Quantification provides a conceptual basis for convergent evolution

While much of evolutionary biology attempts to explain the processes of diversification, there is an important place for the study of phenotypic similarity across life forms. When similar phenotypes evolve independently in different lineages this is referred to as convergent evolution. Although long recognised, evolutionary convergence is receiving a resurgence of interest. This is in part because new genomic data sets allow detailed and tractable analysis of the genetic underpinnings of convergent phenotypes, and in part because of renewed recognition that convergence may reflect limitations in the diversification of life. In this review we propose that although convergent evolution itself does not require a new evolutionary framework, none the less there is room to generate a more systematic approach which will enable evaluation of the importance of convergent phenotypes in limiting the diversity of life's forms. We therefore propose that quantification of the frequency and strength of convergence, rather than simply identifying cases of convergence, should be considered central to its systematic comprehension. We provide a non‐technical review of existing methods that could be used to measure evolutionary convergence, bringing together a wide range of methods. We then argue that quantification also requires clear specification of the level at which the phenotype is being considered, and argue that the most constrained examples of convergence show similarity both in function and in several layers of underlying form. Finally, we argue that the most important and impressive examples of convergence are those that pertain, in form and function, across a wide diversity of selective contexts as these persist in the likely presence of different selection pressures within the environment.     

Mechanisms of bacterial morphogenesis: Evolutionary cell biology approaches provide new insights

How Darwin's “endless forms most beautiful” have evolved remains one of the most exciting questions in biology. The significant variety of bacterial shapes is most likely due to the specific advantages they confer with respect to the diverse environments they occupy. While our understanding of the mechanisms generating relatively simple shapes has improved tremendously in the last few years, the molecular mechanisms underlying the generation of complex shapes and the evolution of shape diversity are largely unknown. The emerging field of bacterial evolutionary cell biology provides a novel strategy to answer this question in a comparative phylogenetic framework. This relatively novel approach provides hypotheses and insights into cell biological mechanisms, such as morphogenesis, and their evolution that would have been difficult to obtain by studying only model organisms. We discuss the necessary steps, challenges, and impact of integrating “evolutionary thinking” into bacterial cell biology in the genomic era.     

生物进化研究的回顾与展望

生物进化是自然科学的永恒之迷。随着历史的发展和科学的进步,生物进化思想从早期的萌芽,到自然选择学说、新达尔文主义,从现代综合理论,到分子进化的中性学说。再到新灾变论和点断平衡论等。当前,由于生物学各分支学科的飞速发展．它们就各自的研究对象在宏观和微观上不断地拓展和深入,并在不同的层次上形成了广泛的交叉、渗透和融合,现代的进化生物学研究从宏观的表型到微观的分子,从群体遗传改变的微进化到成种事件以及地史上生物类群谱系演化的宏进化,从直接的化石证据到基于形态性状、分子证据和环境变迁的综合推理,从基于遗传基础的比较基因组学到演化机理的进化发育生物学等。可以预见,在新的世纪里,在哲学和具体方法论(如系统论、控制论和信息论)的指导下,在生命科学、其他自然科学乃至社会科学工作者的通力合作下,综合遗传、发育和进化等研究领域的各种理论成果,生物进化理论即将出现也一定会出现的一个新的大综合和新的大统一。     

The strain concept in phytoplankton ecology

Laboratory cultures are important tools for investigating the biology of microalgae, allowing experimentation under controlled conditions. This control is critical for comparative studies, such as those often used to investigate intra-specific variation in properties of interest. By holding the environment constant, the experimentalist can gain insight into the genetic basis of phytoplankton phenotypes and by extension, into the adaptive history of those genotypes. In most cases the adaptations of interest are those that the algae have evolved in response to their natural environment. However, here it is argued that such experiments may instead reveal evolutionary adaptations to, and/or non-adaptive changes induced by, the culture conditions under which the alga is maintained. We present a review of the processes of evolution as they pertain to microalgal culture, and illustrate this discussion with examples of in-culture evolution from both within and outside the field of phycology. With these considerations in mind, recommendations are made for experimental practice focusing on comparative physiology, for which the effects of in-culture evolution are particularly confounding. Finally we argue that, although problematic in some contexts, the evolutionary propensities of phytoplankton cultures actually present an important opportunity for experimental evolutionary research with direct environmental significance.     

