Science, religion, and society: the problem of evolution in america

American resistance to accepting evolution is uniquely high among First World countries. This is due largely to the extreme religiosity of the United States, which is much higher than that of comparably advanced nations, and to the resistance of many religious people to the facts and supposed implications of evolution. The prevalence of religious belief in the United States suggests that outreach by scientists alone will not have a huge effect in increasing the acceptance of evolution, nor will the strategy of trying to convince the faithful that evolution is compatible with their religion. Because creationism is a symptom of religion, another strategy to promote evolution involves loosening the grip of faith on America. This is easier said than done, for recent sociological surveys show that religion is highly correlated with the dysfunctionality of a society, and various measures of societal health show that the United States is one of the most socially dysfunctional First World countries. Widespread acceptance of evolution in America, then, may have to await profound social change.     

Modeling the evolution of interconnected processes: It is the song and the singers

Recently, Doolittle and Inkpen formulated a thought provoking theory, asserting that evolution by natural selection was responsible for the sideways evolution of two radically different kinds of selective units (also called Domains). The former entities, termed singers, correspond to the usual objects studied by evolutionary biologists (gene, genomes, individuals, species, etc.), whereas the later, termed songs, correspond to re‐produced biological and ecosystemic functions, processes, information, and memes. Singers perform songs through selected patterns of interactions, meaning that a wealth of critical phenomena might receive novel evolutionary explanations. However, this theory did not provide an empirical approach to study evolution in such a broadened context. Here, we show that analyzing songs and singers, using patterns of interaction networks as a common ontology for both, offers a novel, actionable, inclusive and mathematical way to analyze not only the re‐production but also the evolution and fitness of biological and ecosystemic interconnected processes.     

A generalised approach to the study and understanding of adaptive evolution

Evolutionary theory has made large impacts on our understanding and management of the world, in part because it has been able to incorporate new data and new insights successfully. Nonetheless, there is currently a tension between certain biological phenomena and mainstream evolutionary theory. For example, how does the inheritance of molecular epigenetic changes fit into mainstream evolutionary theory? Is niche construction an evolutionary process? Is local adaptation via habitat choice also adaptive evolution? These examples suggest there is scope (and perhaps even a need) to broaden our views on evolution. We identify three aspects whose incorporation into a single framework would enable a more generalised approach to the understanding and study of adaptive evolution: (i) a broadened view of extended phenotypes; (ii) that traits can respond to each other; and (iii) that inheritance can be non-genetic. We use causal modelling to integrate these three aspects with established views on the variables and mechanisms that drive and allow for adaptive evolution. Our causal model identifies natural selection and non-genetic inheritance of adaptive parental responses as two complementary yet distinct and independent drivers of adaptive evolution. Both drivers are compatible with the Price equation; specifically, non-genetic inheritance of parental responses is captured by an often-neglected component of the Price equation. Our causal model is general and simplified, but can be adjusted flexibly in terms of variables and causal connections, depending on the research question and/or biological system. By revisiting the three examples given above, we show how to use it as a heuristic tool to clarify conceptual issues and to help design empirical research. In contrast to a gene-centric view defining evolution only in terms of genetic change, our generalised approach allows us to see evolution as a change in the whole causal structure, consisting not just of genetic but also of phenotypic and environmental variables.     

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

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

DG指数在定量多样性时的缺陷及其内涵解析

生物多样性通常使用物种丰富度、Simpson指数、Shannon-Wiener多样性指数等来进行度量, 但是在土壤动物群落研究中, 由于使用了粗水平的分类方法, 因此即使生境变化很大, 这些多样性指数在评估群落多样性变化时仍然是不适当的。为了克服这种限制, 廖崇惠(1990, 2009)提出用DG指数来代替这些标准的多样性指数, 并在土壤动物生态学领域得到了广泛应用。然而笔者分析发现DG指数与Pielou均匀度指数呈显著的负相关关系(r = –0.534, P = 0.000), 即, 高的均匀度反而有低的多样性。另外, DG指数与类群数(r = 0.648, P = 0.000)和类群密度(r = 0.487, P = 0.000)呈明显的正相关, 类群数的下降可以通过部分类群密度的上升而获得补偿, 群落的类群丢失后却可以获得一个不变的甚至更高的多样性值。因此, 笔者不支持DG指数用于测度生物多样性, 提议使用各类群实际群势与潜在群势比值的平均值来估计群落潜在多度的实现程度。如果继续使用DG指数作为实际生境条件的一个指标, 那么与以往不同, DG指数测度的是该生境群落多度增长的一种潜力。     

Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data

Understanding the evolution of gene function is a primary challenge of modern evolutionary biology. Despite an expanding database from genomic and developmental studies, we are lacking quantitative methods for analyzing the evolution of some important measures of gene function, such as gene-expression patterns. Here, we introduce phylogenetic comparative methods to compare different models of gene-expression evolution in a maximum-likelihood framework. We find that expression of duplicated genes has evolved according to a nonphylogenetic model, where closely related genes are no more likely than more distantly related genes to share common expression patterns. These results are consistent with previous studies that found rapid evolution of gene expression during the history of yeast. The comparative methods presented here are general enough to test a wide range of evolutionary hypotheses using genomic-scale data from any organism.     

