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PubMed2004

Comparative analysis of neural crest cell death, migration, and function during vertebrate embryogenesis.

Cranial neural crest cells are a multipotent, migratory population that generates most of the cartilage, bone, connective tissue and peripheral nervous system in the vertebrate head. Proper neural crest cell patterning is essential for normal craniofacial morphogenesis and is highly conserved among vertebrates. Neural crest cell patterning is intimately connected to the early segmentation of the neural tube, such that neural crest cells migrate in discrete segregated streams. Recent advances in live embryo imaging have begun to reveal the complex behaviour of neural crest cells which involve intricate cell-cell and cell-environment interactions. Despite the overall similarity in neural crest cell migration between distinct vertebrates species there are important mechanistic differences. Apoptosis for example, is important for neural crest cell patterning in chick embryos but not in mouse, frog or fish embryos. In this paper we highlight the potential evolutionary significance of such interspecies differences in jaw development and evolution. Developmental Dynamics 229:14-29, 2004.

Ambystoma↗
PubMed2005

"Word" preference in the genomic text and genome evolution: different modes of n-tuplet usage in coding and noncoding sequences.

Extensive work on n-tuplet occurrence in genomic sequences has revealed the correlation of their usage with sequence origin. Parallel to that, there exist different restrictions in the nucleotide composition of coding and noncoding sequences that may result in distinct modes of usage of n-tuplets. The relatively simple approaches described herein focus on such differences. They are based on simple summation measures of n-tuplet frequencies, computed after filtering the background nucleotide composition. Among the main targets of this work is to draw some conclusions on the qualitative differences in the composition of genomic sequences depending on their functionality. Moreover, an evolutionary model is formulated, including simple forms of ubiquitous events of genome dynamics: genomic fusions, genome shuffling due to transpositions, replication slippage, and point mutations. This model is shown to be able to reproduce all the statistical features of genomic sequences discussed herein.

Base Sequence↗
PubMed2004

Are natural microcosms useful model systems for ecology?

Several recent, high-impact ecological studies feature natural microcosms as tools for testing effects of fragmentation, metacommunity theory or links between biodiversity and ecosystem processes. These studies combine the microcosm advantages of small size, short generation times, contained structure and hierarchical spatial arrangement with advantages of field studies: natural environmental variance, 'openness' and realistic species combinations with shared evolutionary histories. This enables tests of theory pertaining to spatial and temporal dynamics, for example, the effects of neighboring communities on local diversity, or the effects of biodiversity on ecosystem function. Using examples, we comment on the position of natural microcosms in the roster of ecological research strategies and tools. We conclude that natural microcosms are as versatile as artificial microcosms, but as complex and biologically realistic as other natural systems. Research to date combined with inherent attributes of natural microcosms make them strong candidate model systems for ecology.

Journal Article↗
PubMed1990

Age structure, environmental fluctuations, and hermaphroditic sex allocation.

This paper studies sex allocation in an age-structured population of hermaphrodites living in a temporally fluctuating environment. The general condition for the evolutionary stable state (ESS) of allocation is derived for density-independent dynamics. This condition is used to determine the effect on the deterministic ESS of a dependence of survival rates on allocation. It is also used to identify the special conditions under which a stochastic ESS is given by a product rule and show how demographic structure and the correlation structure of vital rates determines the stochastic ESS.

Biological Evolution↗
PubMed1978

Structural analysis of the ADHS electromorph of Drosophila melanogaster.

Population geneticists have often determined the fitness differences that account for the dynamics of naturally occurring genetic polymorphisms. However, to understand causal aspects of evolutionary processes requires, in addition, investigation of the physiological and molecular structural differences underlying adaptively significant genetic polymorphisms. The characteristics of the alcohol dehydrogenase gene--enzyme system in Drosophila melanogaster make it well suited for this kind of study. Natural populations of this species are polymorphic for two electrophoretically detectable variants, ADHF and ADHS, of the enzyme. Structural studies reported here reveal that the two variants differ by (at least) a single amino acid replacement, threonine in ADHF for lysine in ADHS.

Alcohol Oxidoreductases↗
PubMed2005

Poor maternal environment enhances offspring disease resistance in an invertebrate.

