The Loss of Genetic Diversity in Sichuan Taimen as Revealed by DNA Fingerprinting

Species endangerment often derives from the “endangerment” of genetic diversity, thus loss of genetic diversity is an important cause of species extinction. Since historical specimens were unavailable, previous studies mainly described the genetic diversity status in the current population rather than the loss of genetic variation over time. In this study, we collected samples during1998–1999 and obtained historical specimens from 1957 to 1958. Based on the two sets of fish, we determined the changes in genetic diversity of Sichuan taimen using DNA fingerprinting. The differences in genetic parameters between the present samples and historical taimens revealed their loss of genetic variation. As a result, the existing populations have lower viability, and proper management has to be implemented to preserve genetic diversity.     

Associations between floral specialization and species diversity: cause, effect, or correlation?

It has been proposed frequently, from Darwin’s time onwards, that specialized pollination increases speciation rates and thus the diversity of plant species (i.e. clade species richness). We suggest here that the correlation between clade species richness and floral specialization is real, but that clade species richness is frequently the cause, not the result of floral specialization. We urge a broader, variance-partitioning perspective for assessing the causes of this correlation by suggesting four models of how the diversity-specialization correlation might come about: (1) floral specialization promotes initial reproductive isolation (“Initial-RI” model), (2) floral specialization promotes reinforcement of reproductive isolation upon secondary contact (“Reinforcement” model), (3) floral specialization reduces the extinction rate by promoting tighter species packing (“Extinction” model), (4) floral specialization is the result of high clade species richness, which increases the number of related species in communities, and thus selects for floral character displacement (“Character-Displacement” model). These hypotheses are evaluated by comparing the relationships between species richness, speciation mechanisms, and pollination precision, accuracy, and specialization in the broader literature and, more specifically, in four study systems: Dalechampia (Euphorbiaceae), Collinsia (Plantaginaceae), Burmeistera (Campanulaceae), and Stylidium (Stylidiaceae). These systems provide stronger support for the character-displacement hypothesis, wherein local species diversity drives the evolution of specialized pollination. Although the two reproductive-isolation hypotheses may hold for plants like orchids, with extremely precise pollination systems, the reproductive character-displacement hypothesis seems likely to be more important for plant groups with less precise pollination systems.     

Interplay between humans and infective agents: a population genetic study

The genetic composition of present day human populations is determined largely by the interaction between the human host and infective agents. Therefore, theoretical analysis of the host-infective-agent system is required in order for us to be able to understand human evolution. Classical population genetics has been confined largely to analysing the interplay of various mechanisms, such as selection, mutation and drift, in one species at a time. Unfortunately, there have been few studies of such interactive systems. In the present investigation, these studies have been enlarged, with problems of human genetics in mind, by mathematical examination of a model in which a diploid host with three alleles interacts with a haploid infective agent with two alleles. The results are compared with those obtained from simpler models analysed in the past. The assumptions inherent in such “gene for gene” models and our results are discussed. An increase in the number of alleles appears to enhance the chances for the establishment of permanent genetic polymorphisms, improving genetic “elasticity” of a population for coping with changing challenges by various infective agents. Interaction between two haploid species leads to a loss of polymorphism in both of them and, hence, to a severe loss of evolutionary elasticity. The hypothesis that the evolution of diploidy might have been favoured by a selective advantage of diploid organisms interacting with environmental challenges, such as infective agents, is supported. Received: 6 October 1997 / Accepted: 26 November 1997     

Sexes,species, and genomes: why males and females are not like humans and chimpanzees

This paper describes, analyzes, and critiques the construction of separate “male” and “female” genomes in current human genome research. Comparative genomic work on human sex differences conceives of the sexes as like different species, with different genomes. I argue that this construct is empirically unsound, distortive to research, and ethically questionable. I propose a conceptual model of biological sex that clarifies the distinction between species and sexes as genetic classes. The dynamic interdependence of the sexes makes them “dyadic kinds” that are not like species, which are “individual kinds.” The concept of sex as a “dyadic kind” may be fruitful as a remedy to the tendency to conceive of the sexes as distinct, binary classes in biological research on sex more generally.     

