Macroevolutionary Approaches Research Articles

Archaeology and cultural macroevolution

Given the numerous parallels between the archaeological and paleontological records, it is not surprising to find a considerable fit between macroevolutionary approaches and methods used in biology – for example, cladistics and clade-diversity measures – and some of those that have long been used in archaeology – for example, seriation. Key, however, is recognizing that this methodological congruence is illusory in terms of how evolution has traditionally been viewed in biology and archaeology.

A Hybrid Micro–Macroevolutionary Approach to Gene Tree Reconstruction

Gene family evolution is determined by microevolutionary processes (e.g., point mutations) and macroevolutionary processes (e.g., gene duplication and loss), yet macroevolutionary considerations are rarely incorporated into gene phylogeny reconstruction methods. We present a dynamic program to find the most parsimonious gene family tree with respect to a macroevolutionary optimization criterion, the weighted sum of the number of gene duplications and losses. The existence of a polynomial delay algorithm for duplication/loss phylogeny reconstruction stands in contrast to most formulations of phylogeny reconstruction, which are NP-complete. We next extend this result to obtain a two-phase method for gene tree reconstruction that takes both micro- and macroevolution into account. In the first phase, a gene tree is constructed from sequence data, using any of the previously known algorithms for gene phylogeny construction. In the second phase, the tree is refined by rearranging regions of the tree that do not have strong support in the sequence data to minimize the duplication/lost cost. Components of the tree with strong support are left intact. This hybrid approach incorporates both micro- and macroevolutionary considerations, yet its computational requirements are modest in practice because the two-phase approach constrains the search space. Our hybrid algorithm can also be used to resolve nonbinary nodes in a multifurcating gene tree. We have implemented these algorithms in a software tool, NOTUNG 2.0, that can be used as a unified framework for gene tree reconstruction or as an exploratory analysis tool that can be applied post hoc to any rooted tree with bootstrap values. The NOTUNG 2.0 graphical user interface can be used to visualize alternate duplication/loss histories, root trees according to duplication and loss parsimony, manipulate and annotate gene trees, and estimate gene duplication times. It also offers a command line option that enables high-throughput analysis of a large number of trees.

Is self‐fertilization an evolutionary dead end? Revisiting an old hypothesis with genetic theories and a macroevolutionary approach

G. Ledyard Stebbins suggested that self-fertilization (selfing) may be an evolutionary dead end because it may result in the loss of genetic diversity and consequently preclude adaptation to changing environments. While the basic premise of selfing as a dead end is widely accepted, there have been few rigorous evaluations of the hypothesis. We examine the foundations of the dead-end hypothesis by considering theoretical advances in the study of mating-system evolution. We discuss theories predicting the irreversibility of self-fertilization and the extinction of selfing lineages through the loss of adaptive potential and genetic degradation. In the second portion of the review, focusing on the irreversibility of selfing, we summarize the contribution of phylogenetic studies of mating-system evolution to determine if evolutionary history supports this well-established hypothesis. Most studies are in accord with the hypothesis; no single study unequivocally demonstrates the transition from highly selfing to outcrossing lineages. Finally, we discuss the problems encountered when phylogenetic studies rely on reconstruction of ancestral mating systems. To avoid some of these problems, we applied likelihood ratio tests of irreversibility of mating-system evolution to several data sets and found that current data sets are probably too small for this test.

Mating-system evolution in flowering plants: micro- and macroevolutionary approaches*

SUMMARY The hermaphroditism of most plants and their reliance on vectors for pollen dispersal complicates mating patterns in comparison with most animal groups. Since Darwin's early work there has been considerable interest in the causes and consequences of self- and cross-fertilization in plant populations. Most research on this topic has been ahistorical in perspective and conducted almost exclusively within a selectionist framework. It is suggested that a broadened view encompassing both micro- and macroevolutionary analysis is necessary for a comprehensive understanding of how and why mating systems evolve from one state to another. An attempt to illustrate the diverse approaches that can be used in studying mating-system evolution in flowering plants is presented using the heterostylous, aquatic genus Eichhornia as a model system. Evidence from molecular phylogenetic reconstruction, large-scale surveys of geographical variation and manipulations of experimental populations are used to address the issue of how often the shift from outcrossing to selfing has occurred and what evolutionary mechanisms are involved. Results indicate that selfing has originated on several occasions in the genus and that interactions between genetic drift and natural selection cause destabilization of heterostyly and the evolution of predominant self-fertilization. It is argued that geographical patterns of intraspecific variation in reproductive traits are likely to provide the critical link between micro- and macroevolutionary approaches to the study of plant mating systems.