The end of regressive evolution: examining and interpreting the evidence from cave fishes

The evolution of hypogean fauna in general and hypogean fishes in particular has been controversial. Explanations regarding the reduction or loss of phenotypic characters such as eyes and pigmentation range from neo‐Lamarckism to neutral mutations, with 'regressive evolution' being a catch‐all characterization for such processes. The assumptions required for special evolutionary mechanisms underlying the evolution of cave dwellers have been based on generalizations about the animals and their environments drawn from relatively few observations. The evidence offered for notions such as pre‐adaptation of colonizing fauna and the purported impoverished nutrients in all caves is examined and it appears that the generalizations cannot be supported. Some major accomplishments in field and laboratory studies of hypogean fishes are summarized, including work highlighting developmental phenotypic plasticity. At the end, it is argued that evolution of hypogean fauna can be explained by well‐known mechanisms within the current context of evolutionary biology.     

Reconsidering the taxomony of several Ostrinia species in the light of reproductive isolation: a tale for Ernst Mayr

We reconsider the taxonomy of a group of closely related Ostrinia spp., illustrating how useful Mayr's biological species concept remains for studying speciation patterns and processes. We review and re-analyse recent data on Ostrinia scapulalis , Ostrinia nubilalis , Ostrinia narynensis and Ostrinia orientalis , along with those obtained over > 45 years in the former Soviet Union. The ten species of the 'trilobed uncus' group in the Ostrinia genus are classified into subgroups according to male mid-tibia morphology. However, none of the characters that further discriminate between them (female sex pheromones, male genitalia and calling time) varies together with male mid-tibia morphology, and neither do molecular markers. Moreover, male mid-tibia morphology appears to depend on only two diallelic loci and seems to be unrelated to reproductive isolation between Ostrinia taxa. By contrast, reproductive isolation is strongly related to host-plant type. In accordance with Mayr's species concept, we thus propose a revision of the trilobed uncus Ostrinia spp. based primarily on host-plant type. We propose that O. narynensis Mutuura & Munroe, 1970 ( syn. nov. ) and O. orientalis Mutuura & Munroe, 1970 ( syn. nov. ) be synonymized with O. scapulalis (Walker, 1859). We further demonstrate that O. nubilalis auctt. pro parte feeding on mugwort, hop, and several other dicotyledons (previously called the ' O. nubilalis mugwort-race' in France) also belongs to O. scapulalis . Consequently, we propose that only O. nubilalis specimens feeding on maize (the former French ' O. nubilalis maize-race') belong to O. nubilalis (Hübner, 1796). The implications of this revision are discussed.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 49–72.     

Neotropical bird evolution and 100 years of the enduring ideas of Frank M. Chapman

The processes of bird diversification in South America have long been a focus of evolutionary biologists and this paper partly acts as an introduction to a selection of such work published in the Biological Journal of the Linnean Society and collated into a Virtual Issue ( http://wileyonlinelibrary.com/bij/neotropical-bird-evolution ). At the beginning of the 20^th century, Frank M. Chapman, curator of birds at the American Museum of Natural History, conducted a series of expeditions in Colombia and Ecuador to ‘discover the geographic origins of South American bird‐life’. The expeditions produced almost 30 000 specimens, obtained in a sampling scheme aimed at revealing the geographical and elevational distributions of birds. Chapman proposed a series of ideas about the evolutionary origins of the tropical Andean avifauna. Despite being nearly 100 years old, Chapman's evolutionary hypotheses on the role of the appearance of new environments and geographical barriers on speciation, have an enduring influence. With the development of molecular methods and tools for the study of the mechanisms and timing of speciation events, Chapman's hypotheses have seen a revival in the recent scientific literature. Recent work has provided support for some of Chapman's hypotheses, but has also revealed greatly complex processes of biotic differentiation in the Neotropics. What is remarkable is that with means that today seem precarious, Chapman envisioned evolutionary processes at a continental scale that remain valid, in fields that currently advance at an accelerated rhythm and soon render older ideas obsolete.     