Notes from a snail island: Littorinid evolution and adaptation

The most successful study systems are built on a foundation of decades of research on the basic biology, ecology and life history of the organisms in question. Combined with new technologies, this can provide a formidable means to address important issues in evolutionary biology and molecular ecology. Littorinid marine snails are a good example of this, with a rich literature on their taxonomy, speciation, thermal tolerance and behavioural adaptations. In August 2017, an international meeting on Littorinid evolution was held at the Tjärnö Marine Research Laboratory in Western Sweden. In this meeting review, I provide a summary of some of the exciting work on parallel evolution, sexual selection and adaptation to environmental stress presented there. I argue that newly available genomic resources present an opportunity for integrating the traditionally divergent fields of speciation and environmental adaptation in Littorinid research.     

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.     

A multilevel analytical framework for studying cultural evolution in prehistoric hunter–gatherer societies

Over the past decade, a major debate has taken place on the underpinnings of cultural changes in human societies. A growing array of evidence in behavioural and evolutionary biology has revealed that social connectivity among populations and within them affects, and is affected by, culture. Yet the interplay between prehistoric hunter–gatherer social structure and cultural transmission has typically been overlooked. Interestingly, the archaeological record contains large data sets, allowing us to track cultural changes over thousands of years: they thus offer a unique opportunity to shed light on long‐term cultural transmission processes. In this review, we demonstrate how well‐developed methods for social structure analysis can increase our understanding of the selective pressures underlying cumulative culture. We propose a multilevel analytical framework that considers finer aspects of the complex social structure in which regional groups of prehistoric hunter–gatherers were embedded. We put forward predictions of cultural transmission based on local‐ and global‐level network metrics of small‐scale societies and their potential effects on cumulative culture. By bridging the gaps between network science, palaeodemography and cultural evolution, we draw attention to the use of the archaeological record to depict patterns of social interactions and transmission variability. We argue that this new framework will contribute to improving our understanding of social interaction patterns, as well as the contexts in which cultural changes occur. Ultimately, this may provide insights into the evolution of human behaviour.     

Transformationalism,taxism, and developmental biology in systematics

Issues concerning transformational and taxic comparisons are central to understanding the impact of the recent proliferation of molecular developmental data on evolutionary biology. More importantly, an understanding of taxism and transformationalism in comparative biology is critical to assessing the impact of the recent developmental data on systematic theory and practice. We examine the philosophical and practical aspects of the transformational approach and the relevance of this approach to recent molecular-based developmental data. We also examine the theoretical basis of the taxic approach to molecular developmental data and suggest that developmental data are perfectly amenable to the taxic approach. Two recent examples from the molecular developmental biology literature--the evolution of insect wings and the evolution of dorsal ventral inversion in vertebrates and invertebrates--are used to compare the taxic and transformational approaches. We conclude that the transformational approach is entirely appropriate for ontogenetic studies and furthermore can serve as an excellent source of hypotheses about the evolution of characters. However, the taxic approach is the ultimate arbiter of these hypotheses.     

Early evolution of the Eukaryota

The evolution of eukaryotes represents one of the most fundamental transitions in the history of life on Earth; however, there is little consensus as to when or over what timescale it occurred. Review of recent hypotheses and data in a phylogenetic context yields a broadly coherent account. Critical re‐assessment of the palaeontological record provides convincing evidence for the presence of crown‐group eukaryotes in the late Palaeoproterozic, and stem‐group eukaryotes extending back to the early Archaean. Despite their relatively early establishment, crown‐eukaryotes appear not to have become ecologically significant until the middle Neoproterozoic. I argue that this billion‐year delay was due to the singular, contingent evolution of crown‐group animals and their unique capacity to drive co‐evolutionary change.     

