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PubMed2004

Aligning multiple genomic sequences with the threaded blockset aligner.

We define a "threaded blockset," which is a novel generalization of the classic notion of a multiple alignment. A new computer program called TBA (for "threaded blockset aligner") builds a threaded blockset under the assumption that all matching segments occur in the same order and orientation in the given sequences; inversions and duplications are not addressed. TBA is designed to be appropriate for aligning many, but by no means all, megabase-sized regions of multiple mammalian genomes. The output of TBA can be projected onto any genome chosen as a reference, thus guaranteeing that different projections present consistent predictions of which genomic positions are orthologous. This capability is illustrated using a new visualization tool to view TBA-generated alignments of vertebrate Hox clusters from both the mammalian and fish perspectives. Experimental evaluation of alignment quality, using a program that simulates evolutionary change in genomic sequences, indicates that TBA is more accurate than earlier programs. To perform the dynamic-programming alignment step, TBA runs a stand-alone program called MULTIZ, which can be used to align highly rearranged or incompletely sequenced genomes. We describe our use of MULTIZ to produce the whole-genome multiple alignments at the Santa Cruz Genome Browser.

Animals↗
PubMed2006

Extensive low-affinity transcriptional interactions in the yeast genome.

Major experimental and computational efforts are targeted at the characterization of transcriptional networks on a genomic scale. The ultimate goal of many of these studies is to construct networks associating transcription factors with genes via well-defined binding sites. Weaker regulatory interactions other than those occurring at high-affinity binding sites are largely ignored and are not well understood. Here I show that low-affinity interactions are abundant in vivo and quantifiable from current high-throughput ChIP experiments. I develop algorithms that predict DNA-binding energies from sequences and ChIP data across a wide dynamic range of affinities and use them to reveal widespread functionality of low-affinity transcription factor binding. Evolutionary analysis suggests that binding energies of many transcription factors are conserved even in promoters lacking classical binding sites. Gene expression analysis shows that such promoters can generate significant expression. I estimate that while only a small percentage of the genome is strongly regulated by a typical transcription factor, up to an order of magnitude more may be involved in weaker interactions. Low-affinity transcription factor-DNA interaction may therefore be important both evolutionarily and functionally.

Algorithms↗
PubMed1998

A comparison of the linear tuning properties of two classes of axons in the bullfrog lagena.

Various vertebrate inner-ear end organs appear to have switched their sensory function between equilibrium sensing and acoustic sensing over the courses of various lines of evolution. It is possible that all that is required to make this transition is to provide an end organ with access to the appropriate stimulus mode and frequency range. If, as we believe, however, the adaptive advantage of an acoustic sensory system lies in its ability to sort the total acoustic input into components that correspond to individual acoustic sources, and the adaptive advantage of an equilibrium sensory system lies in its ability to compute the total orientation and motion of the head without regard to the individual sources contributing to that orientation and motion, then it is easy to argue that the differences between acoustic and equilibrium sensors should be more profound than simply access to the appropriate stimuli. Effective signal-sorting requires high resolution in both time and frequency; to achieve this resolution, a peripheral tuning structure must be one of high dynamic order (i.e., constructed from multiple independent energy storage elements). If the peripheral tuning structure simply converts head acceleration to head displacement, velocity, or jerk (i.e., provides one or two steps of integration or differentiation with respect to time, where one energy storage element per step is required), then high dynamic order is inappropriate. Because the bullfrog lagena possesses both acoustic and equilibrium sensitive regions, it is especially suited for comparing these two sensor types and addressing the question of dynamic order of tuning. In this paper we report observations of the linear tuning properties of bullfrog lagenar primary afferent nerve fibers obtained by stimulating the lagena with random, dorsoventral micromotion over the frequency range from 10 Hz to 1.0 kHz. Tuning curves obtained by reverse correlation analysis and discrete Fourier transformation were used to estimate the dynamic order of each fiber's associated peripheral tuning structure. We found two classes of lagenar afferent axons--those with lowpass amplitude tuning characteristics (44 units) and those with bandpass amplitude tuning characteristics (73 units). Lowpass units were found to originate at the equilibrium region of the macula, and they exhibited low dynamic order--summed low- and high-frequency slopes (absolute values) ranged from 10 dB/decade to 64 dB/decade, implying dynamic orders of less than one to three (the modal value was equal to one). Bandpass units were found to originate at the acoustic region of the macula, and they exhibited higher dynamic order than lowpass units--summed low- and high-frequency slopes (absolute values) ranged from 53 dB/decade to 185 dB/decade, implying dynamic orders of three to nine (the modal value was equal to five). It appears that while lagenar equilibrium and acoustic sensors both possess access to signals in the acoustic frequency range, lagenar acoustic sensors are tuned by means of peripheral structures with markedly greater dynamic order and consequently markedly greater physical complexity. These results suggest that steep-sloped (high-dynamic-order) tuning properties reflect special adaptations in acoustic sensors not found in equilibrium sensors, and that any evolutionary transition between the two sensor types must have involved profound structural changes.