Natural populations vary tremendously in their susceptibility to infectious disease agents. The factors (environmental or genetic) that underlie this variation determine the impact of disease on host population dynamics and evolution, and affect our capacity to contain disease outbreaks and to enhance resistance in agricultural animals and disease vectors. Here, we show that changes in the environmental conditions under which female Daphnia magna are kept can more than halve the susceptibility of their offspring to bacterial infection. Counter-intuitively, and unlike the effects typically observed in vertebrates for transfer of immunity, mothers producing offspring under poor conditions produced more resistant offspring than did mothers producing offspring in favourable conditions. This effect occurred when mothers who were well provisioned during their own development then found themselves reproducing in poor conditions. These effects likely reflect adaptive optimal resource allocation where better quality offspring are produced in poor environments to enhance survival. Maternal exposure to parasites also reduced offspring susceptibility, depending on host genotype and offspring food levels. These maternal responses to environmental conditions mean that studies focused on a single generation, and those in which environmental variation is experimentally minimized, may fail to describe the crucial parameters that influence the spread of disease. The large maternal effects we report here will, if they are widespread in nature, affect disease dynamics, the level of genetic polymorphism in populations, and likely weaken the evolutionary response to parasite-mediated selection.

Animals↗
PubMed2004

What are symbols symbols of? Situated action, mythological bootstrapping and the emergence of the Self.

This paper addresses the question of how symbols should be understood in analytical psychology and psychoanalysis. The point of view examined focuses on the recent turn to more cognitive and developmental models in both disciplines and briefly reviews and critiques the evolutionary and cognitive arguments. The paper then presents an argument based on dynamic systems theory in which no pre-existing template or structure for either mind or behaviour is assumed. Within the dynamic systems model the Self is viewed as an emergent phenomenon deriving from the dynamic patterns existing in a complex system that includes the physiological characteristics of the infant, the intentional attributions of the caregiver and the cultural or symbolic resources that constitute the environment. The symbol can then be seen as a discrete, and in important ways an autonomous, element in the dynamic system. Conclusions are drawn for further research into the nature of the symbol with implications for both theory and practice in analytical psychology and psychoanalysis.

Ego↗
PubMed1998

Near-saddle-node bifurcation behavior as dynamics in working memory for goal-directed behavior.

In consideration of working memory as a means for goal-directed behavior in nonstationary environments, we argue that the dynamics of working memory should satisfy two opposing demands: long-term maintenance and quick transition. These two characteristics are contradictory within the linear domain. We propose the near-saddle-node bifurcation behavior of a sigmoidal unit with a self-connection as a candidate of the dynamical mechanism that satisfies both of these demands. It is shown in evolutionary programming experiments that the near-saddle-node bifurcation behavior can be found in recurrent networks optimized for a task that requires efficient use of working memory. The results suggests that the near-saddle-node bifurcation behavior may be a functional necessity for survival in nonstationary environments.

Animals↗
PubMed2006

Is mammalian chromosomal evolution driven by regions of genome fragility?

BACKGROUND: A fundamental question in comparative genomics concerns the identification of mechanisms that underpin chromosomal change. In an attempt to shed light on the dynamics of mammalian genome evolution, we analyzed the distribution of syntenic blocks, evolutionary breakpoint regions, and evolutionary breakpoints taken from public databases available for seven eutherian species (mouse, rat, cattle, dog, pig, cat, and horse) and the chicken, and examined these for correspondence with human fragile sites and tandem repeats. RESULTS: Our results confirm previous investigations that showed the presence of chromosomal regions in the human genome that have been repeatedly used as illustrated by a high breakpoint accumulation in certain chromosomes and chromosomal bands. We show, however, that there is a striking correspondence between fragile site location, the positions of evolutionary breakpoints, and the distribution of tandem repeats throughout the human genome, which similarly reflect a non-uniform pattern of occurrence. CONCLUSION: These observations provide further evidence that certain chromosomal regions in the human genome have been repeatedly used in the evolutionary process. As a consequence, the genome is a composite of fragile regions prone to reorganization that have been conserved in different lineages, and genomic tracts that do not exhibit the same levels of evolutionary plasticity.

Animals↗
PubMed2005

Prevalence-dependent costs of parasite virulence.

