Advances In Evolutionary Biology Research Articles

Opportunities and challenges of macrogenetic studies.

The rapidly emerging field of macrogenetics focuses on analysing publicly accessible genetic datasets from thousands of species to explore large-scale patterns and predictors of intraspecific genetic variation. Facilitated by advances in evolutionary biology, technology, data infrastructure, statistics and open science, macrogenetics addresses core evolutionary hypotheses (such as disentangling environmental and life-history effects on genetic variation) with a global focus. Yet, there are important, often overlooked, limitations to this approach and best practices need to be considered and adopted if macrogenetics is to continue its exciting trajectory and reach its full potential in fields such as biodiversity monitoring and conservation. Here, we review the history of this rapidly growing field, highlight knowledge gaps and future directions, and provide guidelines for further research.

The Cognitive Lens: a primer on conceptual tools for analysing information processing in developmental and regenerative morphogenesis.

Brains exhibit plasticity, multi-scale integration of information, computation and memory, having evolved by specialization of non-neural cells that already possessed many of the same molecular components and functions. The emerging field of basal cognition provides many examples of decision-making throughout a wide range of non-neural systems. How can biological information processing across scales of size and complexity be quantitatively characterized and exploited in biomedical settings? We use pattern regulation as a context in which to introduce the Cognitive Lens-a strategy using well-established concepts from cognitive and computer science to complement mechanistic investigation in biology. To facilitate the assimilation and application of these approaches across biology, we review tools from various quantitative disciplines, including dynamical systems, information theory and least-action principles. We propose that these tools can be extended beyond neural settings to predict and control systems-level outcomes, and to understand biological patterning as a form of primitive cognition. We hypothesize that a cognitive-level information-processing view of the functions of living systems can complement reductive perspectives, improving efficient top-down control of organism-level outcomes. Exploration of the deep parallels across diverse quantitative paradigms will drive integrative advances in evolutionary biology, regenerative medicine, synthetic bioengineering, cognitive neuroscience and artificial intelligence. This article is part of the theme issue 'Liquid brains, solid brains: How distributed cognitive architectures process information'.

Speciation within Columnea section Angustiflora (Gesneriaceae): Islands, pollinators and climate

Despite many advances in evolutionary biology, understanding the proximate mechanisms that lead to speciation for many taxonomic groups remains elusive. Phylogenetic analyses provide a means to generate well-supported estimates of species relationships. Understanding how genetic isolation (restricted gene flow) occurred in the past requires not only a well-supported molecular phylogenetic analysis, but also an understanding of when character states that define species may have changed. In this study, phylogenetic trees resolve species level relationships for fourteen of the fifteen species within Columnea section Angustiflorae (Gesneriaceae). The distributions of sister species pairs are compared and ancestral character states are reconstructed using Bayesian stochastic mapping. Climate variables were also assessed and shifts in ancestral climate conditions were mapped using SEEVA. The relationships between morphological character states and climate variables were assessed with correlation analyses. These results indicate that species in section Angustiflorae have likely diverged as a result of allopatric, parapatric, and sympatric speciation, with both biotic and abiotic forces driving morphological and phenological divergence.

Reason, emotion, compassion: can altruism survive professionalisation in the humanitarian sector?

The humanitarian sector has grown enormously over the past two decades. Some fear that professionalisation comes at the expense of altruistic volunteering. This may be a valid concern if altruism is the product of organisational culture and individual experiences rather than an innate trait. This paper examines advances in evolutionary biology and neurology that provide evidence in support of both the nature and nurture arguments, echoing earlier insights from social sciences. It then questions to what extent humanitarian principles build on altruistic impulses or instead seek to constrain them, and reviews recruitment profiles of selected humanitarian organisations and applicants' letters accordingly. This initial investigation warrants further research to identify how altruism as a personal trait and an organisational principle has influenced diverse humanitarian actors and traditions. This paper outlines how training curricula and organisational reward systems can build on-rather than stifle-natural altruism to nurture critical, reflexive practitioners.

Private funding for molecular evolution.