POTENTIAL PITFALLS OF RECONSTRUCTING DEEP TIME EVOLUTIONARY HISTORY WITH ONLY EXTANT DATA,A CASE STUDY USING THE CANIDAE (MAMMALIA,CARNIVORA)

Reconstructing evolutionary patterns and their underlying processes is a central goal in biology. Yet many analyses of deep evolutionary histories assume that data from the fossil record is too incomplete to include, and rely solely on databases of extant taxa. Excluding fossil taxa assumes that character state distributions across living taxa are faithful representations of a clade's entire evolutionary history. Many factors can make this assumption problematic. Fossil taxa do not simply lead‐up to extant taxa; they represent now‐extinct lineages that can substantially impact interpretations of character evolution for extant groups. Here, we analyze body mass data for extant and fossil canids (dogs, foxes, and relatives) for changes in mean and variance through time. AIC‐based model selection recovered distinct models for each of eight canid subgroups. We compared model fit of parameter estimates for (1) extant data alone and (2) extant and fossil data, demonstrating that the latter performs significantly better. Moreover, extant‐only analyses result in unrealistically low estimates of ancestral mass. Although fossil data are not always available, reconstructions of deep‐time organismal evolution in the absence of deep‐time data can be highly inaccurate, and we argue that every effort should be made to include fossil data in macroevolutionary studies.     

Broadening the application of evolutionarily based genetic pest management

Insect- and tick-vectored diseases such as malaria, dengue fever, and Lyme disease cause human suffering, and current approaches for prevention are not adequate. Invasive plants and animals such as Scotch broom, zebra mussels, and gypsy moths continue to cause environmental damage and economic losses in agriculture and forestry. Rodents transmit diseases and cause major pre- and postharvest losses, especially in less affluent countries. Each of these problems might benefit from the developing field of Genetic Pest Management that is conceptually based on principles of evolutionary biology. This article briefly describes the history of this field, new molecular tools in this field, and potential applications of those tools. There will be a need for evolutionary biologists to interact with researchers and practitioners in a variety of other fields to determine the most appropriate targets for genetic pest management, the most appropriate methods for specific targets, and the potential of natural selection to diminish the effectiveness of genetic pest management. In addition to producing environmentally sustainable pest management solutions, research efforts in this area could lead to new insights about the evolution of selfish genetic elements in natural systems and will provide students with the opportunity to develop a more sophisticated understanding of the role of evolutionary biology in solving societal problems.     

A role for convergent evolution in the secretory life of cells

The role of convergent evolution in biological adaptation is increasingly appreciated. Many clear examples have been described at the level of individual proteins and for organismal morphology, and convergent mechanisms have even been invoked to account for similar community structures that are shared between ecosystems. At the cellular level, an important area that has received scant attention is the potential influence of convergent evolution on complex subcellular features, such as organelles. Here, we show that existing data strongly argue that convergent evolution underlies the similar properties of specialized secretory vesicles, called dense core granules, in the animal and ciliate lineages. We discuss both the criteria for judging convergent evolution and the contribution that such evolutionary analysis can make to improve our understanding of processes in cell biology. The elucidation of these underlying evolutionary relationships is vital because cellular structures that are assumed to be analogous, owing to shared features, might in fact be governed by different molecular mechanisms.     

Evolutionary Psychology: The Burdens of Proof

I discuss two types of evidential problems with the most widely touted experiments in evolutionary psychology, those performed by Leda Cosmides and interpreted by Cosmides and John Tooby. First, and despite Cosmides and Tooby's claims to the contrary, these experiments don't fulfil the standards of evidence of evolutionary biology. Second Cosmides and Tooby claim to have performed a crucial experiment, and to have eliminated rival approaches. Though they claim that their results are consistent with their theory but contradictory to the leading non-evolutionary alternative, Pragmatic Reasoning Schemas theory, I argue that this claim is unsupported. In addition, some of Cosmides and Tooby's interpretations arise from misguided and simplistic understandings of evolutionary biology. While I endorse the incorporation of evolutionary approaches into psychology, I reject the claims of Cosmides and Tooby that a modular approach is the only one supported by evolutionary biology. Lewontin's critical examinations of the applications of adaptationist thinking provide a background of evidentiary standards against which to view the currently fashionable claims of evolutionary psychology.     