Osteoporosis: an evolutionary perspective

Increased life expectancy has led to an overall aging of the population and greater numbers of elderly people. Therefore, the number of people with osteoporosis has increased substantially, accompanied with an epidemic of hip fractures. Osteoporosis is an age-related systemic condition that naturally occurs, among mammals, only in humans. Osteoporosis is known to be highly heritable. However, assuming a genetic determinant for this post-reproductive disease to be transmitted from one generation to the next is counter-intuitive, based on the principles of human evolution, I will attempt to provide an explanation of the phenomenon from the point of view of evolution, selection, and changed environment in humans, which contributed to human longevity, while on other hand, contribute to diseases of civilization, including osteoporosis. There is a need to delve into evolution of human species in search for adaptive patterns to a specific environment that humans are operating in the last couple of millennia, to clarify whether “good” and “bad” genes exist, and how to find and correct them. The answer to the above questions will help us to identify causes of the current epidemic of osteoporosis and to pin-point a tailored treatment.     

The advantages and disadvantages of being introduced

Introduced species, those dispersed outside their natural ranges by humans, now cause almost all biological invasions, i.e., entry of organisms into habitats with negative effects on organisms already there. Knowing whether introduction tends to give organisms specific ecological advantages or disadvantages in their new habitats could help understand and control invasions. Even if no specific species traits are associated with introduction, introduced species might out-compete native ones just because the pool of introduced species is very large (“global competition hypothesis”). Especially in the case of intentional introduction, high initial propagule pressure might further increase the chance of establishment, and repeated introductions from different source populations might increase the fitness of introduced species through hybridization. Intentional introduction screens species for usefulness to humans and so might select for rapid growth and reproduction or carry species to suitable habitats, all which could promote invasiveness. However, trade offs between growth and tolerance might make introduced species vulnerable to extreme climatic events and cause some invasions to be transient (“reckless invader hypothesis”). Unintentional introduction may screen for species associated with human-disturbed habitats, and human disturbance of their new habitats may make these species more invasive. Introduction and natural long-distance dispersal both imply that species have neither undergone adaptation in their new habitats nor been adapted to by other species there. These two characteristics are the basis for many well-known hypotheses about invasion, including the “biotic resistance”, “enemy release”, “evolution of increased competitive ability” and “novel weapon” hypotheses, each of which has been shown to help explain some invasions. To the extent that biotic resistance depends upon local adaption by native species, altering selection pressures could reduce resistance and promote invasion (“local adaptation hypothesis”), and restoring natural regimes could reverse this effect.     

“Green water” microalgae: the leading sector in world aquaculture

Freshwater fish culture is generally considered the largest sector in world aquaculture. Several of the leading species consume “green water” plankton. This plankton—mostly microalgae (phytoplankton) and also bacteria, protozoa and zooplankton—grows in man-made fertilized water impoundments. The quantity of “green water” microalgae consumed by fish and shrimp is estimated here at a quarter billion ton fresh weight a year, about three and a half times as much as the entire recognized aquaculture. This estimate is based on the quantities of the microalgae consumed and the efficiencies of their use for growth by the main species in aquaculture. The cost of producing “green water” microalgae by the aquaculturists—mostly in SE Asia—is low. The populations in “green water” are biologically managed by the cultured fish themselves. The fish with their different feeding habits help “manage” the composition of the plankton and the overall water quality as they grow. The aquaculturists further manage “green water” through simple means, including water exchange and fertilization. Cost is remunerated partially by the income from sales of the fish and partially by bio mitigation services that “green water” polyculture ponds provide the aquaculturists in treating farm and household waste. A comprehension of the scale and importance of the microalgae sector to world aquaculture should lead to more research to improve understanding of algal population dynamics, growth factors, and efficiency of food chains. The consequent improved control of the plankton’s interaction with fish and shrimp production in “green water” will undoubtedly contribute much to the expansion in production of seafood.     