Testing heterochrony: Connecting skull shape ontogeny and evolution of feeding adaptations in baleen whales

Ontogeny plays a key role in the evolution of organisms, as changes during the complex processes of development can allow for new traits to arise. Identifying changes in ontogenetic allometry—the relationship between skull shape and size during growth—can reveal the processes underlying major evolutionary transformations. Baleen whales (Mysticeti, Cetacea) underwent major morphological changes in transitioning from their ancestral raptorial feeding mode to the three specialized filter-feeding modes observed in extant taxa. Heterochronic processes have been implicated in the evolution of these feeding modes, and their associated specialized cranial morphologies, but their role has never been tested with quantitative data. Here, we quantified skull shapes ontogeny and reconstructed ancestral allometric trajectories using 3D geometric morphometrics and phylogenetic comparative methods on sample representing modern mysticetes diversity. Our results demonstrate that Mysticeti, while having a common developmental trajectory, present distinct cranial shapes from early in their ontogeny corresponding to their different feeding ecologies. Size is the main driver of shape disparity across mysticetes. Disparate heterochronic processes are evident in the evolution of the group: skim feeders present accelerated growth relative to the ancestral nodes, while Balaenopteridae have overall slower growth, or pedomorphosis. Gray whales are the only taxon with a relatively faster rate of growth in this group, which might be connected to its unique benthic feeding strategy. Reconstructed ancestral allometries and related skull shapes indicate that extinct taxa used less specialized filter-feeding modes, a finding broadly in line with the available fossil evidence.     

Influence of ambient light on the evolution of colour signals: comparative analysis of a Neotropical rainforest bird community

Rainforests offer two contrasted light environments: a bright canopy rich in blue and UV and a dark understorey, rich in green and orange. Therefore, natural selection for crypsis should favour dark brown signals in understorey and bright green signals in canopy, whereas sexual selection for conspicuousness should favour bright yellow‐red signals in understorey and dark blue and UV signals in canopy. Using spectrometry and comparative analyses, we examined the relationship between ambient light and colour signals in a bird community of French Guiana. It appears that brightness and hue are mostly naturally selected, while UV content of plumage is more likely sexually selected. At each height, both sexes present similar coloration but males display more conspicuous sexually selected patterns than females. These results show that ambient light drives the evolution of colour signals at community scale, and should be considered when studying signalling in other communities and light‐contrasted ecosystems.     

Investigation of the microbial community structure and activity as indicators of compost stability and composting process evolution

In a bid to identify suitable microbial indicators of compost stability, the process evolution during windrow composting of poultry manure (PM), green waste (GW) and biowaste was studied. Treatments were monitored with regard to abiotic factors, respiration activity (determined using the SOUR test) and functional microflora. The composting process went through typical changes in temperature, moisture content and microbial properties, despite the inherent feedstock differences. Nitrobacter and pathogen indicators varied as a monotonous function of processing time. Some microbial groups have shown a potential to serve as fingerprints of the different process stages, but still they should be examined in context with respirometric tests and abiotic parameters. Respiration activity reflected well the process stage, verifying the value of respirometric tests to access compost stability. SOUR values below 1 mg O₂/g VS/h were achieved for the PM and the GW compost.     

Twenty years of phylogeography: the state of the field and the challenges for the Southern Hemisphere

Phylogeography is a young, vigorous and integrative field of study that uses genetic data to understand the history of populations. This field has recently expanded into many areas of biology and also into several historical disciplines of Earth sciences. In this review, I present a numerical synthesis of the phylogeography literature based on an examination of over 3000 articles published during the first 20 years of the field (i.e. from 1987 to 2006). Information from several topics needed to evaluate the progress, tendencies and deficiencies of the field is summarized for 10 major groups of organisms and at a global scale. The topics include the geography of phylogeographic surveys, comparative nature of studies, temporal scales and major environments investigated, and genetic markers used. I also identify disparities in research productivity between the developing and the developed world, and propose ways to reduce some of the challenges faced by phylogeographers from less affluent countries. Phylogeography has experienced explosive growth in recent years fuelled by developments in DNA technology, theory and statistical analysis. I argue that the intellectual maturation of the field will eventually depend not only on these recent developments, but also on syntheses of comparative information across different regions of the globe. For this to become a reality, many empirical phylogeographic surveys in regions of the Southern Hemisphere (and in developing countries of the Northern Hemisphere) are needed. I expect the information and views presented here will assist in promoting international collaborative work in phylogeography and in guiding research efforts at both regional and global levels.     