In this issue of the Journal of Molecular Evolution, two papers appear from research efforts that were partially or wholly funded from a private foundation. As funding for research from governmental sources gets increasingly scarce, scientists are turning to alternative sources to keep the lights on in their laboratories. This affects many disciplines of course, but molecular evolutionary studies are especially vulnerable. On the one hand, the pursuit of an understanding of the Earth’s evolutionary history is somewhat of a philosophical pursuit, and of course evolutionary thinking per se has had a rocky path to acceptance by the general (read: tax-paying) public. Many in the field can point to many practical applications of advances in evolutionary biology—two obvious examples being an appreciation for the spread of bacterial resistance to antibiotics and an appreciation for the problems faced by overuse of pesticides; however, for the average person on the street, there may be little benefit to paying for knowing what happened millions or billions of years ago. And on the other hand, molecular evolution in particular has a hard time from benefitting from ‘‘warm and fuzzy’’ money, which is to say that organismal evolutionary biologists can at least appeal to a shared sense among most that our plant and animal brethren deserve a helping hand. Molecular evolutionists, tracing the fate of minute nano-scale structures as they change over time, are hard-pressed to drum up governmental support in lean economies. Fortunately there are encouraging signs that private foundations, and even individual philanthropists, are seeing the enormous value of our field. For many years, the Alfred P. Sloan Foundation specifically supported molecular evolution and offered valuable funding such as their Young Investigator Awards. While Sloan no longer specifically targets molecular evolutionists, they do still advocate, and support, basic research in other disciplines. Other foundations have filled some of the void left when these Young Investigator Awards were discontinued. The John Templeton Foundation, and more recently, the Simons Foundation have promoted basic evolutionary biology research. And in some sense, the broader and more fundamental the studies, the more eager these organizations seem to be to provide support. Auspiciously, there are even signs that the general public at a more grass-roots level may be interested in stepping up to help molecular evolution. Crowd funding is an exciting new option for relatively small amounts of funding for any sort of pursuit, and surely young molecular evolutionists could be kick started through such means, although I do not yet know of any specific cases of this. Another wonderful example are the efforts of one Mr. Harry Lonsdale, who personally initiated and funded the ‘‘Origins of Life Challenge’’ that led to the support of the research in this issue of JME. These works are those of Ritson & Sutherland and of DeGuzman et al., q.v. The senior author on the first of these, Dr. John Sutherland, was one of the two winners (along with Dr. Matthew Powner) of the Origins of Life Challenge in 2012. There is little doubt that Dr. Sutherland is most appreciative of the support given by Mr. Lonsdale who, for his part, has said, ‘‘Over the past five centuries, so many of the mysteries of antiquity have been solved ... but not the origin of life on Earth. The solution to that problem will have a profound impact and far-reaching consequences.’’ (personal communication). Clearly, this is an enlightened view of our pursuit as human beings, and hopefully it will serve to N. Lehman (&) Department of Chemistry, Portland State University, PO Box 751, Portland, OR 97201, USA e-mail: jme1@pdx.edu; niles@pdx.edu

English

Introduction We summarize briefly contemporary scientific advances in evolutionary biology and epigenetics, and discuss their implications for revising scholarly understanding of human development, especially when framed within relational developmental systems theories. We contrast the evidence in support of a relationally-integrated approach to biological and behavioural (psychological and social) processes with claims about links between evolution and human development emanating from an area of social/behavioural science, Evolutionary Psychology. We note the conceptual and empirical problems of Evolutionary Psychologyand, in turn, highlight the empirical utility of integrated biological and developmental science research framed by relational developmental systems theories. Conclusion We make recommendations for future, multidisciplinary research framed by relational developmental systems theories, and point to the implications of data derived from such work for applications to social policies and programmes.

Evolutionary molecular medicine

Evolution has long provided a foundation for population genetics, but some major advances in evolutionary biology from the twentieth century that provide foundations for evolutionary medicine are only now being applied in molecular medicine. They include the need for both proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, competition between alleles, co-evolution, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are transforming evolutionary biology in ways that create even more opportunities for progress at its interfaces with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and related principles to speed the development of evolutionary molecular medicine.