Acoustic Maculae↗
PubMed2003

The evolution of human phenotypic plasticity: age and nutritional status at maturity.

Several evolutionary optimal models of human plasticity in age and nutritional status at reproductive maturation are proposed and their dynamics examined. These models differ from previously published models because fertility is not assumed to be a function of body size or nutritional status. Further, the models are based on explicitly human demographic patterns, that is, model human life-tables, model human fertility tables, and, a nutrient flow-based model of maternal nutritional status. Infant survival (instead of fertility as in previous models) is assumed to be a function of maternal nutritional status. Two basic models are examined. In the first the cost of reproduction is assumed to be a constant proportion of total nutrient flow. In the second the cost of reproduction is constant for each birth. The constant proportion model predicts a negative slope of age and nutritional status at maturation. The constant cost per birth model predicts a positive slope of age and nutritional status at maturation. Either model can account for the secular decline in menarche observed over the last several centuries in Europe. A search of the growth literature failed to find definitive empirical documentation of human phenotypic plasticity in age and nutritional status at maturation. Most research strategies confound genetics with phenotypic plasticity. The one study that reports secular trends suggests a marginally insignificant, but positive slope. This view tends to support the constant cost per birth model.

Age Factors↗
PubMed2002

Adaptive elastic segmentation of brain MRI via shape-model-guided evolutionary programming.

This paper presents a fully automated segmentation method for medical images. The goal is to localize and parameterize a variety of types of structure in these images for subsequent quantitative analysis. We propose a new hybrid strategy that combines a general elastic template matching approach and an evolutionary heuristic. The evolutionary algorithm uses prior statistical information about the shape of the target structure to control the behavior of a number of deformable templates. Each template, modeled in the form of a B-spline, is warped in a potential field which is itself dynamically adapted. Such a hybrid scheme proves to be promising: by maintaining a population of templates, we cover a large domain of the solution space under the global guidance of the evolutionary heuristic, and thoroughly explore interesting areas. We address key issues of automated image segmentation systems. The potential fields are initially designed based on the spatial features of the edges in the input image, and are subjected to spatially adaptive diffusion to guarantee the deformation of the template. This also improves its global consistency and convergence speed. The deformation algorithm can modify the internal structure of the templates to allow a better match. We investigate in detail the preprocessing phase that the images undergo before they can be used more effectively in the iterative elastic matching procedure: a texture classifier, trained via linear discriminant analysis of a learning set, is used to enhance the contrast of the target structure with respect to surrounding tissues. We show how these techniques interact within a statistically driven evolutionary scheme to achieve a better tradeoff between template flexibility and sensitivity to noise and outliers. We focus on understanding the features of template matching that are most beneficial in terms of the achieved match. Examples from simulated and real image data are discussed, with considerations of algorithmic efficiency.

Algorithms↗
PubMed2025

Integrating hotspot dynamics and centers of diversity: a review of Indo-Australian Archipelago biogeographic evolution and conservation.

