The Cambrian radiation of bilaterians: Evolutionary origins and palaeontological emergence; earth history change and biotic factors

Evidence from a variety of research areas, including phylogenetic palaeobiogeographic studies of trilobites, indicates that there may be a fuse to the Cambrian radiation, with a duration on the order of 20–70 myr. Evolution in trilobites appears to have been powerfully influenced by the tectonic changes occurring at the end of the Neoproterozoic: especially the breakup of Pannotia. This continental fragmentation may have also elevated opportunities for vicariance and speciation in trilobites, and other metazoans, given that speciation rates at this time period were high, though not phenomenally so. This provides clear evidence that abiotic factors played an important role in motivating evolution during this key episode in the history of life; biotic factors probably also played a role. The evidence for the role of biotic factors is considered in light of information from some problematic Cambrian taxa. These may show affinities with modern problematic pseudocoelomate phyla, although Cambrian and modern exponents differ dramatically in body size.     

Adaptive Radiations in the Context of Macroevolutionary Theory: A Paleontological Perspective

Adaptive radiations are often invoked anytime clades show significant bursts of diversification, but it is important to not simply assume that any radiating clade constitutes an adaptive radiation. In addition, several highly relevant macroevolutionary concepts including the Turnover Pulse Hypothesis, the Effect Hypothesis, exaptation, and species selection, have not been considered in the adaptive radiations literature. Here, these concepts are integrated into the theory of evolutionary radiations in general, and adaptive radiations in particular, and different types of evolutionary radiations are identified, including geographic radiations. Special emphasis is placed on considering the role that abiotic as opposed to biotic factors may play in motivating diversification during evolutionary radiations. Further, recent paleontological data suggesting that rather than organismal adaptation it may be principally abiotic factors, such as climate change and a taxon??s presence in a geographically complex region, that cause clades to diversify will be described. The fossil record, the source of the initial hallmark examples of adaptive radiation, now appears to show little concrete support for this phenomenon.     

Cultural and climatic changes shape the evolutionary history of the Uralic languages

Quantitative phylogenetic methods have been used to study the evolutionary relationships and divergence times of biological species, and recently, these have also been applied to linguistic data to elucidate the evolutionary history of language families. In biology, the factors driving macroevolutionary processes are assumed to be either mainly biotic (the Red Queen model) or mainly abiotic (the Court Jester model) or a combination of both. The applicability of these models is assumed to depend on the temporal and spatial scale observed as biotic factors act on species divergence faster and in smaller spatial scale than the abiotic factors. Here, we used the Uralic language family to investigate whether both ‘biotic’ interactions (i.e. cultural interactions) and abiotic changes (i.e. climatic fluctuations) are also connected to language diversification. We estimated the times of divergence using Bayesian phylogenetics with a relaxed‐clock method and related our results to climatic, historical and archaeological information. Our timing results paralleled the previous linguistic studies but suggested a later divergence of Finno‐Ugric, Finnic and Saami languages. Some of the divergences co‐occurred with climatic fluctuation and some with cultural interaction and migrations of populations. Thus, we suggest that both ‘biotic’ and abiotic factors contribute either directly or indirectly to the diversification of languages and that both models can be applied when studying language evolution.     

亚热带-温带过渡区秦岭落叶阔叶林幼苗存活机制

【目的】物种幼苗的存活与各种生物和非生物因素密切相关,研究关键因素对幼苗存活的影响有助于理解群落物种共存的主要作用机制。【方法】以秦岭落叶阔叶林25 hm²固定样地的木本植物幼苗为对象,对11 408棵幼苗的生存动态开展连续5年(2015—2019年)的监测,利用广义线性混合模型(GLMMs)在群落水平上对影响不同年龄阶段幼苗存活的主要生物与非生物因素进行分析。【结果】(1)从群落水平来看,对幼苗存活影响最大的是生物因素,幼苗存活率与同种幼苗邻体密度和同种大树邻体胸高断面积呈显著负相关,与异种幼苗邻体密度呈显著正相关,表明物种在幼苗时期受到强烈的负密度制约效应;(2)从苗龄水平上来看,除了生物因素,影响幼苗存活的主要因素还包括海拔等非生物因素,但非生物因素的影响随着苗龄增大而减小。【结论】影响幼苗存活因素是多样的,其中生物因素的影响更显著,促进秦岭大样地中幼苗共存的主要机制为负密度制约效应。     

