The tree, the network, and the species

To enrich the Hennigian internodal conception of species, a new formalization of the definition of the species concept is proposed. This rigorous definition allows for considerable unification of the various, and sometimes conflicting, techniques of species delimitation used in practice. First, the domain of such a definition is set out, namely, the set of all organisms on Earth, past, present, and future. Next, the focus is on the genealogical relationship among organisms, which provides the key to analysing the giant or global genealogical network (GGN) connecting all these organisms. This leads to the construction of an algorithm revealing the topological structure of the GGN, from families to lineages, ending up with a definition of species as equivalence classes of organisms corresponding to branches of the 'tree of life'. Such a theoretical definition of the species concept must be accompanied by various recognition criteria to be operational. These criteria are, for example, the ill-named 'biological species concepts', 'phylogenetic species concepts', etc., usually, but wrongly, presented as definitions of the species concept. Besides clarifying this disputed point, the definition in the present study displays the huge diversity of the scales (time-scale and population size) involved in actual species, thus explaining away the classical problems raised by previous attempts at defining the species concept (uniparental reproduction, temporal depth of species, and hybridization).  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 509–521.     

Glossopteridae, Angiospermidae and the evidence for angiosperm origin

The reproductive units of the Glossopteridae are unisexual gonophylls, some with the potential for direct conversion into angiosperm flowers. Compound fructifications in both major taxa may be anthostrobili or the newly defined anthofasciculi. The enclosure of ovules in the angiosperm manner, but with extrorse orientation, places the beginning of angiospermy in the Permian. A few angiosperm gynoecia are extrorse. The presence of the leaf + branch berberoid unit is traced throughout the plant and accounts for the presence of protostelic bundles in the ventral traces and other parts of the flower. This evidence invalidates the carpel theory, but supports the gonophyll theory. The extensive evidence for relationship from reproductive organs is supported by leaf and petal venation patterns forming a continuous series linking the two taxa.     

Physical violence,child abuse,and child homicide

The study of child abuse and child homicide has been based on the often implicit assumption that there is a continuum of violence ranging from mild physical punishment to severe abuse and homicide. Empirical data supporting this assumption are sparse. Existing data can be shown, however, to support an assumption that there are distinct forms of violence, not a continuum. This paper reviews these data and discusses their implications for the study of violence, abuse, and homicide in terms of substantive and methodological explanations. In addition, the implications of the assumption that violence consists of distinct behaviors as opposed to a continuum are discussed in light of sociobiological and evolutionary explanations of child abuse and child homicide. This paper was written under the auspices of the Family Violence Research Program at the University of Rhode Island. A complete list of books and articles is available upon request. Richard J. Gelles is Professor of Sociology and Anthropology and the Director of the Family Violence Research Program at the University of Rhode Island. He is the author or coauthor of 14 books and more than 90 articles and chapters on family violence. His most recent books areIntimate Violence, published in 1988 by Simon and Schuster;Physical Violence in American Families: Risk Factors and Adaptations in 8,145 Families, published by Transaction Books in 1990; andIntimate Violence in Families, published in 1990 by Sage Publications.     

Strategies, Conflict, and the Emergence of Territoriality: The Case of the Maine Lobster Industry

In this article, we use game theory to understand the emergence of various kinds of territorial arrangements in the Maine lobster fishery during the past century. Using the Nash equilibria of models of the fishery as our theoretical framework, we show that informal territorial arrangements in this fishery went through three sequential stages. These stages are the result of decisions by groups of lobster fishermen to defend fishing areas or invade those of other groups. A large number of factors influence these defensive and offensive strategies: concentrations of lobsters, the adoption of better technology, transportation costs, ecological changes, trap monitoring costs, the ability to organize defensive and offensive groups, and better law enforcement---all of which are captured by crucial parameters of our model. We argue that this technique can be applied to elucidate territorial changes more generally.     

