries and propose an integrated framework for managing biophysical processes and human ecology, focusing on the dynamics of interaction webs in a spatially constrained environment.
Abstract: Fishing remains one of the largest factors modifying marine ecosystems. Because fisheries constitute only one of many anthropogenic effects, management is shifting from single-species approaches toward ecosystem-based management. Interaction webs are a critical nexus to understand linkages, to model ecosystem change, and to apply management directives. Ecosystem-based management requires consideration of both direct and indirect effects of commercial fisheries. But it must also include impacts of bycatch, recreational fisheries, artisanal fisheries, and environmental change that can be large but unanticipated. Synergistic effects of fishing, environmental variation, and climate change increasingly threaten marine ecosystems and complicate management. Here we review the global effects of fisheries and propose an integrated framework for managing biophysical processes and human ecology. To incorporate the multitude of effects, this emerging approach focuses on the dynamics of interaction webs in a spatially...
TL;DR: The considerable information about the possible source of cryptospores and trilete spores especially from the well-preserved mesofossils of the Late Silurian and Early Devonian is summarized.
Abstract: Considerable progress has been made in documenting evidence of very early plants starting in the basal Ordovician employing dispersed spore, phytodebris, and mesofossil data. Macrofossil evidence is sparse until Late Silurian, but recent new data are improving our understanding of aspects of earliest plants. The considerable information about the possible source of cryptospores and trilete spores especially from the well-preserved mesofossils of the Late Silurian and Early Devonian is summarized. Promising avenues of research are the study of spore ultrastructure, and neo-paleo comparisons between newly discovered resistant components of extant bryophytes and fragmentary fossil remains. Recent macrofossil discoveries in the Late Silurian advance our understanding of early events in plant evolution and raise new questions about the timing of evolution or relationships among earliest (mostly vascular) plants.
TL;DR: The most notable success of the Endangered Species Act (ESA) is that listed species improve in status through time as discussed by the authors, and the fraction of listed species responding positively is remarkable.
Abstract: Arguably the most notable success of the Endangered Species Act (ESA) is that listed species improve in status through time. More species are downlisted than the converse; more species transition from stable to improving status than the converse. Although some listed species have gone extinct, this number is smaller than expected. Given modest recovery funding, the fraction of listed species responding positively is remarkable. Several factors have been linked to improving species status including recovery expenditures, critical habitat listing, and time spent under protection. The inability of government to fully empower the agencies to implement the law has been the most notable failure of the ESA. Listing of species has not matched need, recovery expenditures do not match need or agency-set priorities, and critical habitat determinations have lagged. Alternative protection strategies to listing may be having a positive effect, but are difficult to assess because of sparse data.
TL;DR: Two conspicuous differences between these species groups are their effective population sizes and population structure, which may explain lower levels of selective constraint in coding and noncoding DNA of Arabidopsis, and more evidence for balancing selection and less evidence for canonical signature of positive selection.
Abstract: Species in the Drosophila and Arabidopsis species groups share the feature of having relatively small, streamlined genomes. In Drosophila, evidence for pervasive negative and positive selection is overturning long-held views about the functional significance of noncoding DNA, the frequency of positive selection, and the extent to which coding and noncoding polymorphism and divergence between species is neutral. However, despite sharing some similarities with Drosophila, Arabidopsis shows quite distinct patterns of selective constraint and positive selection. Two conspicuous differences between these species groups are their effective population sizes and population structure, which may explain lower levels of selective constraint in coding and noncoding DNA of Arabidopsis, more evidence for balancing selection and less evidence for canonical signature of positive selection than in Drosophila species. As more comparative genomic data accumulate in the Arabidopsis group, the combination of polymorphism and ...
TL;DR: Research emphasis can now shift to broader-based questions, including the whole of the early tetrapod radiation, from the divergence from other lobed-finned fishes to the origins of modern amphibians and amniotes.