The Indo-Australian Archipelago (IAA) is the world's preeminent marine biodiversity hotspot, distinguished by its exceptional species richness in tropical shallow waters. This biodiversity has spurred extensive research into its evolutionary and biogeographic origins. Two prominent theoretical frameworks dominate explanations for the IAA's biodiversity: the "centers-of hypotheses" and the "hopping hotspot hypothesis". The "centers-of hypotheses" posits that specific regions serve as key sources of IAA biodiversity, either through the accumulation and overlap of species from external areas or via elevated rates of local speciation. In contrast, the "hopping hotspot hypothesis" asserts that biodiversity hotspots are dynamic, shifting across geological timescales in response to tectonic and environmental changes. This review synthesizes these contrasting perspectives into an integrated framework, the "Dynamic Centers Hypothesis," which proposes that as biodiversity hotspots migrate over time, the IAA's role in generating and sustaining biodiversity has evolved, with varying contributions from different sources dominating distinct historical phases. By synthesizing the evidence for both hypotheses and incorporating recent findings, including fossil and phylogeography data, we propose the "Dynamic Centers Hypothesis" as a comprehensive and unifying explanation for the IAA's biodiversity. The review further explores biogeographic delineation, aligning tropical marine realms with the IAA's evolutionary trajectory, from its Tethyan roots to its modern Indo-West Pacific dominance. Looking forward, advances in DNA barcoding and genomics are uncovering vast cryptic diversity, revolutionizing our comprehension of IAA phylogeographic history. These discoveries underscore the imperative for a multidimensional conservation framework, integrating phylogenetic, and functional diversity, to preserve this biodiversity hotspot amid escalating global change.

Biogeography↗
PubMed2026

Proteobacteria with chemosynthetic potential are highly prevalent in the gills of Hypoplectrus reef fishes.

Fishes host a diverse microbiome in their gills, but a broad characterization of this microbiome at the metagenomic level is lacking. Here, we apply genome-resolved metagenomics to the gills of the hamlets (Hypoplectrus spp), a group of reef fishes from the Greater Caribbean. The analysis of 353 gill samples from 15 hamlet species collected at eight locations over 13 years revealed a stark contrast between the gill microbiota and reef water microbial communities, indicating a distinct and specific gill microbiome. A total of 70 gill-associated metagenome-assembled genomes (MAGs) were recovered. These MAGs belong to 17 lineages, most of which are novel. They relate to known fish gill pathogens, fish gut microbes, free-living and biofilm-associated taxa, indicating that the gill microbiome was assembled from a collection of distinct eco-evolutionary trajectories. The MAGs harbor diverse metabolic modules, involved notably in nitrogen cycling, antibiotic production and biofilm formation, revealing a highly dynamic microbial ecosystem. One lineage in the Burkholderiaceae family was outstandingly prevalent across fish host species, sampling locations and years. Its genome encoded complete metabolic modules for carbon fixation and sulfur oxidation, indicating chemosynthetic potential. To the best of our knowledge, this is the first line of evidence that fishes may host sulfur-oxidizing chemosynthetic bacteria in their gills. The functional significance of this chemosynthetic potential for the fish host or other members of the gill microbiome remains to be established. The high prevalence of this lineage allowed to build a pangenome. It revealed large-scale geographic structure (western Caribbean, eastern Caribbean and Gulf of Mexico), which parallels the phylogenomic pattern observed in the hamlets. Overall, our findings point to complex fish host-microbe and microbe-microbe eco-evolutionary interactions in the gills that may influence fish physiology, homeostasis and immune response.

Animals↗
PubMed2006

Local genetic diversity of sorghum in a village in northern Cameroon: structure and dynamics of landraces.

We present the first study of patterns of genetic diversity of sorghum landraces at the local scale. Understanding landrace diversity aids in deciphering evolutionary forces under domestication, and has applications in the conservation of genetic resources and their use in breeding programs. Duupa farmers in a village in Northern Cameroon distinguished 59 named sorghum taxa, representing 46 landraces. In each field, seeds are sown as a mixture of landraces (mean of 12 landraces per field), giving the potential for extensive gene flow. What level of genetic diversity underlies the great morphological diversity observed among landraces? Given the potential for gene flow, how well defined genetically is each landrace? To answer these questions, we recorded spatial patterns of planting and farmers' perceptions of landraces, and characterized 21 landraces using SSR markers. Analysis using distance and clustering methods grouped the 21 landraces studied into four clusters. These clusters correspond to functionally and ecologically distinct groups of landraces. Within-landrace genetic variation accounted for 30% of total variation. The average F(is) over landraces was 0.68, suggesting high inbreeding within landraces. Differentiation among landraces was substantial and significant (F(st) = 0.36). Historical factors, variation in breeding systems, and farmers' practices all affected patterns of genetic variation. Farmers' practices are key to the maintenance, despite gene flow, of landraces with different combinations of agronomically and ecologically pertinent traits. They must be taken into account in strategies of conservation and use of genetic resources.