What people prefer and what they think they prefer in short- and long-term partners. The effects of the phase of the menstrual cycle,hormonal contraception,pregnancy, and the marital and the parenthood status on partner preferences

The issue with most studies concerned with mate selection preferences in humans is that they rely on declarations and rational actions of experimental subjects, which are affected by their pre-conceived opinions and prejudices. Moreover, current research suggests that subcortical structures and processes, rather than the neocortex, play the principal role in actual partner choice behaviour. Consequently, we have only limited information on how relevant our current knowledge is in relation to real-life human ethology. To address these issues, we surveyed 2718 women and 4073 men between the ages of 16–50 and compared their declared and observed preferences for various properties in short-term and long-term partners. We found differences between what the subjects declared to prefer and what they preferred in reality: for example, men declared that wealth was the second least desirable property out of eleven in short-term partners, but we observed that in reality, they considered wealth the third most important factor after charisma and sense of humour. Similarly, while women declared that dominance and masculinity were desirable properties in short-term partners, in the observational part of the study, they showed little preference for these traits. Furthermore, we investigated the effects of the phase of the menstrual cycle, hormonal contraception, pregnancy, and partnership and parenthood status on these preferences. We found some support for the good parents hypothesis and no support for the good genes and the immunocompetence handicap hypotheses when observed, rather than declared preferences were considered. We also detected that hormonal contraception, and parenthood and partnership status influenced declared preferences in considerable ways, but had only a small, if any, impact on observed preferences. We suggest interpreting the results of studies reliant on declarations and rational actions of experimental subjects with great caution.     

The K-factor,Covitality, and personality

We present a psychometric test of life history theory as applied to human individual differences using MIDUS survey data (Brim et al. 2000). Twenty scales measuring cognitive and behavioral dimensions theoretically related to life history strategy were constructed using items from the MIDUS survey. These scales were used to construct a single common factor, the K-factor, which accounted for 70% of the reliable variance. The scales used included measures of personal, familial, and social function. A second common factor, Covitality, was constructed from scales for physical and mental health. Finally, a single general factor, Personality, was constructed from scales for the “Big Five” factors of personality. The K-factor, covitality factor, and general personality factor correlated significantly with each other, supporting the prediction that high K predicts high somatic effort and also manifests in behavioral display. Thus, a single higher-order common factor, the Super-K factor, was constructed that consisted of the K-factor, covitality factor, and personality factor.     

Sodium,protons, and energy coupling in the methanogenic bacteria

In this review, I focus on the bioenergetics of the methanogenic bacteria, with particular attention directed to the roles of transmembrane electrochemical gradients of sodium and proton. In addition, the mechanism of coupling ATP synthesis to methanogenic electron transfer is addressed. Evidence is reviewed which suggests that the methanogens possess great diversity in their bioenergetic machinery. In particular, in some methanogens the primary ion which is translocated coupled to metabolic energy is the proton, while others appear to utilize sodium. In addition, ATP synthesis driven by methanogenic electron transfer is accomplished in some organisms by a chemiosmotic mechanism and is coupled by a more direct mechanism in others. A possible explanation for this diversity (which is consistent with the relatedness of these organisms to each other and to other members of the Archaebacteria as determined by molecular biological techniques) is discussed.     

Construction and maintenance of the optimal photosynthetic systems of the leaf, herbaceous plant and tree: an eco-developmental treatise

BACKGROUND AND AIMS: The paper by Monsi and Saeki in 1953 (Japanese Journal of Botany 14: 22-52) was pioneering not only in mathematical modelling of canopy photosynthesis but also in eco-developmental studies of seasonal changes in leaf canopies. SCOPE: Construction and maintenance mechanisms of efficient photosynthetic systems at three different scaling levels--single leaves, herbaceous plants and trees--are reviewed mainly based on the nitrogen optimization theory. First, the nitrogen optimization theory with respect to the canopy and the single leaf is briefly introduced. Secondly, significance of leaf thickness in CO2 diffusion in the leaf and in leaf photosynthesis is discussed. Thirdly, mechanisms of adjustment of photosynthetic properties of the leaf within the herbaceous plant individual throughout its life are discussed. In particular, roles of sugar sensing, redox control and of cytokinin are highlighted. Finally, the development of a tree is considered. CONCLUSIONS: Various mechanisms contribute to construction and maintenance of efficient photosynthetic systems. Molecular backgrounds of these ecologically important mechanisms should be clarified. The construction mechanisms of the tree cannot be explained solely by the nitrogen optimization theory. It is proposed that the pipe model theory in its differential form could be a potential tool in future studies in this research area.     