Diversity dynamics of post‐Palaeozoic crinoids – in quest of the factors affecting crinoid macroevolution

Following the end‐Permian biotic crisis which led to the near extinction of crinoids, this echinoderm class rebounded rapidly during the Mesozoic, resulting in forms with important morphological and behavioural novelties. However, quantitative patterns of crinoid diversity during the Mesozoic remain largely unexplored. Here, we report results of analyses of the evolutionary dynamics of post‐Palaeozoic crinoid genera spanning a time interval between 250 and 70 Myr. We show that crinoids reached their Mesozoic peak of genus‐level richness during the Late Jurassic. We also document a major reorganization of different ecological crinoid groups in the Mesozoic. More specifically, the diversity of sessile forms generally increased towards the mid‐Mesozoic but decreased significantly starting in the Cretaceous, whereas the number of motile crinoid genera increased linearly during the Mesozoic. The possible role of biotic and abiotic factors in crinoid evolution is discussed.     

The niche, biogeography and species interactions

In this paper, I review the relevance of the niche to biogeography, and what biogeography may tell us about the niche. The niche is defined as the combination of abiotic and biotic conditions where a species can persist. I argue that most biogeographic patterns are created by niche differences over space, and that even ‘geographic barriers’ must have an ecological basis. However, we know little about specific ecological factors underlying most biogeographic patterns. Some evidence supports the importance of abiotic factors, whereas few examples exist of large-scale patterns created by biotic interactions. I also show how incorporating biogeography may offer new perspectives on resource-related niches and species interactions. Several examples demonstrate that even after a major evolutionary radiation within a region, the region can still be invaded by ecologically similar species from another clade, countering the long-standing idea that communities and regions are generally ‘saturated’ with species. I also describe the somewhat paradoxical situation where competition seems to limit trait evolution in a group, but does not prevent co-occurrence of species with similar values for that trait (called here the ‘competition–divergence–co-occurrence conundrum’). In general, the interface of biogeography and ecology could be a major area for research in both fields.     

Relative contributions of biotic and abiotic factors to the spatial variation of litter stock in a mature subtropical forest

Aims Dead plant material (i.e. litter) is the major source of soil organic matter and thus plays a fundamental role in regulating soil carbon cycling in global forest ecosystems. The storage of litter is jointly determined by its production from plants and decomposition in a given environment. However, only few studies have explored the relative importance of environmental (i.e. abiotic) and plant (i.e. biotic) factors in driving the spatial variation of litter mass. The objective of this study is to quantify the relative contributions of biotic and abiotic factors in affecting the spatial variation of aboveground litter stock in a mature subtropical forest.     

Evolution of herbicide resistance in weeds: vertically transmitted fungal endophytes as genetic entities

The appearance of heritable resistance to herbicides in weeds is an evolutionary process driven by human selection. Assuming that spontaneous and random mutations originate herbicide resistance genes, which are selected by selection pressure imposed by herbicides, is the simplest model to understand how this phenomenon appears and increases in weed populations. However, the rate of herbicide resistance evolution is not only determined by the amount of genetic variation within the populations and the selection pressure exerted by herbicides, but also by factors related to genetics, biology and ecology of weeds. The inheritance of the resistance genes, the mating patterns of the populations, the relative fitness of susceptible and resistant phenotypes and gene flow processes also control the mentioned rate. Many cool season grasses are often infected by fungal symbiotic endophytes (Neotyphodium spp.). These organisms modify the physiology, ecology and reproductive biology of their hosts, conferring greater tolerance to biotic and abiotic stresses, greater competitive ability and the capacity of reducing ecosystem biodiversity. In this work, we present new empirical data and propose new theoretical support on how these microbial symbionts can modulate the evolution of herbicide resistance in weeds. Fungal endophytes are vertically transmitted, and may act as genetic entities altering the evolution of herbicide resistance by reducing herbicide efficacy (delaying effect on evolution). In addition, indirect evidence suggests that fungal endophytes might reduce the fitness penalty associated with the newly arisen resistant phenotypes. The importance and dynamic of these opposite effects is discussed.     