Cameroon↗
PubMed2025

The complex evolution and genomic dynamics of mating-type loci in Cryptococcus and Kwoniella.

Sexual reproduction in basidiomycete fungi is governed by MAT loci (P/R and HD), which exhibit remarkable evolutionary plasticity, characterized by expansions, rearrangements, and gene losses often associated with mating system transitions. The sister genera Cryptococcus and Kwoniella provide a powerful framework for studying MAT loci evolution owing to their diverse reproductive strategies and distinct architectures, spanning bipolar and tetrapolar systems with either linked or unlinked MAT loci. Building on recent comparative genomic analyses, we generated additional chromosome-level assemblies, uncovering distinct trajectories shaping MAT loci organization. Contrasting with the small-scale expansions and gene acquisitions observed in Kwoniella, our analyses revealed independent expansions of the P/R locus in tetrapolar Cryptococcus, possibly driven by pheromone gene duplications. Notably, these expansions coincided with a pronounced GC-content reduction best explained by reduced GC-biased gene conversion following recombination suppression, rather than relaxed codon usage selection. Diverse modes of MAT locus linkage were also identified, including three previously unrecognized transitions: one resulting in a pseudobipolar arrangement and two leading to bipolarity. All three transitions involved translocations. In the pseudobipolar configuration, the P/R and HD loci remained on the same chromosome but genetically unlinked, whereas the bipolar transitions additionally featured rearrangements that fused the two loci into a nonrecombining region. Mating assays confirmed a sexual cycle in Cryptococcus decagattii, demonstrating its ability to undergo mating and sporulation. Progeny analysis in Kwoniella mangrovensis revealed substantial ploidy variation and aneuploidy, likely stemming from haploid-diploid mating, yet evidence of recombination and loss of heterozygosity indicates that meiotic exchange occurs despite irregular chromosome segregation. Our findings underscore the importance of continued diversity sampling and provide further evidence for convergent evolution of fused MAT loci in basidiomycetes, offering new insights into the genetic and chromosomal changes driving reproductive transitions.

Genes, Mating Type, Fungal↗
PubMed2002

Cross-scale ecological dynamics and microbial size spectra in marine ecosystems.

Evaluating the component features of 'scaling' planktonic size spectra, commonly observed in marine ecosystems, is crucial for understanding the ecological and evolutionary processes from which they emerge. Here, we develop a theoretical framework that describes such spectra in terms of the size distributions of individual species, and test it against actual datasets of microbial size spectra from the Atlantic Ocean. We describe characteristics of size probability distributions of component species that are sufficient to support the observational evidence and infer that, when a power law describes the community size spectrum (thus suggesting critical self-organization of microbial ecosystem structure and function), a related power law links the total number of individuals of a given species to its mean size.

Animals↗
PubMed2005

Link between population dynamics and dynamics of Darwinian evolution.

We provide the link between population dynamics and the dynamics of Darwinian evolution via studying the joint population dynamics of similar populations. Similarity implies that the relative dynamics of the populations is slow compared to, and decoupled from, their aggregated dynamics. The relative dynamics is simple, and captured by a Taylor expansion in the difference between the populations. The emerging evolution is directional, except at the singular points of the evolutionary state space. Here "evolutionary branching" may occur. The diversification of life forms thus is demonstrated to be a natural consequence of the Darwinian process.

Biodiversity↗
PubMed2004

The life history legacy of evolutionary body size change in carnivores.