Pulses of movement across the sea ice: population connectivity and temporal genetic structure in the arctic fox

Lemmings are involved in several important functions in the Arctic ecosystem. The Arctic fox (Vulpes lagopus) can be divided into two discrete ecotypes: “lemming foxes” and “coastal foxes”. Crashes in lemming abundance can result in pulses of “lemming fox” movement across the Arctic sea ice and immigration into coastal habitats in search for food. These pulses can influence the genetic structure of the receiving population. We have tested the impact of immigration on the genetic structure of the “coastal fox” population in Svalbard by recording microsatellite variation in seven loci for 162 Arctic foxes sampled during the summer and winter over a 5-year period. Genetic heterogeneity and temporal genetic shifts, as inferred by STRUCTURE simulations and deviations from Hardy–Weinberg proportions, respectively, were recorded. Maximum likelihood estimates of movement as well as STRUCTURE simulations suggested that both immigration and genetic mixture are higher in Svalbard than in the neighbouring “lemming fox” populations. The STRUCTURE simulations and AMOVA revealed there are differences in genetic composition of the population between summer and winter seasons, indicating that immigrants are not present in the reproductive portion of the Svalbard population. Based on these results, we conclude that Arctic fox population structure varies with time and is influenced by immigration from neighbouring populations. The lemming cycle is likely an important factor shaping Arctic fox movement across sea ice and the subsequent population genetic structure, but is also likely to influence local adaptation to the coastal habitat and the prevalence of diseases.     

Ecological explanations for successful invasion of exotic plants

The intentional introduction of exotic species can increase the level of local biodiversity, enrich people’s material lives, and bring significant social and economic benefits that are also the symbols of human progress. However, along with the frequent intercourse among countries and regions, the frequency of uncontrolled crossregional migration of species is increased and there is a lack of scientific management strategy for the intentional introduction of exotic species. Exotic species invasion, which is behind habitat fragmentation, has become the second largest threatening factor to the maintenance of the global-scale level of biological diversity. Exotic species invasion can destroy the structure of an ecosystem, disturb the economic life of a society, and do harm to human health. In this paper, the authors review some of the ecological explanations for issues such as “what causes or mechanisms have led to the successful invasion of exotic species”, including the “ideal weeds characteristics”, “biodiversity resistance hypothesis”, “enemies release hypothesis”, “evolution of increased competitive ability hypothesis”, “niche opportunity hypothesis”, and “novel weapon hypothesis”. The authors also analyze and evaluate the background and theoretical basis of the hypotheses, providing explanations for some phenomena, as well as the deficiencies of these explanations.     

Edward Hitchcock’s Pre-Darwinian (1840) “Tree of Life”

The “tree of life” iconography, representing the history of life, dates from at least the latter half of the 18th century, but evolution as the mechanism providing this bifurcating history of life did not appear until the early 19th century. There was also a shift from the straight line, scala naturae view of change in nature to a more bifurcating or tree-like view. Throughout the 19th century authors presented tree-like diagrams, some regarding the Deity as the mechanism of change while others argued for evolution. Straight-line or anagenetic evolution and bifurcating or cladogenetic evolution are known in biology today, but are often misrepresented in popular culture, especially with anagenesis being confounded with scala naturae. Although well known in the mid 19th century, the geologist Edward Hitchcock has been forgotten as an early, if not the first author to publish a paleontologically based “tree of life” beginning in 1840 in the first edition of his popular general geology text Elementary Geology. At least 31 editions were published and those between 1840 and 1859 had this “paleontological chart” showing two trees, one for fossil and living plants and another for animals set within a context of geological time. Although the chart did not vary in later editions, the text explaining the chart did change to reflect newer ideas in paleontology and geology. Whereas Lamarck, Chambers, Bronn, Darwin, and Haeckel saw some form of transmutation as the mechanism that created their “trees of life,” Hitchcock, like his contemporaries Agassiz and Miller, who also produced “trees of life,” saw a deity as the agent of change. Through each edition of his book Hitchcock denounced the newer transmutationist hypotheses of Lamarck, then Chambers, and finally Darwin in an 1860 edition that no longer presented his tree-like “paleontological chart.”     

