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PubMed2006

[Biological evolution and ancient DNA].

Twenty years after the advent of ancient DNA studies, this discipline seems to have reached the maturity formerly lacking to the fulfilment of its objectives. In its early development paleogenetics, as it is now acknowledged, had to cope with very limited data due to the technical limitations of molecular biology. It led to phylogenetic assumptions often limited in their scope and sometimes non-focused or even spurious results that cast the reluctance of the scientific community. This time seems now over and huge amounts of sequences have become available which overcome the former limitations and bridge the gap between paleogenetics, genomics and population biology. The recent studies over the charismatic woolly mammoth (independent sequencing of the whole mitochondrial genome and of millions of base pairs of the nuclear genome) exemplify the growing accuracy of ancient DNA studies thanks to new molecular approaches. From the earliest publications up to now, the number of mammoth nucleotides was multiplied by 100,000. Likewise, populational approaches of ice-age taxa provide new historical scenarios about the diversification and extinction of the Pleistocene megafauna on the one hand, and about the processes of domestication of animal and vegetal species by Man on the other. They also shed light on the differential structure of molecular diversity between short-term populational research (below 2 My) and long-term (over 2 My) phylogenetic approaches. All those results confirm the growing importance of paleogenetics among the evolutionary biology disciplines.

Animals↗

PubMed1994

Phylogenetic analysis of green plant rbcL sequences.

DNA and derived amino acid sequences of the rbcL gene from selected photosynthetic bacteria, green algae, bryophytes, "fern allies," ferns, and seed plants were used to construct phylogenetic trees using parsimony algorithms. Internal support of clades was determined by the bootstrap and decay indices. External support was judged by comparison of trees with previous morphological and molecular cladograms. Some clades on all the trees are supported both internally and externally, but all of the trees are characterized by unsupported relationships of the bryophytes and fern allies. Trees produced by analyses of all three DNA positions have the highest levels of internal support, but many clades are still not supported externally or internally. Analyses using only the first and second positions of the DNA sequences and derived amino acid sequences produced trees with odd groupings and low levels of internal support for most of the clades. These results indicate that rbcL sequences may be too divergent to test phylogenetic relationships among major groups of green plants. Additional problems with constructing phylogenetic trees from rbcL sequences may be caused by RNA editing, pseudogenes, unequal rates of evolution, and inadequate taxon sampling. Whether RNA editing is a problem can be determined by sequencing amplified RNAs from selected taxa. If pseudogenes are suspected, purified chloroplast DNA should be used for amplification. It may be beneficial to include more taxa in subsequent analyses, but there are indications that historical extinctions will prevent adequate sampling of some groups, such as the bryophytes and fern allies.

Amino Acid Sequence↗

PubMed1998

A reconsideration of Galton's problem (using a two-sex population).

The main purposes of this paper are to promote and expound the bisexual Galton-Watson branching process as a relevant model for the consideration of Francis Galton's problem regarding the extinction of surnames of "men of note." A scheme for adapting the bisexual process to consider Galton's problem is introduced. A necessary and sufficient condition for the certain extinction of a male-induced property in a two-sex species is presented. An approach for calculating the extinction of a male-generated characteristic in the two-sex species is proposed. That approach is then used to find the probability of the extinction of surnames in a bisexual population for Alfred Lotka's data based on an United States Census. Finally, these results are then compared with the classic extinction probabilities (from Lotka) associated with the traditional Galton-Watson branching process using asexual reproduction.

Female↗

PubMed2000

Two SIS epidemiologic models with delays.

The SIS epidemiologic models have a delay corresponding to the infectious period, and disease-related deaths, so that the population size is variable. The population dynamics structures are either logistic or recruitment with natural deaths. Here the thresholds and equilibria are determined, and stabilities are examined. In a similar SIS model with exponential population dynamics, the delay destabilized the endemic equilibrium and led to periodic solutions. In the model with logistic dynamics, periodic solutions in the infectious fraction can occur as the population approaches extinction for a small set of parameter values.

