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PubMed2006

Neuronal implementation of hippocampal-mediated spatial behavior: a comparative evolutionary perspective.

The hippocampal formation (HF) of mammals and birds plays a strikingly similar role in the representation of space. This evolutionarily conserved property, however, belies the contrasting spatial ecology of animals such as rats and homing pigeons, differing spatial ecologies that should have promoted the evolution of group-specific adaptations to the HF representation of space. However, the spatial response properties of pigeon and rat HF neurons reveal surprising similarity in the contribution of position, direction, and trajectory toward explaining spatial variation in firing rate. By contrast, the asymmetrical distribution of neuronal response properties in the left and right HF of homing pigeons, but not rats, indicates a difference in network organization. The authors propose that hippocampal evolution may be characterized by inertia with respect to changes in the basic spatial elements that determine the response properties of neurons but considerable plasticity in how the neuronal response elements are organized into functional networks.

Animals↗

PubMed2025

Gene and Genome Duplication in Spiders.

Gene and genome duplications are widely observed across various organisms, including plants, yeasts, and animals. Numerous studies link gene duplications to the emergence of novel phenotypes, supporting the hypothesis that duplication events are advantageous for adaptive evolution. Whole-genome duplications (WGD) are especially prevalent in plants and have also occurred ancestrally in vertebrates. However, large-scale duplication events in other animal groups remain understudied, partly due to limited genomic resources. Arthropods, particularly insects, represent one of the most diverse animal clades in terms of both species and phenotypic diversity. With increasing availability of chromosome-level genomes, large-scale duplications appear to be rare in insects but are more frequent in chelicerates (e.g. spiders, scorpions, and horseshoe crabs). This makes chelicerates an intriguing group for comparing the mechanisms, fates, and evolutionary impacts of large-scale duplications with those seen in plants and vertebrates. In this review, we synthesize and discuss current research on WGD in spiders and discuss different scenarios for genes following gene duplication events (conservation, nonfunctionalization, subfunctionalization, specialization, drift, neofunctionalization) in the context of experimental studies. We hypothesize if there might be common trajectories after duplication and how these could be tested.

Animals↗

PubMed1997

Comparative diversification dynamics among palaeocontinents during the Ordovician Radiation.

The Ordovician Radiation was among the most extensive intervals of diversification in the history of life. However, a delineation of the proximal cause(s) of the Radiation remains elusive. Any such determination should involve an analysis of geographic overprints on diversification: did the Radiation occur randomly around the world or, alternatively, was it focused in particular geographic or depositional regimes? Here, I present a comparative evaluation of Ordovician diversification among several palaeocontinents to determine whether biotas associated with certain palaeocontinents exhibited different diversification patterns than others; in part, this involves a numerical "correction" to raw diversity trajectories. Clear disparities among palaeocontinents are indicated by the data, which appear to reflect differences in the extent of siliciclastic input partly in association with tectonic activity. Further testing will be required to fully substantiate the implication that siliciclastic influx was a predominant factor in the Ordovician Radiation, affecting a variety of higher taxa among all three Phanerozoic evolutionary faunas.

Animals↗

PubMed2006

Insulin signaling and limb-patterning: candidate pathways for the origin and evolutionary diversification of beetle 'horns'.

Beetle 'horns' are rigid outgrowths of the insect cuticle used as weapons in contests for access to mates. Relative to their body size, beetle horns can be enormous. They protrude from any of five different regions of the head or thorax; they are curved, straight, branched or bladed; and their development is often coupled with the nutrient environment (male dimorphism) or with sex (sexual dimorphism). Here, we show that this extraordinary diversity of horns can be distilled down to four trajectories of morphological change--horn location, shape, allometry and dimorphism--and we illustrate how the developmental mechanisms regulating horn growth could generate each of these types of horn evolution. Specifically, we review two developmental pathways known to regulate growth of morphological structures in Drosophila and other insects: a limb-patterning pathway that specifies the location and shape of a structure, and the insulin pathway, which modulates trait growth in response to larval nutrition. We summarize preliminary evidence indicating that these pathways are associated with the development of beetle horns, and we show how subtle changes in the relative activities of these two pathways would be sufficient to generate most of the extant diversity of horn forms. Our objective is to intuitively connect genotype with phenotype, and to advocate an informed 'candidate gene' approach to studies of the developmental basis of evolution. We end by using this insight from development to offer a solution to the long-standing mystery of the scarabs: the observation by Darwin, Lameere, Arrow and others that this one family of beetles appeared to have a 'special tendency' towards the evolution of horns.

Animals↗

PubMed1993

A symmetric inhibitor binds HIV-1 protease asymmetrically.