The Origin of the Vertebrate Eye

In his considerations of “organs of extreme perfection,” Charles Darwin described the evidence that would be necessary to support the evolutionary origin of the eye, namely, demonstration of the existence of “numerous gradations” from the most primitive eye to the most perfect one, where each such tiny change had provided a survival advantage (however slight) to the organism possessing the subtly altered form. In this paper, we discuss evidence indicating that the vertebrate eye did indeed evolve through numerous subtle changes. The great majority of the gradual transitions that did occur have not been preserved to the present time, either in the fossil record or in extant species; yet clear evidence of their occurrence remains. We discuss the remarkable “eye” of the hagfish, which has features intermediate between a simple light detector and an image-forming camera-like eye and which may represent a step in the evolution of our eye that can now be studied by modern methods. We also describe the important clues to the evolutionary origin of the vertebrate eye that can be found by studying the embryological development of our own eye, by examining the molecular genetic record preserved in our own genes and in the genes of other vertebrates, and through consideration of the imperfections (or evolutionary “scars”) in the construction of our eye. Taking these findings together, it is possible to discuss in some detail how the vertebrate eye evolved.     

A population facing climate change: joint influences of Allee effects and environmental boundary geometry

As a result of climate change, many populations have to modify their range to follow the suitable areas—their “climate envelope”—often risking extinction. During this migration process, they may face absolute boundaries to dispersal because of external environmental factors. Consequently, not only the position, but also the shape of the climate envelope can be modified. We use a reaction-diffusion model to analyse the effects on population persistence of simultaneous changes in the position and shape of the climate envelope. When the growth term is of logistic type, we show that extinction and persistence are principally conditioned by the species mobility and the speed of climate change, but not by the shape of the climate envelope. However, with a growth term taking an Allee effect into account, we find a high sensitivity to variations in the shape of the climate envelope. In this case, the species which have a high mobility, although they could more easily follow the migration of the climate envelope, would be at risk of extinction when encountering a local narrowing of the boundary geometry. This effect can be attenuated by a progressive opening at the exit of the narrowing into the available space, even though this leads temporarily to a diminished area of the climate envelope.     

Mammalian Faunal Dynamics During the Last 1.8 Million Years of the Cretaceous in Garfield County, Montana

This study provides an analysis of biotic change in successive mammalian communities during the last 1.8 million years of the Cretaceous (67.3–65.58 Ma) from the Hell Creek Formation in Garfield County, Montana. Results show changes in relative abundances of species, mean individual body size, and to some extent taxonomic composition through the Hell Creek Formation. These results are interpreted as “normal” mammalian responses to fluctuating temperatures during the latest Cretaceous. By contrast, the extinction of 22–27 mammalian species at or near the Cretaceous-Tertiary (K-T) boundary cannot be explained by the coincident cooling interval alone. At the scale of temporal resolution available, these fossil data are inconsistent with an extended gradual pattern of extinction (linear-response) and are most consistent with either a non-linear response pattern for the K-T extinction, resulting from the accumulated stress of multiple long- and short-term environmental perturbations (e.g., climate change, sea-level regression, volcanism, an extraterrestrial impact), or a single, short-term cause (an extraterrestrial impact).     

Evolutionary ontogenetic aspects of pathogenetics of chronic human diseases

This article is a review of scientific publications, in which issues of pathogenetics of multifactorial diseases (MFDs) are considered from the viewpoint of evolution and ontogeny. Concepts explaining significance of evolutionary processes in the formation of genetic architecture of human chronic diseases (“thrifty” genomes and phenotypes, “drifty genes,” decanalization) are analyzed. The roles of natural selection and genetic drift in the formation of hereditary diversity of genes for susceptibility to MFDs are considered. The modern concept of “disease ontogeny” (somatic mosaicism, loss of heterozygosity, paradominant inheritance, epigenetic variability) is discussed. It is demonstrated that the evolutionary and ontogenetic approaches to analysis of genimuc and other “-omic” data are essential for understanding the biology of diseases.     