Genetics and evolution of infectious diseases

The brilliance of Darwin's theory of evolution arises largely from his connection of pattern—the diversity and affiliations of organisms—with process: natural selection. Since Darwin, the great advances in evolutionary biology have merged pattern with process. The most important advance was the integration of genetics with evolution. This “modern synthesis” began during the 1930s and has developed since then with ever more detailed understanding of molecular mechanisms of genetic regulation and expression, genomic composition, and genetic variation in and between populations.

Prospect Theory and Political Decision Making

Risk is a central feature of political decision making. Prospect theory, an empirically correct theory of choice under risk that deals precisely with this condition, therefore seems to have much to offer political science. Prospect theory's central finding is that individuals’ attitude toward risk depends on whether they face losses or gains. Confronting gains, individuals are risk averse in their decision making; confronting losses, they are risk accepting. Where do these preferences come from? Do they also hold for collective decision making? How can prospect theory help us to solve puzzles in political science? This article addresses these questions by discussing some advances in evolutionary biology, behavioural economics, psychology, neuro-economics and political science. The article shows that there is increasing evidence that prospect theory preferences have an evolutionary origin and that these preferences extend to collective decision making. Moreover, it demonstrates that political science can indeed gain from applying prospect theory, as insights from prospect theory help to solve puzzles such as why some governments pursue electorally risky welfare state reform but others do not.

Successful development of microsatellite markers in a challenging species: the horizontal borerAustroplatypus incompertus(Coleoptera: Curculionidae)

The analysis of microsatellite loci has allowed significant advances in evolutionary biology and pest management. However, until very recently, the potential benefits have been compromised by the high costs of developing these neutral markers. High-throughput sequencing provides a solution to this problem. We describe the development of 13 microsatellite markers for the eusocial ambrosia beetle, Austroplatypus incompertus, a significant pest of forests in southeast Australia. The frequency of microsatellite repeats in the genome of A. incompertus was determined to be low, and previous attempts at microsatellite isolation using a traditional genomic library were problematic. Here, we utilised two protocols, microsatellite-enriched genomic library construction and high-throughput 454 sequencing and characterised 13 loci which were polymorphic among 32 individuals. Numbers of alleles per locus ranged from 2 to 17, and observed and expected heterozygosities from 0.344 to 0.767 and from 0.507 to 0.860, respectively. These microsatellites have the resolution required to analyse fine-scale colony and population genetic structure. Our work demonstrates the utility of next-generation 454 sequencing as a method for rapid and cost-effective acquisition of microsatellites where other techniques have failed, or for taxa where marker development has historically been both complicated and expensive.

Scientific drilling and biological evolution in ancient lakes: lessons learned and recommendations for the future

Scientific drilling to recover sediment core and fossil samples is a promising approach to increasing our understanding of species evolution in ancient lakes. Most lake drilling efforts to date have focused on paleoclimate reconstruction. However, it is clear from the excellent fossil preservation and high temporal resolution typical of lake beds that significant advances in evolutionary biology can be made through drill core studies coordinated with phylogenetic work on appropriate taxa. Geological records can be used to constrain the age of specific lakes and the timing of evolutionarily significant events (such as lake level fluctuations and salinity crises). Fossil data can be used to test speciation and biogeographic hypotheses and flesh out phylogenetic trees, using a better-resolved fossil record to estimate timing of phylogenetic divergences. The extraordinary preservation of many fossils in anoxic lake beds holds the hope of collecting fossil DNA from the same body fossils that improve our understanding of morphological character evolution and adaptation. Moreover, fossils allow calibration of molecular clocks, which are currently largely inferential. Lake Malawi Drilling Project results provide some guideposts on what might be expected in a drilling project for studies of evolution. The extreme variability in lake level and environmental history that most ancient lakes experience (exemplified by the Lake Malawi record) demonstrates that no one drilling locality is likely to provide a complete record of phylogenetic history for a radiating lineage. Evolutionary biologists should take an active role in the design of drilling projects, which typically have interdisciplinary objectives, to ensure their sampling needs will be met by whatever sites in a lake are ultimately drilled.