Evolution. A case of system dynamics

It is contended that the Darwinian theory of evolution is merely a special case of the obsolete Newtonian paradigm. A modern vision of reality, consistent with structuralism in biology, is presented. Some well-known neo-Darwinist explanations of the evolutionary process are quoted accompanied by structuralist interpretations of the same cases. These lead to a different 'mechanism' of evolution, based on internal factors, consistent with contemporary science. It is argued that a great number of specialists who dismiss the Darwinian theory of evolution share a common reason for rejecting it, but differ widely in guessing the motivating factor or factors of evolution.     

Biotic and abiotic constraints that facilitate host exclusivity of Gondwanamyces and Ophiostoma on Protea

Estimations of global fungal diversity are hampered by a limited understanding of the forces that dictate host exclusivity in saprobic microfungi. To consider this problem for Gondwanamyces and Ophiostoma found in the flower heads of Protea in South Africa, we determined the role of various factors thought to influence their host exclusivity. Results showed that various biotic and abiotic factors influence the growth and survival of these fungi in vitro. Monitoring temperature and relative humidity (RH) fluctuations within infructescences in vivo revealed considerable microclimatic differences between different Protea spp. Fungal growth and survival at different RH levels experienced in the field suggested that this factor does not play a major role in host exclusivity of these fungi. Maximum temperatures within infructescences and host preferences of the vectors of Gondwanamyces and Ophiostoma appear to play a substantial part in determining colonisation of Protea in general. However, these factors did not explain host exclusivity of specific fungal species towards particular Protea hosts. In contrast, differential growth of fungal species on media containing macerated tissue of Protea showed that Gondwanamyces and Ophiostoma grow best on tissue from their natural hosts. Thus, host chemistry plays a role in host exclusivity of these fungi, although some species grew vigorously on tissue of Protea spp. with which they are not naturally associated. A combination of host chemistry and temperature partially explains host exclusivity, but the relationship for these factors on the tested saprobic microfungi and their hosts is clearly complex and most likely includes combinations of various biotic and abiotic factors including those emerging from this study.     

Spatio‐temporal variation of biotic factors underpins contemporary range dynamics of congeners

Species’ ranges are complex often exhibiting multidirectional shifts over space and time. Despite the strong fingerprint of recent historical climate change on species’ distributions, biotic factors such as loss of vegetative habitat and the presence of potential competitors constitute important yet often overlooked drivers of range dynamics. Furthermore, short‐term changes in environmental conditions can influence the underlying processes of local extinction and local colonization that drive range shifts, yet are rarely considered at broad scales. We used dynamic state‐space occupancy models to test multiple hypotheses of the relative importance of major drivers of range shifts of Golden‐winged Warblers (Vermivora chrysoptera) and Blue‐winged Warblers (V. cyanoptera) between 1983 and 2012 across North America: warming temperatures; habitat changes; and occurrence of congeneric species, used here as proxy for biotic interactions. Dynamic occupancies for both species were most influenced by spatial relative to temporal variation in temperature and habitat. However, temporal variation in temperature anomalies and biotic interactions remained important. The two biotic factors considered, habitat change and biotic interactions, had the largest relative effect on estimated extinction rates followed by abiotic temperature anomalies. For the Golden‐winged Warbler, the predicted presence of the Blue‐winged Warbler, a hypothesized competitor, most influenced extinction probabilities, contributing to evidence supporting its role in site‐level species replacement. Given the overall importance of biotic factors on range‐wide dynamic occupancies, their consideration alongside abiotic factors should not be overlooked. Our results suggest that warming compounds the negative effect of habitat loss emphasizing species’ need for habitat to adapt to a changing climate. Notably, even closely related species exhibited individual responses to abiotic and biotic factors considered.     

Temporal dynamics of biotic and abiotic drivers of litter decomposition

Climate, litter quality and decomposers drive litter decomposition. However, little is known about whether their relative contribution changes at different decomposition stages. To fill this gap, we evaluated the relative importance of leaf litter polyphenols, decomposer communities and soil moisture for litter C and N loss at different stages throughout the decomposition process. Although both microbial and nematode communities regulated litter C and N loss in the early decomposition stages, soil moisture and legacy effects of initial differences in litter quality played a major role in the late stages of the process. Our results provide strong evidence for substantial shifts in how biotic and abiotic factors control litter C and N dynamics during decomposition. Taking into account such temporal dynamics will increase the predictive power of decomposition models that are currently limited by a single‐pool approach applying control variables uniformly to the entire decay process.     

All stressed out and nowhere to go: does evolvability limit adaptation in invasive species?