Structure of the bank vole (<Emphasis Type="Italic">Myodes glareolus</Emphasis>) population cycles in the core and periphery of its species area

The results of long-term studies of two bank vole (Myodes glareolus) populations in stationary sites in the central part and periphery of its species area are described. Four phases of a multiannual population cycle and two of its structural parts have been detected for both populations. The first part of the cycle is “determined,” with the “peak” phase passing into a “depression” (population collapse). This transition is mainly determined by intrapopulation processes and is weakly dependent on the external conditions of each individual year. The second part is “stochastic,” starting from a stable point in the cycle in the depression phase. The duration of the second part is determined by the state of the population and its ability to increase its size, as well as by the weather and food factors, predation pressure, and location of the population within the species area. The transition from the peak phase to the depression phase (the determined part) for both populations takes place during one fall-winter-spring season and has no effect on the cycle duration. The duration of the stochastic part in the core of the species area (the period from depression phase to peak phase) is 1–3 years and in the periphery, 2–4 years.     

The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random

Protein evolution is not a random process. Views which attribute randomness to molecular change, deleterious nature to single-gene mutations, insufficient geological time, or population size for molecular improvements to occur, or invoke “design creationism” to account for complexity in molecular structures and biological processes, are unfounded. Scientific evidence suggests that natural selection tinkers with molecular improvements by retaining adaptive peptide sequence. We used slot-machine probabilities and ion channels to show biological directionality on molecular change. Because ion channels reside in the lipid bilayer of cell membranes, their residue location must be in balance with the membrane’s hydrophobic/philic nature; a selective “pore” for ion passage is located within the hydrophobic region. We contrasted the random generation of DNA sequence for KcsA, a bacterial two-transmembrane-domain (2TM) potassium channel, from Streptomyces lividans, with an under-selection scenario, the “jackprot,” which predicted much faster evolution than by chance. We wrote a computer program in JAVA APPLET version 1.0 and designed an online interface, The Jackprot Simulation , to model a numerical interaction between mutation rate and natural selection during a scenario of polypeptide evolution. Winning the “jackprot,” or highest-fitness complete-peptide sequence, required cumulative smaller “wins” (rewarded by selection) at the first, second, and third positions in each of the 161 KcsA codons (“jackdons” that led to “jackacids” that led to the “jackprot”). The “jackprot” is a didactic tool to demonstrate how mutation rate coupled with natural selection suffices to explain the evolution of specialized proteins, such as the complex six-transmembrane (6TM) domain potassium, sodium, or calcium channels. Ancestral DNA sequences coding for 2TM-like proteins underwent nucleotide “edition” and gene duplications to generate the 6TMs. Ion channels are essential to the physiology of neurons, ganglia, and brains, and were crucial to the evolutionary advent of consciousness. The Jackprot Simulation illustrates in a computer model that evolution is not and cannot be a random process as conceived by design creationists.     

Local genetic differentiation in Proteopsis argentea (Asteraceae), a perennial herb endemic in Brazil

 Proteopsis argentea (Asteraceae, Vernonieae) is a perennial herb endemic to the “campos rupestres” of the Espinha?o Range in Minas Gerais, Brazil, with fragmented populational distribution. Eleven populations were sampled, throughout the entire distribution of the species, and assayed for isozyme variation. Low intra-population genetic diversity was found (P = 19.2; A = 1.30; He = 0.058) whereas species level diversity was higher (P = 55.5, A = 2.0, He = 0.093). The most geographically isolated population showed exclusive alleles at two loci, whereas two populations less than 2 km apart from each other showed inverted frequencies for two alleles. Mean genetic identity was high (I = 0.974), but the large Fst (0.30) indicates that the species could lose an important part of its genetic variation with the extinction of a single population. Our findings indicate that geographic isolation alone cannot explain population differentiation: localized pollinator behaviour and selection, for example, may be contributing to the patterns observed. Received February 18, 2000 Accepted November 1, 2000     