Costs of parasitism are commonly measured by comparing the performance of infected groups of individuals to that of uninfected control groups. This measure potentially underestimates the cost of parasitism because it ignores indirect costs, which may result from the modification of the competitiveness of the hosts by the parasite. In this context, we used the host-parasite system consisting of the yellow fever mosquito Aedes aegypti and the microsporidian parasite Vavraia culicis to address this question: Do infected individuals exert a more or less intense intraspecific competition than uninfected individuals? Our experimental results show that, indeed, infected hosts incur a direct cost of parasitism: It takes them longer to become adults than uninfected individuals. They also incur an indirect cost, however, which is actually larger than the direct cost: When grown in competition with uninfected individuals they develop even slower. The consequence of this modification of competitiveness is that, in our system, the cost of parasitism is underestimated by the traditional measure. Moreover, because the indirect cost depends on the frequency of interactions between infected and uninfected individuals, our results suggest that the real cost of parasitism, i.e., virulence, is negatively correlated with the prevalence of the parasite. This link between prevalence and virulence may have dynamical consequences, such as reducing the invasion threshold of the parasite, and evolutionary consequences, such as creating a selection pressure maintaining the host's constitutive resistance to the parasite.

Aedes↗
PubMed2025

Surveillance of tick-borne viruses in the border regions of the Tumen River Basin: Co-circulation in ticks and livestock.

BACKGROUND: The unique eco-geographical patterns and climatic conditions of the China-Tumen River border region, combined with frequent cross-border tourism and trade activities, collectively establish this area as a recognized hotspot for tick-borne disease outbreaks. However, critical knowledge gaps persist regarding the eco-epidemiology of emerging tick-borne viruses and the distribution of their potential reservoir hosts within this trinational ecosystem spanning China, North Korea, and Russia. METHODS: We collected a total of 2,004 ticks from the study area, along with blood samples obtained from 42 sheep and 45 cattle. Following viral metagenomic analysis of the ticks, dual verification of target pathogens in all samples was performed using qRT-PCR and RT-PCR assays. Phylogenetic trees were constructed and nucleotide sequences were analyzed to delineate relationships between the obtained virus strains and reference sequences. RESULTS: Viral metagenomics identified three viruses in ticks: Dabieshan tick virus (DBTV), Songling virus (SGLV), and Yanggou tick virus (YGTV). PCR analysis detected DBTV exclusively in Hunchun ticks (minimum infection rates, MIR:4.73%) and YGTV in Antu specimens (MIR:0.97%). Conversely, SGLV was detected in ticks from all four regions, with MIR of 1.68% (Helong), 0.74% (Hunchun), 1.61% (Antu), and 4.79% (Longjing). Concurrently, SGLV was detected in 19 sheep blood samples from Longjing, yielding a positivity rate of 45.24%, while YGTV was identified in 13 cattle blood samples from Antu, with a positivity rate of 28.89%. Phylogenetically, the DBTV strain clustered with previously reported DBTV and Yongjia tick virus 1 isolates. Sheep-derived SGLV strains shared close evolutionary ties with tick-borne SGLV, whereas YGTV from cattle and ticks formed a distinct cluster with Russian strains but diverged into two branches from Chinese variants, suggesting evolutionary instability. CONCLUSION: These findings address critical knowledge gaps in the transmission dynamics and genetic diversity of emerging arboviruses while providing vital insights for developing cross-border surveillance strategies with significant public health implications.

Animals↗
PubMed2002

[Evolutionary epidemiological thought on infections].

The objective of the study is to analyse the main aspects of current epidemiological knowledge on the evolutionary status of infections. Living organisms in the biosphere are part of dynamic systems of variable intensities. Some of these systems are on the surface while others take place inside the genome core. Parasitism is a phenomenon commonly seen in nature. Infective parasites relate to each other through several mechanisms, such as genetic DNA exchange, and because of the connections established communities of infectious agents are not isolated. The internalization process allows the parasites to get into their hosts' cells, which is accomplished through the phagocytosis of infectious agents or other more sophisticated mechanisms such as pill production. To leave the intracellular medium, some organisms make use of apoptosis, a highly specialized genetic mechanism that makes possible to destroy macrophages. It is currently accepted that molecular DNA can flow into the blood stream as the so-called infectrons. Thus it is hypothesized the existence of infection networks that allows the coadaptability of parasites and their hosts, and creates coevolutionary forces between hosts and their parasites facilitating the emergence of new pathogens.