We estimate the body sizes of direct ancestors of extant carnivores, and examine selected aspects of life history as a function not only of species' current size, but also of recent changes in size. Carnivore species that have undergone marked recent evolutionary size change show life history characteristics typically associated with species closer to the ancestral body size. Thus, phyletic giants tend to mature earlier and have larger litters of smaller offspring at shorter intervals than do species of the same body size that are not phyletic giants. Phyletic dwarfs, by contrast, have slower life histories than nondwarf species of the same body size. We discuss two possible mechanisms for the legacy of recent size change: lag (in which life history variables cannot evolve as quickly as body size, leading to species having the 'wrong' life history for their body size) and body size optimization (in which life history and hence body size evolve in response to changes in energy availability); at present, we cannot distinguish between these alternatives. Our finding that recent body size changes help explain residual variation around life history allometries shows that a more dynamic view of character change enables comparative studies to make more precise predictions about species traits in the context of their evolutionary background.

Age Factors↗
PubMed2005

Biological sensitivity to context: I. An evolutionary-developmental theory of the origins and functions of stress reactivity.

Biological reactivity to psychological stressors comprises a complex, integrated, and highly conserved repertoire of central neural and peripheral neuroendocrine responses designed to prepare the organism for challenge or threat. Developmental experience plays a role, along with heritable, polygenic variation, in calibrating the response dynamics of these systems, with early adversity biasing their combined effects toward a profile of heightened or prolonged reactivity. Conventional views of such high reactivity suggest that it is an atavistic and pathogenic legacy of an evolutionary past in which threats to survival were more prevalent and severe. Recent evidence, however, indicates that (a) stress reactivity is not a unitary process, but rather incorporates counterregulatory circuits serving to modify or temper physiological arousal, and (b) the effects of high reactivity phenotypes on psychiatric and biomedical outcomes are bivalent, rather than univalent, in character, exerting both risk-augmenting and risk-protective effects in a context-dependent manner. These observations suggest that heightened stress reactivity may reflect, not simply exaggerated arousal under challenge, but rather an increased biological sensitivity to context, with potential for negative health effects under conditions of adversity and positive effects under conditions of support and protection. From an evolutionary perspective, the developmental plasticity of the stress response systems, along with their structured, context-dependent effects, suggests that these systems may constitute conditional adaptations: evolved psychobiological mechanisms that monitor specific features of childhood environments as a basis for calibrating the development of stress response systems to adaptively match those environments. Taken together, these theoretical perspectives generate a novel hypothesis: that there is a curvilinear, U-shaped relation between early exposures to adversity and the development of stress-reactive profiles, with high reactivity phenotypes disproportionately emerging within both highly stressful and highly protected early social environments.

Environment↗
PubMed2004

Pineal attrition, loss of cognitive plasticity, and onset of puberty during the teen years: is it a modern maladaptation exposed by evolutionary displacement?

Cognitive plasticity, a developmental trait that promotes acquisition of complex skills such as language or playing musical instruments, diminishes substantially during puberty. The loss of plasticity has been attributed to surge of sex steroids during adolescence, but the phenomenon remains poorly understood. We hypothesize that pineal involution during puberty may contribute to plasticity decay. The pineal gland produces melatonin, the level of which declines dramatically during onset of puberty. Emerging evidence suggest that melatonin may modulate cognitive plasticity, independent of the effects of sex steroids, and low sex steroids and high melatonin may be simultaneously required to maintain cognitive plasticity. Potential mechanisms by which melatonin may modulate plasticity are examined within the sleep and hippocampal long-term potentiation frameworks. Implications for psychiatric conditions that involve sleep disorders and learning dysfunctions such as schizophrenia and autism are discussed, and the potential adaptive roles of postprandial and postcoital sleep are explored. From the Darwinian perspective, development and reproductive maturity may represent distinct phases that require tailored cognitive strategies to maximize fitness. While cognitive flexibility and susceptibility to new skills may be paramount during development, reduced cognitive flexibility and increased cognitive determinism may enable more efficient responses to stimuli during adulthood. Thus, cognitive plasticity and cognitive determinism may represent trade-off adaptations and different dimensions of intelligence. The decline of plasticity and emergence of puberty during the second decade may be relics of prehistoric times when the human lifespan was short and the environment was relatively simple and static. Today, when the environment is more complex and dynamic, and humans are living far longer, the early obsolescence of plasticity during puberty may represent a Darwinian inefficiency exposed by evolutionary displacement. Regulation of plasticity may be a systemic phenomenon, as exemplified by the association of learning disability with allergic conditions, a form of immune plasticity dysfunction. Ramifications for other plastic functions that decline during puberty such as wound healing and hyaline cartilage regeneration are explored. Like the plasticity of immunity and cognition, the plasticity of hyaline cartilage during youth may enable hosts to respond to ecologic opportunities and generate the optimally adapted adult phenotype. Pineal involution may represent a potential target for therapeutic extension or restoration of plasticity after puberty. Extending plasticity may have far-reaching consequences for human evolution.