MORAL APES, HUMAN UNIQUENESS, AND THE IMAGE OF GOD

Abstract.Recent advances in evolutionary biology and ethology suggest that humans are not the only species capable of empathy and possibly morality. These findings are of no little consequence for theology, given that a nonhuman animal as a free moral agent would beg the question if human beings are indeed uniquely created in God's image. I argue that apes and some other mammals have moral agency and that a traditional interpretation of the imago Dei is incorrectly equating specialness with exclusivity. By framing the problem in terms of metaphor, following the work of Paul Ricoeur and Sallie McFague, I propose that the concept of the imago Dei could be extended to accommodate moral species other than our own.

An alternative approach to medical genetics based on modern evolutionary biology. Part 1: mutation and symbiogenesis.

The need to understand the genetic underpinning of common diseases, such as cancer, diabetes and autoimmune disorders, is a major challenge facing medical genetics. While many disorders involve a complex interaction between genetic traits and environmental influences, a significant proportion involve specific genetic causes that are diagnosable and thus amenable to therapeutic approaches, including family counselling, specific lines of chemically-directed therapy and even the possibility of addressing the underlying genetic causation through specific genetic therapy. The genetic approach to medicine has always found commonalities with the disciplines of evolutionary biology: only when we understand the evolutionary origins of the human genome can we aspire to understand how ‘normality’, in terms of genetics and epigenetics, becomes subverted in disease. Since the 1930s, mutation has been assumed to be the exclusive explanation of the hereditary basis of disease. But advances in evolutionary biology over the last two decades have introduced three additional, and important, sources of hereditary variation, namely symbiogenesis, particularly symbiogenesis involving viruses, epigenetics and hybridogenesis, all of which are now seen to have played important roles in the evolution of biodiversity. These additional mechanisms have played a major role in the evolution of the human genome – indeed they help to explain what would otherwise appear to be some paradoxical aspects of its construction and make-up. In this paper, and the four linked papers that follow it, I shall explain the evolutionary advances and show how, together with the knowledge already accrued from the study of mutation, they provide a more comprehensive understanding of the hereditary basis of human disease.

It's a Bull's Market

Research on domesticated livestock heralds new advances in evolutionary biology, animal breeding, and animal models for human diseases.

Natural selection drives the fine-scale divergence of a coevolutionary arms race involving a long-mouthed weevil and its obligate host plant

BackgroundOne of the major recent advances in evolutionary biology is the recognition that evolutionary interactions between species are substantially differentiated among geographic populations. To date, several authors have revealed natural selection pressures mediating the geographically-divergent processes of coevolution. How local, then, is the geographic structuring of natural selection in coevolutionary systems?ResultsI examined the spatial scale of a "geographic selection mosaic," focusing on a system involving a seed-predatory insect, the camellia weevil (Curculio camelliae), and its host plant, the Japanese camellia (Camellia japonica). In this system, female weevils excavate camellia fruits with their extremely-long mouthparts to lay eggs into seeds, while camellia seeds are protected by thick pericarps. Quantitative evaluation of natural selection demonstrated that thicker camellia pericarps are significantly favored in some, but not all, populations within a small island (Yakushima Island, Japan; diameter ca. 30 km). At the extreme, camellia populations separated by only several kilometers were subject to different selection pressures. Interestingly, in a population with the thickest pericarps, camellia individuals with intermediate pericarp thickness had relatively high fitness when the potential costs of producing thick pericarps were considered. Also importantly, some parameters of the weevil - camellia interaction such as the severity of seed infestation showed clines along temperature, suggesting the effects of climate on the fine-scale geographic differentiation of the coevolutionary processes.ConclusionThese results show that natural selection can drive the geographic differentiation of interspecific interactions at surprisingly small spatial scales. Future studies should reveal the evolutionary/ecological outcomes of the "fine scale geographic mosaics" in biological communities.