Explaining the global biodiversity gradient: energy, area, history and natural selection

Hubbell's neutral theory of biodiversity is used to investigate the decline in species richness from the tropics to the poles. On this basis, biodiversity should correlate with productivity or climate (there is strong statistical evidence for this), with the latitudinal width of the continents (insufficiently investigated as yet), and with the speciation rate (which may not vary in such a way as to produce a planetary gradient). According to the neutral, model biodiversity will vary with the area of the “metacommunity”: it is suggested that at higher latitudes species disperse most readily east–west, within their climatic belt, but that the relatively uniform temperature across the intertropical belt allows isotropic dispersal there. Metacommunities within the tropics may therefore be an order of magnitude larger than those at other latitudes. This could explain the extra bulge in the gradient in the tropics. It is further possible that long-term and cyclical climate change generates a tropic-pole gradient. Niche assembly models will also explain tropical biodiversity, but the enhanced division of habitat may be the result, not the cause, of the species richness. The neutrality–competition debate in ecology closely parallels the neutrality–natural selection debate in evolution and may be equally hard to resolve.

Zusammenfassung

Hubbells neutrale Theorie der Biodiversität wird genutzt um den Rückgang des Artenreichtums von den Tropen zu den Polen zu untersuchen. Auf dieser Basis sollte die Biodiversität mit der Produktivität oder dem Klima (es gibt überzeugende statistische Beweise dafür) korrelieren, mit der Ausdehnung der Kontinente in geografischer Breite (bisher unzureichend untersucht) und mit der Artbildungsrate (welche möglicherweise nicht in der Weise variiert, als dass sie einen planetarischen Gradienten erzeugen kann).Dem neutralen Model entsprechend wird die Biodiversität mit dem Areal der “Metagemeinschaft” variieren. Es wird behauptet, dass sich Arten in höheren Breiten am leichtesten innerhalb ihres klimatischen Gürtels in Ost–West-Richtung ausbreiten, dass aber die relativ gleichmäßige Temperatur des innertropischen Gürtels dort eine isotrope Ausbreitung erlaubt.Metagemeinschaften in den Tropen können daher um eine Größenordnung größer sein als in anderen Breiten. Dies könnte die zusätzliche Ausdehnung des Gradienten in den Tropen erklären. Es ist darüber hinaus möglich, dass langfristige und zyklische Klimaveränderungen einen Gradienten von den Tropen zu den Polen generieren. Modelle der Nischenanordnung erklären ebenfalls tropische Biodiversität. Die verstärkte Habitataufteilung könnte jedoch das Ergebnis und nicht der Grund des Artenreichtums sein. Die Neutralitäts–Konkurrenz-Debatte in der Ökologie ähnelt sehr der Neutralitäts–Selektions-Debatte in der Evolution und mag ähnlich schwer zu lösen sein.     

Information Theory in Living Systems,Methods, Applications,and Challenges

Living systems are distinguished in nature by their ability to maintain stable, ordered states far from equilibrium. This is despite constant buffeting by thermodynamic forces that, if unopposed, will inevitably increase disorder. Cells maintain a steep transmembrane entropy gradient by continuous application of information that permits cellular components to carry out highly specific tasks that import energy and export entropy. Thus, the study of information storage, flow and utilization is critical for understanding first principles that govern the dynamics of life. Initial biological applications of information theory (IT) used Shannon’s methods to measure the information content in strings of monomers such as genes, RNA, and proteins. Recent work has used bioinformatic and dynamical systems to provide remarkable insights into the topology and dynamics of intracellular information networks. Novel applications of Fisher-, Shannon-, and Kullback–Leibler informations are promoting increased understanding of the mechanisms by which genetic information is converted to work and order. Insights into evolution may be gained by analysis of the the fitness contributions from specific segments of genetic information as well as the optimization process in which the fitness are constrained by the substrate cost for its storage and utilization. Recent IT applications have recognized the possible role of nontraditional information storage structures including lipids and ion gradients as well as information transmission by molecular flux across cell membranes. Many fascinating challenges remain, including defining the intercellular information dynamics of multicellular organisms and the role of disordered information storage and flow in disease.     

Hubrecht,Macfarlane, Jensen and Willmer: on the nature and testability of four versions of the nemertean theory of vertebrate origins

Four authors (A. A. W. Hubrecht, J. M. Macfarlane, D. D. Jensen and E. N. Willmer) have argued that nemerteans are the proximal invertebrate ancestors of vertebrates. While all these authors accept certain homologies (i.e. vertebrate pituitary and notochord with nemertean proboscis invagination and proboscis sheath or mesoderm), there is considerable variation among them in the derivation of the vertebrate nervous system, sense organs and foregut apertures. For example, Hubrecht suggests that the vertebrate nervous system developed from a solid dorsal nerve found in some nemerteans; Macfarlane suggests it developed by fusion of the left and right solid brains of nemerteans; Jensen suggests that the vertebrate tubular nervous system developed by the backward extension of the nemertean frontal organ and fusion with the nemertean dorsal and ventral brain ganglia. Modern EM, histochemical and biochemical methods can test empirically the four theories. Research testing these theories will also test the more popular acraniate theory, since that theory implies that vertebrate head structures evolved de novo in chordates and that no homologies should exist between vertebrate and nemertean head structures.     