Introduced and invasive species are major threats native species and communities and, quite naturally, most scientists and managers think of them in terms of ecological problems. However, species introductions are also experiments in evolution, both for the alien species and for the community that they colonize. We focus here on the introduced species because these offer opportunities to study the properties that allow a species to succeed in a novel habitat and the constraints that limit range expansion. Moreover, an increasing body of evidence from diverse taxa suggests that the introduced species often undergo rapid and observable evolutionary change in their new habitat. Evolution requires genetic variation, which may be decreased or expanded during an invasion, and an evolutionary mechanism such as genetic drift or natural selection. In this volume, we seek to understand how natural selection produces adaptive evolution during invasions. Key questions include what is the role of biotic and abiotic stress in driving adaptation, and what is the source of genetic variation in introduced populations.     

Local-scale drivers of tree survival in a temperate forest

Tree survival plays a central role in forest ecosystems. Although many factors such as tree size, abiotic and biotic neighborhoods have been proposed as being important in explaining patterns of tree survival, their contributions are still subject to debate. We used generalized linear mixed models to examine the relative importance of tree size, local abiotic conditions and the density and identity of neighbors on tree survival in an old-growth temperate forest in northeastern China at three levels (community, guild and species). Tree size and both abiotic and biotic neighborhood variables influenced tree survival under current forest conditions, but their relative importance varied dramatically within and among the community, guild and species levels. Of the variables tested, tree size was typically the most important predictor of tree survival, followed by biotic and then abiotic variables. The effect of tree size on survival varied from strongly positive for small trees (1-20 cm dbh) and medium trees (20-40 cm dbh), to slightly negative for large trees (>40 cm dbh). Among the biotic factors, we found strong evidence for negative density and frequency dependence in this temperate forest, as indicated by negative effects of both total basal area of neighbors and the frequency of conspecific neighbors. Among the abiotic factors tested, soil nutrients tended to be more important in affecting tree survival than topographic variables. Abiotic factors generally influenced survival for species with relatively high abundance, for individuals in smaller size classes and for shade-tolerant species. Our study demonstrates that the relative importance of variables driving patterns of tree survival differs greatly among size classes, species guilds and abundance classes in temperate forest, which can further understanding of forest dynamics and offer important insights into forest management.     

Evolution in caves: Darwin’s ‘wrecks of ancient life’ in the molecular era

Cave animals have historically attracted the attention of evolutionary biologists because of their bizarre ‘regressive’ characters and convergent evolution. However, understanding of their biogeographic and evolutionary history, including mechanisms of speciation, has remained elusive. In the last decade, molecular data have been obtained for subterranean taxa and their surface relatives, which have allowed some of the classical debates on the evolution of cave fauna to be revisited. Here, we review some of the major studies, focusing on the contribution of phylogeography in the following areas: biogeographic history and the relative roles of dispersal and vicariance, colonization history, cryptic species diversity and modes of speciation of cave animals. We further consider the limitations of current research and prospects for the future. Phylogeographic studies have confirmed that cave species are often cryptic, with highly restricted distributions, but have also shown that their divergence and potential speciation may occur despite the presence of gene flow from surface populations. Significantly, phylogeographic studies have provided evidence for speciation and adaptive evolution within the confines of cave environments, questioning the assumption that cave species evolved directly from surface ancestors. Recent technical developments involving ‘next generation’ DNA sequencing and theoretical developments in coalescent and population modelling are likely to revolutionize the field further, particularly in the study of speciation and the genetic basis of adaptation and convergent evolution within subterranean habitats. In summary, phylogeographic studies have provided an unprecedented insight into the evolution of these unique fauna, and the future of the field should be inspiring and data rich.     

Modular assembly of genes and the evolution of new functions

Modular assembly of novel genes from existing genes has long been thought to be an important source of evolutionary novelty. Thanks to major advances in genomic studies it has now become clear that this mechanism contributed significantly to the evolution of novel biological functions in different evolutionary lineages. Analyses of completely sequenced bacterial, archaeal and eukaryotic genomes has revealed that modular assembly of novel constituents of various eukaryotic intracellular signalling pathways played a major role in the evolution of eukaryotes. Comparison of the genomes of single-celled eukaryotes, multicellular plants and animals has also shown that the evolution of multicellularity was accompanied by the assembly of numerous novel extracellular matrix proteins and extracellular signalling proteins that are absolutely essential for multicellularity. There is now strong evidence that exon-shuffling played a general role in the assembly of the modular proteins involved in extracellular communications of metazoa. Although some of these proteins seem to be shared by all major groups of metazoa, others are restricted to certain evolutionary lineages. The genomic features of the chordates appear to have favoured intronic recombination as evidenced by the fact that exon-shuffling continued to be a major source of evolutionary novelty during vertebrate evolution.     