Communicable Diseases↗

PubMed1978

Consequences of helminth aggregation for the dynamics of schistosomiasis.

The distribution of schistosome worms among their human hosts is not random but aggregated. The consequences of introducing aggregation into models of schistosomiasis transmission, especially that of Macdonald, are explored. There are two possibilities for aggregation, with the sexes distributed either independently or together. Both have profound though differing effects on the breakpoint concept, which is largely destroyed when the sexes are aggregated together, and Macdonald's epidemiological conclusions are not robust to variations from the Poisson distribution. The conclusion from his model that if schistosome densities in man are reduced appropriately the infection will spontaneously proceed to extinction even in the presence of conditions suitable for transmission, is also not therefore robust.

Humans↗

PubMed2004

Synchrony & chaos in patchy ecosystems.

The apparent synchronisation of spatially discrete populations is a well documented phenomenon. However, it is not clear what the governing mechanisms are for this synchrony, and whether they are robust over a range of environmental conditions and patch specific population dynamic behaviours. In this paper, we explore two (possibly interacting) modes of coupling, and investigate their theoretically discernible, and perhaps even experimentally measurable, signatures. To aid us in this investigation we employ a planktonic example system, with direct application to plankton patchiness. Furthermore, we address the role of chaos in complex spatio-temporal dynamics; we find that chaos associated with funnel attractors can play a distinguished role, over dynamics less sensitive to small variations, in being more susceptible to generalised synchronisation (such as phase synchronisation) in the presence of small local parameter variation. This is in contrast to the case for coupled systems with identical dynamics, and suggests that non-identically coupled systems are more vulnerable to global extinction events when exhibiting funnel-type chaotic dynamics.

Animals↗

PubMed2004

A structured ancestral population for the evolution of modern humans.

The view that modern humans evolved through a bottleneck from a single founding group of archaic Homo is being challenged by new analyses of contemporary genetic variation. A wide range of middle to late Pleistocene ages for gene genealogies and evidence for early population structures point to a diverse and scattered ancestry associated with a metapopulation history of local extinctions, re-colonization and admixture. A different balance of the same processes has shaped chimpanzee diversity.

Africa↗

PubMed1985

The fixation of chromosomal rearrangements in a subdivided population with local extinction and colonization.

The fixation of major chromosomal rearrangements with a heterozygote disadvantage is modelled as a simple example of Wright's shifting balance process of evolution in a strongly subdivided population. Chromosomal mutations with an inferior heterozygote become fixed in a local population (or deme) by random genetic drift and spread by migration and colonization. Wright postulated a process of selective diffusion in which the numbers of emigrants and colonizers dispersed from a deme increase with the mean fitness of individuals in it. The present models show that interdeme selection during the spread of a mutation depends more on the capacity of the mutant to invade and become established in other demes than on selective diffusion, unless there is rapid local extinction and colonization. The intensity of interdeme selection is reduced by random local extinction and colonization, and when these processes are rapid (with no selective diffusion) the expected fixation rate of spontaneous mutations with a heterozygote disadvantage approaches that in a single isolated deme. Local extinction and colonization, and selection on the homozygotes, accelerate the spread of chromosomal mutations which are destined to be fixed.

Animals↗

PubMed2003

Inbreeding depression in fecundity and inbred line extinction in the bulb mite, Rhizoglyphus robini.