从顶枝学说、中柱学说和子叶节区学说看维管植物的形态演化和起源

作者对当前植物形态学中与维管植物的形态演化和起源有着十分密切关系的顶枝学说,中柱学说与子叶节区学说进行了全面研究。并结合半个多世纪以来国际上著名的植物系统学家的维管植物分类系统,反复进行了比较和研究,对其中认为不妥之处提出了我们的见解,具体反映在文后的“维管植物系统的系统发育图”中。     

Identifying potential conservation areas in the Cuitzeo Lake basin,Mexico by multitemporal analysis of landscape connectivity

Lake Cuitzeo basin is an important ecological area subjected to strong human pressure on forest covers that are key elements for the long-term support of biodiversity. We studied landscape connectivity changes for the years 1975, 1996, 2000, 2003 and 2008 to identify potential conservation areas in the basin. We modeled potential distributions of the Mexican bobcat (Lynx rufus escuinapae) and the ringtail (Bassariscus astutus) – two terrestrial mammal focal species with contrasting dispersal capacities – and we determined their habitat availability and suitability in the basin. We then identified their optimal habitat patches and produced landscape cumulative resistance maps, estimated least-cost paths (graph theory approach), and elaborated current flow maps (circuit theory approach). For evaluation of landscape connectivity, we applied an integral index of connectivity (IIC) to each study period, and determined individual habitat patch contribution to the overall landscape connectivity. The IIC index had very low values associated with reduced availability of focal species habitat. However, our study showed the conservation importance of the surface of optimal habitat patch areas. The combined application of a graph-based approach and current flow mapping were useful, and complementary both in terms of estimating potential dispersal corridors and identifying high probability dispersal areas. This indicated that landscape connectivity analysis is a useful tool for identification of potential conservation areas and for local landscape planning.     

Biodiversity, ecosystem functioning and food webs in fresh waters: assembling the jigsaw puzzle

1. Dramatic advances have been made recently in the study of biodiversity–ecosystem functioning (B-EF) relations and food web ecology. These fields are now starting to converge, and this fusion has the potential to improve our understanding of how environmental stressors modulate ecosystem processes and the supply of 'goods and services'.
2. Food web structure and dynamics can exert particularly strong influences on B-EF relations in fresh waters, as consumer–resource interactions (e.g. trophic cascades) are often more important than horizontal interactions within trophic levels. For instance, many freshwater food webs are size structured, with large organisms tending to occupy the higher trophic levels and often exerting powerful effects on ecosystem processes. However, because they are also vulnerable to perturbations, non-random losses of these large taxa can alter both food web structure and ecosystem functioning profoundly.
3. Recently, the focus of food web research has shifted away from exploring patterns, towards developing an understanding of processes (e.g. quantifying fluxes of individuals, biomass, energy, nutrients) and how the two interact. Many of the best-characterized food webs are from fresh waters, and these ecosystems are now being used to address some of the shortcomings of earlier B-EF studies. I have identified several key gaps in our current knowledge and highlighted potentially fruitful avenues of future B-EF and food web research.
4. A major challenge for this newly emerging research is to place it within a unified theoretical framework. The application of metabolic theory and ecological stoichiometry may help to achieve this goal by considering biological systems within the constraints imposed upon them by physical and chemical laws.     

Signaling,solidarity, and the sacred: The evolution of religious behavior

Anthropologists have repeatedly noted that there has been little theoretical progress in the anthropology of religion over the past fifty years.^1–7 By the 1960s, Geertz² had pronounced the field dead. Recently, however, evolutionary researchers have turned their attention toward understanding the selective pressures that have shaped the human capacity for religious thoughts and behaviors, and appear to be resurrecting this long‐dormant but important area of research.^8–19 This work, which focuses on ultimate evolutionary explanations, is being complemented by advances in neuropsychology and a growing interest among neuroscientists in how ritual, trance, meditation, and other altered states affect brain functioning and development.^20–26 This latter research is providing critical insights into the evolution of the proximate mechanisms responsible for religious behavior. Here we review these literatures and examine both the proximate mechanisms and ultimate evolutionary processes essential for developing a comprehensive evolutionary explanation of religion.     