Defensive Traits in Young Pine Trees Cluster into Two Divergent Syndromes Related to Early Growth Rate

The combination of defensive traits leads to the evolution of ‘plant defense syndromes’ which should provide better protection against herbivores than individual traits on their own. Defense syndromes can be generally driven by plant phylogeny and/or biotic and abiotic factors. However, we lack a solid understanding of (i) the relative importance of shared evolution vs. convergence due to similar ecological conditions and (ii) the role of induced defense strategies in shaping defense syndromes. We investigate the relative roles of evolutionary and ecological factors shaping the deployment of pine defense syndromes including multiple constitutive and induced chemical defense traits. We performed a greenhouse experiment with seedlings of eighteen species of Pinaceae family, and measured plant growth rate, constitutive chemical defenses and their inducibility. Plant growth rate, but not phylogenetic relatedness, determined the deployment of two divergent syndromes. Slow-growing pine species living in harsh environments where tissue replacement is costly allocated more to constitutive defenses (energetically more costly to produce than induced). In contrast, fast-growing species living in resource-rich habitats had greater inducibility of their defenses, consistent with the theory of constitutive-induced defense trade-offs. This study contributes to a better understanding of evolutionary and ecological factors driving the deployment of defense syndromes.     

Evolution and ecology of antibiotic resistance genes

A new perspective on the topic of antibiotic resistance is beginning to emerge based on a broader evolutionary and ecological understanding rather than from the traditional boundaries of clinical research of antibiotic-resistant bacterial pathogens. Phylogenetic insights into the evolution and diversity of several antibiotic resistance genes suggest that at least some of these genes have a long evolutionary history of diversification that began well before the 'antibiotic era'. Besides, there is no indication that lateral gene transfer from antibiotic-producing bacteria has played any significant role in shaping the pool of antibiotic resistance genes in clinically relevant and commensal bacteria. Most likely, the primary antibiotic resistance gene pool originated and diversified within the environmental bacterial communities, from which the genes were mobilized and penetrated into taxonomically and ecologically distant bacterial populations, including pathogens. Dissemination and penetration of antibiotic resistance genes from antibiotic producers were less significant and essentially limited to other high G+C bacteria. Besides direct selection by antibiotics, there is a number of other factors that may contribute to dissemination and maintenance of antibiotic resistance genes in bacterial populations.     

Quorum-sensing regulation of adhesion in Serratia marcescens MG1 is surface dependent

Serratia marcescens is an opportunistic pathogen and a major cause of ocular infections. In previous studies of S. marcescens MG1, we showed that biofilm maturation and sloughing were regulated by N-acyl homoserine lactone (AHL)-based quorum sensing (QS). Because of the importance of adhesion in initiating biofilm formation and infection, the primary goal of this study was to determine whether QS is important in adhesion to both abiotic and biotic surfaces, as assessed by determining the degree of attachment to hydrophilic tissue culture plates and human corneal epithelial (HCE) cells. Our results demonstrate that while adhesion to the abiotic surface was AHL regulated, adhesion to the HCE cell biotic surface was not. Type I fimbriae were identified as the critical adhesin for non-QS-mediated attachment to the biotic HCE cell surface but played no role in adhesion to the abiotic surface. While we were not able to identify a single QS-regulated adhesin essential for attachment to the abiotic surface, four AHL-regulated genes involved in adhesion to the abiotic surface were identified. Interestingly, two of these genes, bsmA and bsmB, were also shown to be involved in adhesion to the biotic surface in a non-QS-controlled fashion. Therefore, the expression of these two genes appears to be cocontrolled by regulators other than the QS system for mediation of attachment to HCE cells. We also found that QS in S. marcescens regulates other potential cell surface adhesins, including exopolysaccharide and the outer membrane protein OmpX. We concluded that S. marcescens MG1 utilizes different regulatory systems and adhesins in attachment to biotic and abiotic surfaces and that QS is a main regulatory pathway in adhesion to an abiotic surface but not in adhesion to a biotic surface.