The neuroeconomic path of the law

Advances in evolutionary biology, experimental economics and neuroscience are shedding new light on age-old questions about right and wrong, justice, freedom, the rule of law and the relationship between the individual and the state. Evidence is beginning to accumulate suggesting that humans evolved certain fundamental behavioural predispositions grounded in our intense social natures, that those predispositions are encoded in our brains as a distribution of probable behaviours, and therefore that there may be a core of universal human law.

When environmental variation short-circuits natural selection

The development of a coherent framework for measuring natural selection was one of the major advances in evolutionary biology in the 1970s and 1980s. However, for evolution to occur, natural selection must act on underlying genetic variation, whereas most measurements of natural selection are limited to phenotypes. Two new papers now show that environmentally induced covariances between phenotypes and fitness can frequently lead to the systematic overestimation of the strength of natural selection.

Deepening the History of Masculinity and the Sexes

The turn of the twenty-first century has brought a tentative yet potentially seismic shift in feminist studies towards re-integrating biology into critical understanding of the behavioral differences between women and men. 1 Until Robert S. McElvaine's book, this movement has barely registered among historians of women and gender. For at least the last thirty-five years, academic historians have made a sharp, principled distinction between sex as a physiological designation and gender as the contingent mental traits, behaviors, social conventions, and institutions that have formed around sex difference. A few important historical works do consider the issue of whether biology influences more than primary sexual characteristics: Gerda Lerner's The Creation of Patriarchy (1986) maintains that the initial division of labor between women and men emerged from different roles in sexual reproduction; Carl Degler's In Search of Human Nature: The Decline and Revival of Darwinism in American Social Thought (1991) provides a valuable analysis of the recent social scientific scholarship that finds innate psychological and behavioral differences between the sexes; and David Courtwright's Violent Land: Single Men and Social Disorder from the Frontier to the Inner City (1996) explains the exceptional levels of American violence through the "sociobiological impulses" of the nation's inordinately large number of un-married men. But, as its title suggests, McElvaine's Eve's Seed: Biology, the Sexes and the Course of History re-synthesizes the full sweep of human history around the concept of sexual difference; it also offers a timely account of what historians risk in continuing to ignore advances in evolutionary biology. Through its attempt to apply "biohistory" to twentieth-century U.S. masculinity, Eve's Seed may presage a second-wave of men's historiography. While I have considerable misgivings about some of the book's particulars, it should be appreciated as an imaginatively written and highly interpretive polemic. It's revisionist history in grand form. [End Page 135]

Hamilton goes empirical: estimation of inclusive fitness from life-history data.

Hamilton's theory of kin selection is one of the most important advances in evolutionary biology since Darwin. Central to the kin-selection theory is the concept of inclusive fitness. However, despite the importance of inclusive fitness in evolutionary theory, empirical estimation of inclusive fitness has remained an elusive task. Using the concept of individual fitness, I present a method for estimating inclusive fitness and its components for diploid organisms with age-structured life histories. The method presented here: (i) allows empirical estimation of inclusive fitness from life-history data; (ii) simultaneously considers all components of fitness, including timing and magnitude of reproduction; (iii) is consistent with Hamilton's definition of inclusive fitness; and (iv) adequately addresses shortcomings of existing methods of estimating inclusive fitness. I also demonstrate the application of this new method for testing Hamilton's rule.

Towards a theory of self‐organization of natural and Social systems: The theory of form

Abstract The study of irreversible processes and states far from thermodynamic equilibrium, the extraordinary advances in evolutionary biology and cognitive sciences, and the fundamental contribution from general systems theory, have made possible a confrontation and rapprochement between scientific areas that traditionally were sharply separated from one another. Today a new perspective of convergence emerges in the study of evolution at the various levels of reality. In this perspective the theory of form aims to interpret the self‐organization of complex systems, both in natural evolution and in the socio‐cultural evolution of mankind. Two basic properties of this self‐organization are underlined: (1) a cognitive capacity which is inherent in the evolutionary process and constructs itself with that process on the basis of an original nature‐knowledge nexus; (2) the historical path that characterizes the evolutionary process of complex systems. In addition, the theory of form is advanced as the transcen...