Origins of the other metazoan body plans: the evolution of larval forms

Bilaterian animal body plan origins are not solely about adult forms. Most animals have larvae with body plans, ontogenies and ecologies distinct from adults. There are two primary hypotheses for larval origins. The first hypothesis suggests that the first animals were small pelagic forms similar to modern larvae, with adult bilaterian body plans evolved subsequently. The second hypothesis suggests that adult bilaterian body plans evolved first and that larval body plans arose by interpolation of features into direct-developing ontogenies. The two hypotheses have different consequences for understanding parsimony in evolution of larvae and of developmental genetic mechanisms. If primitive metazoans were like modern larvae and distinct adult forms evolved independently, there should be little commonality of patterning genes among adult body plans. However, sharing of patterning genes is observed. If larvae arose by co-option of adult bilaterian-expressed genes into independently evolved larval forms, larvae may show morphological convergence, but with distinct patterning genes, and this is observed. Thus, comparative studies of gene expression support independent origins of larval features. Precambrian and Cambrian embryonic fossils are also consistent with direct development of the adult as being primitive, with planktonic larvae arising during the Cambrian. Larvae have continued to co-opt genes and evolve new features, allowing study of developmental evolution.     

The importance of the “Gegenbaur school” for German morphology

Summary The school Carl Gegenbaur cultivated at Heidelberg (1873–1901) was critical to the history of German morphology in multiple ways. During and after his lifetime, the school carried out detailed comparative anatomical and embryological investigations in an evolutionary framework, thereby contributing substantially to the project of vertebrate evolutionary morphology. Its members also defended their mentor when his ideas came under attack. After his death, they labored to perpetuate his program and his memory in the increasingly unwelcoming environment of medical education and research. While the senior members of the school did this largely through institutional means-seeking to place Gegenbaur sympathizers in academic and editorial positions-its junior members absorbed some of the criticisms of the school to develop a modified, more functional approach to evolutionary morphology. The school thus kept the Gegenbaur program alive and active in the German-speaking lands for over fifty years. This paper is drawn largely from Nyhart (1995), esp. chapter 7 (supported by NSF award no. 8910873). Information not otherwise documented derives from this book.     

Phylogenetic diversity as a window into the evolutionary and biogeographic histories of present-day richness gradients for mammals

Phylogenetic diversity (PD) captures the shared ancestry of species, and is increasingly being recognized as a valuable conservation currency. Regionally, PD frequently covaries closely with species richness; however, variation in speciation and extinction rates and/or the biogeographic history of lineages can result in significant deviation. Locally, these differences may be pronounced. Rapid recent speciation or high temporal turnover of lineages can result in low PD but high richness. In contrast, rare dispersal events, for example, between biomes, can elevate PD but have only small impact on richness. To date, environmental predictors of species richness have been well studied but global models explaining variation in PD are lacking. Here, we contrast the global distribution of PD versus species richness for terrestrial mammals. We show that an environmental model of lineage diversification can predict well the discrepancy in the distribution of these two variables in some places, for example, South America and Africa but not others, such as Southeast Asia. When we have information on multiple diversity indices, conservation efforts directed towards maximizing one currency or another (e.g. species richness versus PD) should also consider the underlying processes that have shaped their distributions.     

Response of microbial community structure to the hydrochemical evolution during riverbank filtration: a case study in Shenyang,China

Abstract

Microorganisms are widely involved in the transformation process of physical and chemical properties in the geological and hydrogeological environment. Active participation of microorganisms is important features of the biogeochemical reactions during groundwater exploiting along the riverbank filtration. Hydrodynamic condition has a direct or indirect difference control of the biological effectiveness, chemical activity and mobility of the pollution components, which can affect biogeochemical process. In different biogeochemistry, there will be some exclusive functional bacteria, which is of great significance to understand the biogeochemical mechanism of river water infiltration. This study confirms that there are two main different flow paths from river to the center of the depression cone due to different hydrodynamic conditions and spatial characteristics and scaling effects of redox zonation during riverbank filtration. In different flow paths, the microbial abundance shows obvious spatial heterogeneity. The microbial abundance and species similarity degree of the riverbed and deep flow path sediments has significant correlation. There is a significant correlation between the dominant bacteria and the environmental factors in different hydrodynamic conditions on a spatial scale. This study is the first to reveal the response of microbial community structure to water chemical evolution during riparian filtration. Due to significant positive correlation between the Fe/Mn and As, it brings the potential danger for drinking water.     

New diversity,old anxieties in New Zealand: the complex identity politics and engagement of a settler society

Superdiversity signals the common experience in many countries and cities of the enhanced levels of diversity that are associated with contemporary immigration, yet there are a range of permutations and possibilities. One example of superdiversity – that of a particular group of settler societies represented by New Zealand – is explored, as the colonization of indigenous peoples has occurred alongside a nation-building project that centres on mass immigration, and which in turn has been layered by a more recent immigrant recruitment project that ostensibly values immigrants for the skills that they contribute to economic development. Since the 1970s, there have been limited but still important concessions made in terms of diversity recognition and group rights. This article explores the nature of this settler society superdiversity and its politics.