Adaptation, Biological↗
PubMedDate not supplied

Density-dependent insect-mold interactions: effects on fungal growth and spore production.

Larvae of saprophagous insects often have been suspected of being competitors of filamentous fungi on decaying organic matter, which negatively influence mold development. Of interest, the role of insects in determining fungal growth and the onset of sporulation largely has been ignored. I used Aspergillus niger and the vinegar fly Drosophila melanogaster as an ecological model system to analyze the influence of insect larvae on daily fungal growth and the start of conidiospore production. I used an artificial substrate to test whether the effect of larval density (one, five and 10 larvae) and inoculation date of the mold (2 and 3 d ahead of the addition of larvae) significantly altered fungal growth. Fungal growth (area covered by hyphal tissue of the artificial patch) was affected negatively by the number of larvae and by the time that elapsed between inoculation with fungal spores and transfer of larvae to the patches. Whereas one larva had only a minor effect on fungal growth, five or 10 larvae strongly hampered mold development. As time between inoculation with spores and introduction of fly larvae increased, mold increased, indicating a priority effect for the fungus. When 10 larvae were transferred at the same time as the patches were inoculated with spores, almost no mold was visible within the period of observation (after 12 d). In comparison with control treatment (no insect larvae), an increase in larval density caused an increasing delay of several days in the start of spore production. Thus only minor changes in the density of insect larvae and the time that larvae entered the patches after inoculation with spores had an enormous effect on fungal growth and spore production. Therefore insects co-occurring with mold on ephemeral resources might constitute an important biotic factor driving local fungal population dynamics. The mechanisms leading to the suppression of fungal growth and the evolutionary implications of insect-mold interactions are discussed.

Animals↗
PubMed2005

Floral gene resources from basal angiosperms for comparative genomics research.

BACKGROUND: The Floral Genome Project was initiated to bridge the genomic gap between the most broadly studied plant model systems. Arabidopsis and rice, although now completely sequenced and under intensive comparative genomic investigation, are separated by at least 125 million years of evolutionary time, and cannot in isolation provide a comprehensive perspective on structural and functional aspects of flowering plant genome dynamics. Here we discuss new genomic resources available to the scientific community, comprising cDNA libraries and Expressed Sequence Tag (EST) sequences for a suite of phylogenetically basal angiosperms specifically selected to bridge the evolutionary gaps between model plants and provide insights into gene content and genome structure in the earliest flowering plants. RESULTS: Random sequencing of cDNAs from representatives of phylogenetically important eudicot, non-grass monocot, and gymnosperm lineages has so far (as of 12/1/04) generated 70,514 ESTs and 48,170 assembled unigenes. Efficient sorting of EST sequences into putative gene families based on whole Arabidopsis/rice proteome comparison has permitted ready identification of cDNA clones for finished sequencing. Preliminarily, (i) proportions of functional categories among sequenced floral genes seem representative of the entire Arabidopsis transcriptome, (ii) many known floral gene homologues have been captured, and (iii) phylogenetic analyses of ESTs are providing new insights into the process of gene family evolution in relation to the origin and diversification of the angiosperms. CONCLUSION: Initial comparisons illustrate the utility of the EST data sets toward discovery of the basic floral transcriptome. These first findings also afford the opportunity to address a number of conspicuous evolutionary genomic questions, including reproductive organ transcriptome overlap between angiosperms and gymnosperms, genome-wide duplication history, lineage-specific gene duplication and functional divergence, and analyses of adaptive molecular evolution. Since not all genes in the floral transcriptome will be associated with flowering, these EST resources will also be of interest to plant scientists working on other functions, such as photosynthesis, signal transduction, and metabolic pathways.

Biodiversity↗
PubMed2002

The role of size-specific predation in the evolution and diversification of prey life histories.