Spiritual Foundations for an Ecologically Sustainable Society

This article takes a broad macroevolutionary approach to our changing relationship to Nature in the light of the teachings or the Bahá’í Faith. It suggests that humanity is in a process of evolving consciousness leading to the development of a new planetary culture based on spiritual principles. In an ecological sense, humanity has in many respects appeared to be a delinquent species running out of control. Within a larger vision of humanity’s spiritual and social evolution, however, the present environmental crisis and the race’s reaction to it can be seen as portending a momentous transformation. The process of evolving consciousness that can be discerned in emerging knowledge in physics, ecology, psychology, and other fields of science is leading to the possibility of a mature cooperative relationship between humanity and the ecosphere which gave it birth. After a brief overview of the current range of responses to environmental issues and the view of Nature on which they are based, this article will explore the basic attitudes to Nature contained within the Bahá’í writings. The second part of the article examines how the emergence of an ecologically sustainable social order is linked to basic principles of the Bahá’í Faith. Implicit throughout is the Bahá’í view of the balance and cohesion of material and spiritual realities. * An earlier version of this article appeared in the Journal of Bahá’í Studies 2.1 (1989): 33–57. A special pamphlet version was co-published with the Bahá’í International Community–Office of the Environment and was distributed at the 1992 Earth Summit in Brazil. The updated version in this issue was prepared for Bahá’í World Yearbook 1992-93.

Coevolution: A History of the Macroevolutionary Approach to Studying Host-Parasite Associations

The year 1991 marked 100 yr of coevolution research. I have reviewed the first 90 yr of this history. Three chronological phases are apparent: recognition of predictable associations among hosts and their parasites; search for patterns of association and their underlying causes, emphasizing either correlated biogeographic patterns or correlated phylogenies; and development of objective and repeatable methodologies for reconstructing and interpreting these patterns of association. Von Ihering, an outspoken anti-Darwinian, was undoubtedly the first to recognize and make use of predictable host-parasite associations. Kellogg and Fahrenholz, however, had more profound influence on subsequent generations, but in different directions. Kellogg attempted to meld natural selection with speciation by isolation. He also considered host specificity a component of coevolution, important but variable. His work laid the foundation for future research concentrated on biogeographic interpretations of host-parasite relationships. This emphasis and Metcalf's failed attempts to provide adequate mechanisms for reconstructing phylogenies reduced the biogeographic approach to an empirical research program in the hands of Manter. Fahrenholz, on the other hand, exposed to a strong anti-Darwinian sentiment, emphasized the importance of strict host specificity. This led to Eichler's formulation of the first 3 coevolutionary rules and the conclusion that host specificity was not a component but the cause of coevolution and ultimately the tautology inherent in the phylogenetic approach. All had to rely on 1 assumption, that host and parasite phylogenies were reflected in the taxonomic hierarchy. Hennig criticized this assumption and provided a method whereby phylogenies are reconstructed independently. Brooks melded this new phylogenetic method (cladistics) with an equally new biogeographic method (vicariance biogeography), providing the foundations for the modern macroevolutionary approach to studying host-parasite associations.

Spiritual Foundations for an Ecologically Sustainable Society

This paper takes a broad macroevolutionary approach to our changing relationship to Nature in light of the teachings of the Baha'i Faith. It suggests that humanity is perhaps, after all, not a delinquent species running out of control but is at the very centre of a vast growth process clearly approaching a tremendous transition. Drawing on the teachings of the Baha'i Faith as well as on emerging knowledge in physics, ecology, and psychology, it suggests humanity is in a process of evolving consciousness that is leading to the birth of a new planetary culture. This process subsumes the development of a mature cooperative relationship between humanity and the ecosphere that gave it birth. This examination and synthesis will be accomplished in two parts. In the first part the basic attitudes to Nature that are contained within the Baha'i Writings will be explored and explicated. The second part will examine how the emergence of an ecological consciousness is linked to basic principles of the Baha'i Faith. These principles will be related to tenets for an ecological society being advanced by contemporary social commentators. Implicit throughout is the Baha'i view of the balance and cohesion of material and spiritual realities in approaching every question, whether it be environmental policy, agriculture, development, health, or peace. All areas of human endeavor are interrelated and require an integrated understanding of human purpose. This paper lays no claim to being an authoritative Baha'i position and should be regarded as a preliminary attempt of one mind to grasp some of the deeper meanings latent in the voluminous writings of the Baha'i Faith. Through this attempt it is hoped the reader will be led to a deeper understanding of current environmental dilemmas and will be offered a vision of profound change for which the current crises may be viewed as "forcing functions." As idealistic as this may seem, in this day only the visionary is pragmatic.

Organizational Ecology

Recent research on organizational ecology is reviewed. Three levels of analysis and approaches to evolution are distinguished: (a) the organizational level, which uses a developmental approach; (b) the population level. which uses a selection approach; and (c) the community level, which uses a macroevolutionary approach. Theoretical and empirical research is critiqued within this framework. Proposals to develop organizational taxonomies are considered.