This study investigated the magnitude of inbreeding depression in fecundity, and whether the depression is purged during six generations of sib mating in the bulb mite, Rhizoglyphus robini. The progeny resulting from a single generation of brother-sister mating suffered significant inbreeding depression in fecundity. During the following six generations of continuous sib-mating, 58% lines were lost, 45% because of sterility and 13% because of preadult mortality. The lines were then outcrossed, and their inbreeding depression compared with that of the base population. The inbreeding depression for the outcrossed population was 0.15, and for the base population 0.19, but the difference was not significant. The lack of significant purging of inbreeding depression indicates that it was caused either by detrimental genes of small effect, or by the breaking down of overdominant relations between alleles. However, the large proportion of extinct lines points to the former mechanism as a predominant cause of inbreeding depression. Theory predicts that the probability of line extinction with inbreeding increases with its load of mutations. If phenotypic variation in fecundity was partly because of differences in numbers of mutations carried by individuals, the fecundity of the line founder could be expected to correlate with the probability that the line derived from it will survive long-term inbreeding. Indeed, fecundity of founder females was significantly associated with line survival, which suggests that line extinction rate may be used as a method to study individual mutational loads, for example, in studies of sexual selection.

Animals↗

PubMed2003

Global diversification rates of passerine birds.

The distribution of species richness in families of passerine birds suggests that the net rate of diversification was significantly higher than average in as many as 7 out of 47 families. However, the absence of excess species richness among the 106 tribes within these families indicates that these high rates were transient, perhaps associated in some cases with tectonic movements or dispersal events that extended geographical ranges. Thus, large clade size among passerine birds need not represent intrinsic key innovations that influence the rate of diversification. Approximately 17 families and 30 tribes have too few species relative to other passerine taxa. Many of these are ecologically or geographically marginal, being especially overrepresented in the Australasian region. Observed intervals between lineage splitting suggest that extinction has occurred ca. 90% as frequently as speciation (waiting times of 1.03 and 0.93 Myr) and that the 47 modern families comprising 5712 species descended from approximately 430 passerine lineages extant 24 Myr ago. Speciation and extinction rates among small, marginal families might be 1-2 orders of magnitude lower.

Animals↗

PubMed2006

Modelling the impacts of two exotic invasive species on a native butterfly: top-down vs. bottom-up effects.

1. Exotic invasive species can influence population dynamics of native species through top-down or bottom-up forces. The present study examined separate and interactive effects of multiple exotic species invasions on the native mustard white butterfly, Pieris napi oleracea Harris (Lepidoptera: Pieridae), using a stochastic simulation model. 2. P. n. oleracea populations in North America have decreased regionally since the 1860s. Competition with an exotic congener (P. rapae L.), loss of native host plants and parasitism by the introduced broconid wasp (Cotesia glomerata L.), have been suggested to be independently responsible for its decline. The present study examined these hypotheses, as well as an alternative, invasion by an exotic crucifer, garlic mustard (Alliaria petiolata[Bieb.] Cavara & Grande). 3. A stochastic simulation model of P. n. oleracea population dynamics revealed that decreasing the number of host plants available for oviposition and larval development (i.e. habitat loss), sharply reduced the probability of populations persistence and decreased population size for those that persisted. 4. Simulated invasion by garlic mustard also substantially decreased both probability of persistence (= 0 at approximately 50% cover) and mean population size. Persistence probability never reached zero under any C. glomerata scenarios, even when larval mortality in the second generation due to parasitism was 100%. The impact of garlic mustard was intensified by the addition of C. glomerata parasitism. 5. Results suggest that bottom-up forces, loss of host plants through forest understorey loss and/or garlic mustard invasion are the most important forces driving P. n. oleracea population decline. Parasitism by C. glomerata may interact to reduce P. n. oleracea populations more rapidly, but appears insufficient alone to cause local extinction.

Animals↗

PubMed2001

Nonequilibrium diversity dynamics of the Lesser Antillean avifauna.

MacArthur and Wilson's model of island diversity predicts an increase in the number of species until colonization and extinction are balanced at a long-term steady state. We appraise this model on an evolutionary time scale by molecular phylogenetic analysis of the colonization of the Lesser Antilles by small land birds. The pattern of accumulation of species with time, estimated by genetic divergence between island and source lineages, rejects a homogeneous model of colonization and extinction. Rather, our results suggest an abrupt, roughly 10-fold increase in colonization rate or a 90% mass extinction event 0.55 to 0.75 million years ago.