Adolescent↗
PubMed2005

Active vision and receptive field development in evolutionary robots.

In this paper, we describe the artificial evolution of adaptive neural controllers for an outdoor mobile robot equipped with a mobile camera. The robot can dynamically select the gazing direction by moving the body and/or the camera. The neural control system, which maps visual information to motor commands, is evolved online by means of a genetic algorithm, but the synaptic connections (receptive fields) from visual photoreceptors to internal neurons can also be modified by Hebbian plasticity while the robot moves in the environment. We show that robots evolved in physics-based simulations with Hebbian visual plasticity display more robust adaptive behavior when transferred to real outdoor environments as compared to robots evolved without visual plasticity. We also show that the formation of visual receptive fields is significantly and consistently affected by active vision as compared to the formation of receptive fields with grid sample images in the environment of the robot. Finally, we show that the interplay between active vision and receptive field formation amounts to the selection and exploitation of a small and constant subset of visual features available to the robot.

Artificial Intelligence↗
PubMed1988

Evolutionary development of systems.

The number of HMOs and their enrollment has increased since the inception of managed care and is expected to continue to expand. The dynamic growth in this area has raised concerns whether there are systems available which can handle their needs. Capabilities need to handle the complexities inherent in multiple benefit plans and provider relations.

Health Maintenance Organizations↗
PubMed2002

Human cortical dynamics determined by speech fundamental frequency.

Evidence for speech-specific brain processes has been searched for through the manipulation of formant frequencies which mediate phonetic content and which are, in evolutionary terms, relatively "new" aspects of speech. Here we used whole-head magnetoencephalography and advanced stimulus reproduction methodology to examine the contribution of the fundamental frequency F0 and its harmonic integer multiples in cortical processing. The subjects were presented with a vowel, a frequency-matched counterpart of the vowel lacking in phonetic contents, and a pure tone. The F0 of the stimuli was set at that of a typical male (i.e., 100 Hz), female (200 Hz), or infant (270 Hz) speaker. We found that speech sounds, both with and without phonetic content, elicited the N1m response in human auditory cortex at a constant latency of 120 ms, whereas pure tones matching the speech sounds in frequency, intensity, and duration gave rise to N1m responses whose latency varied between 120 and 160 ms. Thus, it seems that the fundamental frequency F0 and its harmonics determine the temporal dynamics of speech processing in human auditory cortex and that speech specificity arises out of cortical sensitivity to the complex acoustic structure determined by the human sound production apparatus.

Adult↗
PubMed1989

Behavioral evolution and biocultural games: vertical cultural transmission.

We consider an evolutionary game model in which strategies are transmitted culturally from parents to offspring rather than inherited biologically. Our analysis yields two noteworthy results. First, biocultural games show a greater diversity of dynamical behaviors than their purely biological counterparts, including multiple fully polymorphic equilibria. Second, biocultural games on average exhibit greater equilibrium strategy diversity because of the countervailing influences of cultural transmission and natural selection. Therefore, knowledge of a strategy's influence on Darwinian fitness is not sufficient to infer the evolutionary consequences of biocultural games. Further, our results suggest that cultural transmission in the presence of natural selection may be an important mechanism maintaining behavioral diversity in natural populations.

Animals↗