Lessons from the deep: mechanisms behind diversification of eukaryotic protein complexes

Genetic variation is the major mechanism behind adaptation and evolutionary change. As most proteins operate through interactions with other proteins, changes in protein complex composition and subunit sequence provide potentially new functions. Comparative genomics can reveal expansions, losses and sequence divergence within protein-coding genes, but in silico analysis cannot detect subunit substitutions or replacements of entire protein complexes. Insights into these fundamental evolutionary processes require broad and extensive comparative analyses, from both in silico and experimental evidence. Here, we combine data from both approaches and consider the gamut of possible protein complex compositional changes that arise during evolution, citing examples of complete conservation to partial and total replacement by functional analogues. We focus in part on complexes in trypanosomes as they represent one of the better studied non-animal/non-fungal lineages, but extend insights across the eukaryotes by extensive comparative genomic analysis. We argue that gene loss plays an important role in diversification of protein complexes and hence enhancement of eukaryotic diversity.     

The incomplete natural history of mitochondria

Mitochondrial DNA (mtDNA) has been used to study molecular ecology and phylogeography for 25 years. Much important information has been gained in this way, but it is time to reflect on the biology of the mitochondrion itself and consider opportunities for evolutionary studies of the organelle itself and its ecology, biochemistry and physiology. This review has four sections. First, we review aspects of the natural history of mitochondria and their DNA to show that it is a unique molecule with specific characteristics that differ from nuclear DNA. We do not attempt to cover the plethora of differences between mitochondrial and nuclear DNA; rather we spotlight differences that can cause significant bias when inferring demographic properties of populations and/or the evolutionary history of species. We focus on recombination, effective population size and mutation rate. Second, we explore some of the difficulties in interpreting phylogeographical data from mtDNA data alone and suggest a broader use of multiple nuclear markers. We argue that mtDNA is not a sufficient marker for phylogeographical studies if the focus of the investigation is the species and not the organelle. We focus on the potential bias caused by introgression. Third, we show that it is not safe to assume a priori that mtDNA evolves as a strictly neutral marker because both direct and indirect selection influence mitochondria. We outline some of the statistical tests of neutrality that can, and should, be applied to mtDNA sequence data prior to making any global statements concerning the history of the organism. We conclude with a critical examination of the neglected biology of mitochondria and point out several surprising gaps in the state of our knowledge about this important organelle. Here we limelight mitochondrial ecology, sexually antagonistic selection, life-history evolution including ageing and disease, and the evolution of mitochondrial inheritance.     

Antibiotic resistant pathogen outbreak investigation: an interdisciplinary module to teach fundamentals of evolutionary biology

The evolution of resistance to antibiotics provides a timely and relevant topic for teaching undergraduate students evolutionary biology. Here, we present a module incorporating modified sequencing data from eight antibiotic resistant pathogen outbreaks in hospital settings with bioinformatics and phylogenetic analyses. This module uses whole genome sequencing data from hospital outbreaks investigated by the Centers for Disease Control and Prevention to provide examples of antibiotic resistance spread. Students work in groups to analyze outbreak data to identify the bacterial species and antibiotic resistance genes, to infer a phylogenetic tree examining relatedness among isolates, and to determine a possible source of the outbreak. Students then compile their results in individual reports and provide recommendations for preventing the further spread of antibiotic resistant organisms. In addition to providing genomic outbreak data, we include a teaching concepts guide discussing three integral components of the module: how evolutionary biology concepts of natural selection and competition impact antibiotic resistance; outbreak investigation information to aid in phylogenetic analysis and creation of recommendations; and instructions for the bioinformatics protocol. Completion of this module provides students an opportunity to think critically about the evolution of resistance, practice bioinformatics techniques, and relate evolutionary biology to current events.     

Old fossils–young species: evolutionary history of an endemic gastropod assemblage in Lake Malawi

Studies on environmental changes provide important insights into modes of speciation, into the (adaptive) reoccupation of ecological niches and into species turnover. Against this background, we here examine the history of the gastropod genus Lanistes in the African Rift Lake Malawi, guided by four general evolutionary scenarios, and compare it with patterns reported from other endemic Malawian rift taxa. Based on an integrated approach using a mitochondrial DNA phylogeny and a trait-specific molecular clock in combination with insights from the fossil record and palaeoenvironmental data, we demonstrate that the accumulation of extant molecular diversity in the endemic group did not start before approximately 600 000 years ago from a single lineage. Fossils of the genus from the Malawi Rift, however, are over one million years older. We argue that severe drops in the lake level of Lake Malawi in the Pleistocene offer a potential explanation for this pattern. Our results also challenge previously established phylogenetic relationships within the genus by revealing parallel evolution and providing evidence that the endemic Lanistes species are not restricted to the lake proper but are present throughout the Malawi Rift.     