Abstract: The traditional notion of a gap between fishes and amphibians has been closed by a wealth of fish-like fossil tetrapods, many discovered since the mid 1980s. This review summarizes these discoveries and explores their significance relative to changing ideas about early tetrapod phylogeny, biogeography, and ecology. Research emphasis can now shift to broader-based questions, including the whole of the early tetrapod radiation, from the divergence from other lobed-finned fishes to the origins of modern amphibians and amniotes. The fish-to-tetrapod morphological transition occurred within the Upper Devonian; the divergence of modern tetrapod groups is an Early Carboniferous event. Modern tetrapods emerged in the aftermath of one of the five major extinction episodes in the fossil record, but the earlier Devonian tetrapod radiation is not well understood. Tetrapod limbs, paired fins, and comparative developmental data are reviewed; again, research emphasis needs to change to explore the origins of tetrapod diversity.
TL;DR: It is suggested that displacement of genes from the more anterior Hox classes toward the 5 � end of the chromosome leads to control of the later-developing, radially symmetric axial region, which is another way of using colinearity to build the unique echinoderm symmetry.
Abstract: The strangeness of echinoderm pentaradiality results from superposition of radial symmetry onto ancestral deuterostome bilaterality. The ExtraxialAxial Theory shows that echinoderms also have an anterior/posterior (A/P) axis developed independently and ontogenetically before radiality. The A/P axis is first established via coelomic stacking in the extraxial region, with ensuing development of the pentamerous hydrocoel in the axial region. This is strongly correlated with a variety of gene expression patterns. The echinoid Hox cluster is disordered into two different sets of genes. During embryogenesis, members of the posterior class demonstrate temporal, spatial, and genetic colinearity within the extraxial region. We suggest that displacement of genes from the more anterior Hox classes toward the 5 � end of the chromosome leads to control of the later-developing, radially symmetric axial region. Genetic disorder is therefore another way of using colinearity to build the unique echinoderm symmetry.
TL;DR: Stratocladistics offers a methodological context within which temporal data participate along with conventional character data in selecting most-parsimonious hypotheses, and the explanatory power of hypotheses that use both temporal and conventional characterData exceeds that of hypotheses based on character data alone.
Abstract: Debate has long simmered over whether data on the order of appearance of taxa in the stratigraphic record should play any role in analyses of phylogenetic relationships among those taxa. Critics argue that temporal data are in principle inapplicable to questions of cladistic relationship, but specific versions of this claim all seem flawed. Stratocladistics offers a methodological context (patterned after that of cladistics itself) within which temporal data participate along with conventional character data in selecting most-parsimonious hypotheses. Stratocladistics outperforms cladistics in tests based on simulated histories, and additional testing will be facilitated by new software automating stratocladistic searches. As with any body of data, we may decide to include or exclude temporal data for specific reasons, but the explanatory power of hypotheses that use both temporal and conventional character data exceeds that of hypotheses based on character data alone.
TL;DR: Generality emerges, however, by “unpacking” β into within- and between-host opportunities for selection, which is illustrated by evolutionary biology of the bacterium Yersinia pestis, which remains highly virulent and is transmitted by multiple routes, including fleas and direct contacts with infected hosts.
Abstract: Rather than being fixed, pathogen transmission varies and is thus an object of natural selection. I examine how opportunities for selection on pathogen transmission depend on (a) pathogen fitness, (b) genetic variability, and (c) forces acting at within- and between-host levels. The transmission rate, β, influences processes such as epidemic spread, postepidemic fade-outs, and low-level persistence. Complexity of infection processes within hosts leads to different transmission rates among hosts and between types of pathogens (viruses, bacteria, eukaryotic Protozoa). Generality emerges, however, by “unpacking” β into within- and between-host opportunities for selection. This is illustrated by evolutionary biology of the bacterium Yersinia pestis, which causes plague in mammals, remains highly virulent and is transmitted by multiple routes, including fleas and direct contacts with infected hosts. The strength of within-host selection is manifested through infectivity, replication, pathogenicity, and dissemi...