Animals↗

PubMed2005

When Earth started blooming: insights from the fossil record.

Recent palaeobotanical studies have greatly increased the quantity and quality of information available about the structure and relationships of Cretaceous angiosperms. Discoveries of extremely well preserved Cretaceous flowers have been especially informative and, combined with results from phylogenetic analyses of extant angiosperms (based mainly on molecular sequence data), have greatly clarified important aspects of early angiosperm diversification. Nevertheless, many questions still persist. The phylogenetic origin of the group itself remains as enigmatic as ever and, in some cases, newly introduced techniques from molecular biology have given confusing results. In particular, relationships between the five groups of extant seed plants remain uncertain, and it has sometimes proved difficult to reconcile estimates of the time of divergence between extant lineages made using a 'molecular clock' with the fossil record. One result, however, is becoming increasingly clear: a great deal of angiosperm diversity is extinct. Some groups of angiosperms were evidently more diverse in the past than they are today. In other cases, fossils defy assignment to extant groups at the family level or below. This raises the possibility that evolutionary conclusions based solely upon extant taxa that are merely relics of groups that were once much more diverse might be misled by the effects of extinction. It also introduces the possibility that some early enigmatic fossils might represent lineages that diverged from the main line of angiosperm evolution below the most recent common ancestor of all extant taxa. These, and other questions, are among those that need to be addressed by future palaeobotanical research.

Biological Evolution↗

PubMed1993

Associative learning in a network model of Hermissenda crassicornis. II. Experiments.

A companion paper in a previous issue of this journal presented a resistance-capacitance circuit computer model of the four-neuron visual-vestibular network of the invertebrate marine mollusk Hermissenda crassicornis. In the present paper, we demonstrate that changes in the model's output in response to simulated associative training is quantitatively similar to behavioral and electrophysiological changes in response to associative training of Hermissenda crassicornis. Specifically, the model demonstrates many characteristics of conditioning: sensitivity to stimulus contingency, stimulus specificity, extinction, and savings. The model's learning features also are shown to be devoid of non-associative components. Thus, this computational model is an excellent tool for examining the information flow and dynamics of biological associative learning and for uncovering insights concerning associative learning, memory, and recall that can be applied to the development of artificial neural networks.

Animals↗

PubMed2004

The role of density-dependent dispersal in source-sink dynamics.

I investigate two aspects of source-sink theory that have hitherto received little attention: density-dependent dispersal and the cost of dispersal to sources. The cost arises because emigration reduces the per capita growth rate of sources, thus predisposing them to extinction. I show that source-sink persistence depends critically on the interplay between these two factors. When the emigration rate increases with abundance at an accelerating rate, dispersal costs to sources is the lowest and risk of source-sink extinction the least. When the emigration rate increases with abundance at a decelerating rate, dispersal costs to sources is the highest and the risk of source-sink extinction the greatest. Density-independent emigration has an intermediate effect. Thus, density-dependent dispersal per se does not increase or decrease source-sink persistence relative to density-independent dispersal. The exact mode of dispersal is crucial. A key point to appreciate is that these effects of dispersal on source-sink extinction arise from the temporal density-dependence that dispersal induces in the per capita growth rates of source and sink populations. Temporal density-dependence due to dispersal is beneficial at low abundances because it rescues sinks from extinction, and detrimental at high abundances because it drives otherwise viable sources to extinction. These results are robust to the nature of population dynamics in the sink, whether exponential or logistic. They provide a means of assessing the relative costs and benefits of preserving sink habitats given three biological parameters.

Animals↗

PubMed2000

Mercury levels in muscle of two fish species and sediments from the Cartagena Bay and the Ciénaga Grande de Santa Marta, Colombia.