Evolutionary developmental biology and the problem of variation

Abstract. One of the oldest problems in evolutionary biology remains largely unsolved. Which mutations generate evolutionarily relevant phenotypic variation? What kinds of molecular changes do they entail? What are the phenotypic magnitudes, frequencies of origin, and pleiotropic effects of such mutations? How is the genome constructed to allow the observed abundance of phenotypic diversity? Historically, the neo‐Darwinian synthesizers stressed the predominance of micromutations in evolution, whereas others noted the similarities between some dramatic mutations and evolutionary transitions to argue for macromutationism. Arguments on both sides have been biased by misconceptions of the developmental effects of mutations. For example, the traditional view that mutations of important developmental genes always have large pleiotropic effects can now be seen to be a conclusion drawn from observations of a small class of mutations with dramatic effects. It is possible that some mutations, for example, those in cis‐regulatory DNA, have few or no pleiotropic effects and may be the predominant source of morphological evolution. In contrast, mutations causing dramatic phenotypic effects, although superficially similar to hypothesized evolutionary transitions, are unlikely to fairly represent the true path of evolution. Recent developmental studies of gene function provide a new way of conceptualizing and studying variation that contrasts with the traditional genetic view that was incorporated into neo‐Darwinian theory and population genetics. This new approach in developmental biology is as important for micro‐evolutionary studies as the actual results from recent evolutionary developmental studies. In particular, this approach will assist in the task of identifying the specific mutations generating phenotypic variation and elucidating how they alter gene function. These data will provide the current missing link between molecular and phenotypic variation in natural populations.     

An omics evolutionary perspective on phytophagous insect–host plant interactions in Anastrepha obliqua: a review

Phytophagous insects have a close relationship with their host plants. For this reason, their interactions can lead to important changes in insect population dynamics and evolutionary trajectories. Next generation sequencing (NGS) has provided an opportunity to analyze omics data on a large scale, facilitating the change from a classical genetics approach to a more holistic understanding of the underlying molecular mechanisms of host plant use by insects. Most studies have been carried out on model species in Holarctic and temperate zones. In tropical zones, however, the effects of use of various host plants on evolutionary insect history is less understood. In the current review, we describe how omics methodologies help us to understand phytophagous insect–host plant interactions from an evolutionary perspective, using as example the Neotropical phytophagous insect West Indian fruit fly, Anastrepha obliqua (Macquart) (Diptera: Tephritidae), an economically important fruit crop pest in the Americas. Anastrepha obliqua could adopt a generalist or a specialist lifestyle. We first review the adaptive molecular mechanisms of phytophagous insects to host plants, and then describe the main tools to study phytophagous insect–host plant interactions in the era of omics sciences. The omics approaches will advance the understanding of insect molecular mechanisms and their influence on diversification and evolution. Finally, we discuss the importance of a multidisciplinary approach that integrates the use of omics tools and other, more classical methodologies in evolutionary studies.     

Evolution and medicine in undergraduate education: a prescription for all biology students

The interface between evolutionary biology and the biomedical sciences promises to advance understanding of the origins of genetic and infectious diseases in humans, potentially leading to improved medical diagnostics, therapies, and public health practices. The biomedical sciences also provide unparalleled examples for evolutionary biologists to explore. However, gaps persist between evolution and medicine, for historical reasons and because they are often perceived as having disparate goals. Evolutionary biologists have a role in building a bridge between the disciplines by presenting evolutionary biology in the context of human health and medical practice to undergraduates, including premedical and preprofessional students. We suggest that students will find medical examples of evolution engaging. By making the connections between evolution and medicine clear at the undergraduate level, the stage is set for future health providers and biomedical scientists to work productively in this synthetic area. Here, we frame key evolutionary concepts in terms of human health, so that biomedical examples may be more easily incorporated into evolution courses or more specialized courses on evolutionary medicine. Our goal is to aid in building the scientific foundation in evolutionary biology for all students, and to encourage evolutionary biologists to join in the integration of evolution and medicine.