Generic physical mechanisms of morphogenesis and pattern formation as determinants in the evolution of multicellular organization

Early embryos of metazoan species are subject to the same set of physical forces and interactions as any small parcels of semi-solid material, living or nonliving. It is proposed that such “generic” properties of embryonic tissues have played a major role in the evolution of biological form and pattern by providing an array of morphological templates, during the early stages of metazoan phylogeny, upon which natural selection could act. The generic physical mechanisms considered include sedimentation, diffusion, and reaction-diffusion coupling, all of which can give rise to chemical nonuniformities (including periodic patterns) in eggs and small multicellular aggregates, and differential adhesion, which can lead to the formation of boundaries of non-mixing between adjacent cell populations. Generic mechanisms that produce chemical patterns, acting in concern with the capacity of cells to modulate their adhesivity (presumed to be a primitive, defining property of metazoa), could lead to multilayered gastrulae of various types, segmental organization, and many of the other distinguishing characteristics of extant and extinct metazoan body plans. Similar generic mechanisms, acting on small tissue primordia during and subsequent to the establishment of the major body plans, could have given rise to the forms of organs, such as the vertebrate limbs. Generic physical processes acting on a single system of cells and cell products can often produce a widely divergent set of morphological phenotypes, and these are proposed to be the raw material of the evolution of form. The establishment of any ecologically successful form by these mechanisms will be followed, under this hypothesis, by a period of genetic evolution, in which the recruitment of gene products to produce the “generically templated” morphologies by redundant pathways would be favoured by intense selection, leading to extensive genetic change with little impact on the fossil record. In this view, the stabilizing and reinforcing functions of natural selection are more important than its ability to effect incremental change in morphology. Aspects of evolution which are problematic from the standard neo-Darwinian viewpoint, or not considered within that framework, but which follow in a straightforward fashion from the view presented here, include the beginnings of an understanding of why organisms have the structure and appearance they’ do, why homoplasy (the recurrent evolution of certain forms) is so prevalent, why evolution has the tempo and mode it does (“punctuated equilibrium”), and why a “rapid” burst of morphological evolution occurred so soon after the origin of the metazoa.     

Japan and the concept of sustainability

This article describes a sustainable human social adaptation. It provides an example of how a human population responds to environmental stresses and modulates its population given technological abilities for food production and population control. The example used is Japan over the past 500 years. The concept of “sustainability” has become a popular concept used in a variety of conflicting and contradictory contexts and with resulting confusion. This eassay is offered as a point of discussion to produce more precise definitions of the concept of sustainability as it applies to human society.     

Hierarchies and the Sloshing Bucket: Toward the Unification of Evolutionary Biology

Evolutionary biology presents a bewildering array of phenomena to scientists and students alike—ranging from molecules to species and ecosystems; and embracing 3.8 billion years of life’s history on earth. Biological systems are arranged hierarchically, with smaller units forming the components of larger systems. The evolutionary hierarchy, based on replication of genetic information and reproduction, is a complex of genes/organisms/demes/species and higher taxa. The ecological hierarchy, based on patterns of matter–energy transfer, is a complex of proteins/organisms/avatars/local ecosystems/regional ecosystems. All organisms are simultaneously parts of both hierarchical systems. Darwin’s original formulation of natural selection maps smoothly onto a diagram where the two hierarchical systems are placed side-by-side. The “sloshing bucket” theory of evolution emerges from empirical cases in biological history mapped onto this dual hierarchy scheme: little phenotypically discernible evolution occurs with minor ecological disturbance; conversely, greatest concentrations of change in evolutionary history follow mass extinctions, themselves based on physical perturbations of global extent. Most evolution occurs in intermediate-level regional “turnovers,” when species extinction leads to rapid evolution of new species. Hierarchy theory provides a way of integrating all fields of evolutionary biology into an easily understood—and taught—rubric.