Mercury (Hg) content in sediments and muscle from two fish species were determined in Cartagena Bay and Ciénaga Grande de Santa Marta, an industrialized bay and an unpolluted estuary in the Caribbean coast of Colombia. Sampling was conducted four times during March-November 1996, including both the dry and rainy seasons. Significant differences in Hg concentration were detected both for fish and sediments between the two waterbodies. Hg values ranged from 94 to 10,293 microg/kg dry weight (dw) in sediments from Cartagena Bay and between 20 and 109 microg/kg dw in Ciénaga Grande de Santa Marta. Highest Hg concentrations were observed for the omnivorous species Eugerres plumieri, and lowest concentrations were found in the detritivorous Mugil incilis. High Hg concentrations in sediments of Cartagena Bay were detected in front of the sewage discharge of an extinct chlor-alkali plant, with decreasing concentrations in stations far from the source. Our results suggest that Hg can be persistent in the sediments of previously exposed ecosystems and that the use of their biological resources should be avoided until decontamination programs guarantee safe levels of the metal in the environment.

Journal Article↗

PubMedDate not supplied

[A different interpretation of the Oedipus complex].

Is mans fate irrevocable predetermined or have we a certain amout of free will? We assume, that although restricted by his own developed character, and given circumstances, man has a choice and is capable to influence his destiny. According to Freud our actions and behaviour are often unconsciously motivated and frequently incomprehensible for ourselves. They are then independent of our "will" and capacity of decision--making. Freud observes rightly the ambivalence of seelings between father and son, mother and daughter and regards this as the essential factor for the character-formation of the developing child. However his interpretation that these feelings are always based on libidinous wishes and jealousy seems to the author too farfetched and not fully proved in all cases. In the author's opinion the basic problem of life must be an insolvable one and that is the problem of death. Seen from the father's point of view, the son, on one hand represents the only solution for continuation of his life, the only possibility of victory over death, on the other hand however, he will substitute him one day, make him superfluous and eventually take his place. A similar process takes place between mother and daughter who on one hand would like to enjoy the beauty and success of her daughter (whom she regards as her biological continuation)--by whom however she feels as well pushed aside and made older on the other hand. The Problem, how to vanquish death and the wish for continuation of our existance, the resistance against extinction and replacement by someone else, is of fundamental and inescapable importance. If we understand this, we will find a more profound explicaiton of ambivalent feelings between parents and children. The aim of human development should be, to find the right way, how to satisfy our justified urges in accepting the limits of our capacities and possibilities within the framework of reality.--In doing so, our creative capabilities and our desires for change and progress should not be inhibited. The acceptance of our Self, of the reality of life and of our limitations includes however also the acceptance of death. This inside therefore will have its positive effect also on the development of the ambivalent feelings between parents and children, which we could handle better, if we know and understand their meaning.

Aggression↗

PubMed2001

Primate molar crown formation times and life history evolution revisited.

Comparative studies have convincingly demonstrated that the pattern and timing of tooth emergence are highly correlated with life-history variables and brain size. Conversely, a firm relationship between molar formation time and life-history variables has not yet been established. It seems counterintuitive that one aspect of dental development should be correlated with life-history variables, whereas the other should not. In order to shed light on this apparent discrepancy this study analyzed all data on primate molar crown formations available in the published literature in relation to life-history variables, brain size, and female body mass. Crown formation times were found to be particularly highly correlated with both female body mass and brain size. Species that depart from the overall brain/body allometry by being relatively large-bodied, e.g., Gorilla gorilla and later Theropithecus oswaldi, also have shorter molar crown formation times than expected. The reverse is not found for species that depart from the overall brain/body allometry due to their larger brains, i.e., Homo sapiens. This finding is interpreted within an evolutionary and ecological framework. Specifically, by focusing on ecological commonalities, a scenario is proposed which may allow predictions to be made about the evolutionary history of other extinct primates also. If confirmed in future studies, crown formation time may again become a powerful tool in evolutionary enquiry.

Animals↗