Stochasticity, complex spatial structure, and the feasibility of the shifting balance theory

Sewall Wright's shifting balance theory of evolution posits a mechanism by which a structured population may escape local fitness optima and find a global optimum. We examine a one-locus, two-allele model of underdominance in populations with differing spatial arrangements of demes, both analytically and with Monte Carlo simulations. We find that inclusion of variance in interpatch connectivities can significantly reduce the number of generations required for fixation of the more favorable allele relative to island and stepping-stone models. Although time to fixation increases with migration rate in all cases, the presence of one or two relatively isolated demes may reduce the number of generations by 80% or more. These results suggest that the shifting balance process may operate under less restrictive conditions than those found with a simple spatial arrangement of demes.     

Movement patterns, social dynamics, and the evolution of cooperation

The structure of social interactions influences many aspects of social life, including the spread of information and behavior, and the evolution of social phenotypes. After dispersal, organisms move around throughout their lives, and the patterns of their movement influence their social encounters over the course of their lifespan. Though both space and mobility are known to influence social evolution, there is little analysis of the influence of specific movement patterns on evolutionary dynamics. We explored the effects of random movement strategies on the evolution of cooperation using an agent-based prisoner’s dilemma model with mobile agents. This is the first systematic analysis of a model in which cooperators and defectors can use different random movement strategies, which we chose to fall on a spectrum between highly exploratory and highly restricted in their search tendencies. Because limited dispersal and restrictions to local neighborhood size are known to influence the ability of cooperators to effectively assort, we also assessed the robustness of our findings with respect to dispersal and local capacity constraints. We show that differences in patterns of movement can dramatically influence the likelihood of cooperator success, and that the effects of different movement patterns are sensitive to environmental assumptions about offspring dispersal and local space constraints. Since local interactions implicitly generate dynamic social interaction networks, we also measured the average number of unique and total interactions over a lifetime and considered how these emergent network dynamics helped explain the results. This work extends what is known about mobility and the evolution of cooperation, and also has general implications for social models with randomly moving agents.     

Genetic hitchhiking,mitonuclear coadaptation,and the origins of mt DNA barcode gaps

DNA barcoding based on mitochondrial (mt) nucleotide sequences is an enigma. Neutral models of mt evolution predict DNA barcoding cannot work for recently diverged taxa, and yet, mt DNA barcoding accurately delimits species for many bilaterian animals. Meanwhile, mt DNA barcoding often fails for plants and fungi. I propose that because mt gene products must cofunction with nuclear gene products, the evolution of mt genomes is best understood with full consideration of the two environments that impose selective pressure on mt genes: the external environment and the internal genomic environment. Moreover, it is critical to fully consider the potential for adaptive evolution of not just protein products of mt genes but also of mt transfer RNAs and mt ribosomal RNAs. The tight linkage of genes on mt genomes that do not engage in recombination could facilitate selective sweeps whenever there is positive selection on any element in the mt genome, leading to the purging of mt genetic diversity within a population and to the rapid fixation of novel mt DNA sequences. Accordingly, the most important factor determining whether or not mt DNA sequences diagnose species boundaries may be the extent to which the mt chromosomes engage in recombination.     

黄土高原腹地人工林下草本层群落构建机制

群落构建机制是生态学研究的核心论题。生态位理论和中性理论是阐明群落构建的两种主要理论, 但这两种理论分别强调的环境过滤和扩散限制对群落构建的影响尚存争议。该研究以黄土高原人工林下草本层群落为研究对象, 将群落物种组成数据与地理空间、气候、地形以及生物因子相结合, 运用随机森林模型(RF)和基于距离矩阵的多元回归方法(MRM), 探究了各个因子的重要性, 并通过邻体主坐标矩阵(PCNM)和基于距离的冗余分析(db-RDA)分别筛选显著的空间结构和环境因子, 最后结合筛选出的PCNM特征值和环境变量进行变差分解。研究结果显示: 1)林下草本层群落组成相似性随地理距离和生境差异的增加而减小。2)地理距离与生境差异共同解释了群落组成相似性变化的47.8%。其中, 空间因子和环境因子的独立解释率分别为14.1%和9.8%, 两者的联合解释率为23.9%。3)地理距离和年降水量是引起研究区内物种组成变化的关键因子, 且地理距离的重要性大于年降水量。在黄土高原腹地, 扩散限制与环境过滤共同主导了人工林下草本层群落的构建过程。