Some of the best empirical examples of life-history evolution involve responses to predation. Nevertheless, most life-history theory dealing with responses to predation has not been formulated within an explicit dynamic food-web context. In particular, most previous theory does not explicitly consider the coupled population dynamics of the focal species and its predators and resources. Here we present a model of life-history evolution that explores the evolutionary consequences of size-specific predation on small individuals when there is a trade-off between growth and reproduction. The model explicitly describes the population dynamics of a predator, the prey of interest, and its resource. The selective forces that cause life-history evolution in the prey species emerge from the ecological interactions embodied by this model and can involve important elements of frequency dependence. Our results demonstrate that the strength of the coupling between predator and prey in the community determines many aspects of life-history evolution. If the coupling is weak (as is implicitly assumed in many previous models), differences in resource productivity have no effect on the nature of life-history evolution. A single life-history strategy is favored that minimizes the equilibrium resource density (if possible). If the coupling is strong, then higher resource productivities select for faster growth into the predation size refuge. Moreover, under strong coupling it is also possible for natural selection to favor an evolutionary diversification of life histories, possibly resulting in two coexisting species with divergent life-history strategies.

Animals↗
PubMed2005

Population genetic analysis identifies source-sink dynamics for two sympatric garter snake species (Thamnophis elegans and Thamnophis sirtalis).

Population genetic structure can be shaped by multiple ecological and evolutionary factors, but the genetic consequences of these factors for multiple species inhabiting the same environment remain unexplored. We used microsatellite markers to examine the population structures of two coexisting species of garter snake, Thamnophis elegans and Thamnophis sirtalis, to determine if shared landscape and biology imposed similar population genetic structures. These snakes inhabit a series of ponds, lakes and flooded meadows in northern California and tend to converge on prey type wherever they coexist. Both garter snakes had comparable effective population sizes and bidirectional migration rates (estimated using a maximum-likelihood method based on the coalescent) with low but significant levels of genetic differentiation (F(ST) = 0.024 for T. elegans and 0.035 for T. sirtalis). Asymmetrical gene flow revealed large source populations for both species as well as potential sinks, suggesting frequent extinction-recolonization and metapopulation dynamics. In addition, we found a significant correlation between their genetic structures based on both pairwise F(ST)s for shared populations (P = 0.009) and for bidirectional migration rates (P = 0.024). Possible ecological and evolutionary factors influencing similarities and differences in genetic structure for the two species are discussed. Genetic measures of effective population size and migration rates obtained in this study are also compared with estimates obtained from mark-recapture data.

Animal Migration↗
PubMed2004

rVISTA 2.0: evolutionary analysis of transcription factor binding sites.

Identifying and characterizing the transcription factor binding site (TFBS) patterns of cis-regulatory elements represents a challenge, but holds promise to reveal the regulatory language the genome uses to dictate transcriptional dynamics. Several studies have demonstrated that regulatory modules are under positive selection and, therefore, are often conserved between related species. Using this evolutionary principle, we have created a comparative tool, rVISTA, for analyzing the regulatory potential of noncoding sequences. Our ability to experimentally identify functional noncoding sequences is extremely limited, therefore, rVISTA attempts to fill this great gap in genomic analysis by offering a powerful approach for eliminating TFBSs least likely to be biologically relevant. The rVISTA tool combines TFBS predictions, sequence comparisons and cluster analysis to identify noncoding DNA regions that are evolutionarily conserved and present in a specific configuration within genomic sequences. Here, we present the newly developed version 2.0 of the rVISTA tool, which can process alignments generated by both the zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from the ECR Browser and GALA database. The rVISTA web server is closely interconnected with the TRANSFAC database, allowing users to either search for matrices present in the TRANSFAC library collection or search for user-defined consensus sequences. The rVISTA tool is publicly available at http://rvista.dcode.org/.

Algorithms↗
PubMed1992

The roles of ecological and evolutionary influences in providing structure to parasite species assemblages.

Parasite species assemblages currently are thought to range from isolationist to interactive, their dynamic properties being related to the number of species and types of hosts involved. The literature contains few experimental tests of this concept, however, and many of the host/parasite systems studied to date are not amenable to experimental manipulation. In this review, the presence of a parasite species, in a sample of host individuals, is considered to be an evolutionary phenomenon, but the parasite's population structure is considered to be an ecological one. Studies that allow evaluation of these 2 influences are comparative in nature and include data from a series of homogeneous samples of host populations. A lottery model is presented, in which hosts acquire their assemblages of parasites by Monte Carlo type sampling from multiple kind arrays; the major structuring influence is the relative probability of becoming infected by various parasite species. Claims of parasite species interaction need to be supported by studies showing departures from the predictions of this model. The species density and infraassemblage diversity index distributions are recommended as quantitative tools useful in such work.

Animals↗