Potential advantages of C2-symmetric inhibitors designed for the symmetric HIV-1 protease include high selectivity, potency, stability, and bioavailability. Pseudo-C2-symmetric monools and C2-symmetric diols, containing central hydroxymethylene and (R,R)-dihydroxyethylene moieties flanked by a variety of hydrophobic P1/P1' side chains, were studied as HIV-1 protease inhibitors. The monools and diols were synthesized in 8-10 steps from D-(+)-arabitol and D-(+)-mannitol, respectively. Monools with ethyl or isobutyl P1/P1' side chains were weak inhibitors of recombinant HIV-1 protease (Ki > 10 microM), while benzyl P1/P1' side chains afforded a moderately potent inhibitor (apparent Ki = 230 nM). Diols were 100-10,000x more potent than analogous monools, and a wider range of P1/P1' side chains led to potent inhibition. Both classes of compounds exhibited lower apparent Ki values under high-salt conditions. Surprisingly, monool and diol HIV-1 protease inhibitors were potent inhibitors of porcine pepsin, a prototypical asymmetric monomeric aspartic protease. These results were evaluated in the context of the pseudosymmetric structure of monomeric aspartic proteases and their evolutionary kinship with the retroviral proteases. The X-ray crystal structure of HIV-1 protease complexed with a symmetric diol was determined at 2.6 A. Contrary to expectations, the diol binds the protease asymmetrically and exhibits 2-fold disorder in the electron density map. Molecular dynamics simulations were conducted beginning with asymmetric and symmetric HIV-1 protease/inhibitor model complexes. A more stable trajectory resulted from the asymmetric complex, in agreement with the observed asymmetric binding mode. A simple four-point model was used to argue more generally that van der Waals and electrostatic force fields can commonly lead to an asymmetric association between symmetric molecules.

Alcohols↗

PubMed2002

Postcopulatory sexual selection.

The female reproductive tract is where competition between the sperm of different males takes place, aided and abetted by the female herself. Intense postcopulatory sexual selection fosters inter-sexual conflict and drives rapid evolutionary change to generate a startling diversity of morphological, behavioural and physiological adaptations. We identify three main issues that should be resolved to advance our understanding of postcopulatory sexual selection. We need to determine the genetic basis of different male fertility traits and female traits that mediate sperm selection; identify the genes or genomic regions that control these traits; and establish the coevolutionary trajectory of sexes.

Animals↗

PubMed2025

Exploring genetic adaptation and microbial dynamics in engineered anaerobic ecosystems via strain-level metagenomics.

Genetic heterogeneity exists within all microbial populations, with sympatric cells of the same species often exhibiting single-nucleotide variations that influence phenotypic traits, including metabolic efficiency. However, the evolutionary dynamics of these strain-level differences in response to environmental stress remain poorly understood. Here, we present a first-of-its-kind study tracking the adaptive evolution of an anaerobic, carbon-fixing microbiota under a controlled engineered ecosystem focused on carbon dioxide bioconversion into methane. Leveraging strain-resolved metagenomics with an ad hoc variant calling and phasing approach, we mapped mutation trajectories and observed that the two dominant Methanothermobacter species maintained distinct sweeping haplotypes over time, most likely due to niche-specific metabolic roles. By combining population genetic statistics and peptide reconstruction, mer and mcrB genes emerged as potential drivers of archaeal strain-level competition. These findings pave the way for targeted engineering of microbial communities to enhance bioconversion efficiency, with significant implications for sustainable energy and carbon management in anaerobic systems.

Metagenomics↗

PubMed1997

Variation in mate choice and mating preferences: a review of causes and consequences.

The aim of this review is to consider variation in mating preferences among females. We define mating preferences as the sensory and behavioural properties that influence the propensity of individuals to mate with certain phenotypes. Two properties of mating preferences can be distinguished: (1) "preference functions'-the order with which an individual ranks prospective mates and (2) "choosiness'-the effort an individual is prepared to invest in mate assessment. Patterns of mate choices can be altered by changing the costs of choosiness without altering the preference function. We discuss why it is important to study variation in female mating behaviour and identify five main areas of interest: Variation in mating preferences and costs of choosiness could (1) influence the rate and direction of evolution by sexual selection, (2) provide information about the evolutionary history of female preferences, (3) help explain inter-specific differences in the evolution of secondary sexual characteristics, (4) provide information about the level of benefits gained from mate choice, (5) provide information about the underlying mechanisms of mate choice. Variation in mate choice could be due to variability in preference functions, degree of choosiness, or both, and may arise due to genetic differences, developmental trajectories or proximate environmental factors. We review the evidence for genetic variation from genetic studies of heritability and also from data on the repeatability of mate-choice decisions (which can provide information about the upper limits to heritability). There can be problems in interpreting patterns of mate choice in terms of variation in mating preferences and we illustrate two main points. First, some factors can lead to mate choice patterns that mimic heritable variation in preferences and secondly other factors may obscure heritable preferences. These factors are divided into three overlapping classes, environmental, social and the effect of the female phenotype. The environmental factors discussed include predation risk and the costs of sampling; the social factors discussed include the effect of male-male interactions as well as female competition. We review the literature which presents data on how females sample males and discuss the number of cues females use. We conclude that sexual-selection studies have paid far less attention to variation among females than to variation among males, and that there is still much to learn about how females choose males and why different females make different choices. We suggest a number of possible lines for future research.

Animal Communication↗

PubMed2025

Tracing the evolution and genomic dynamics of mating-type loci in Cryptococcus pathogens and closely related species.

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 C. decagattii, demonstrating its ability to undergo mating and sporulation. Progeny analysis in K. 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.

MAT genes↗

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↗

PubMed2003

A "Long Indel" model for evolutionary sequence alignment.

We present a new probabilistic model of sequence evolution, allowing indels of arbitrary length, and give sequence alignment algorithms for our model. Previously implemented evolutionary models have allowed (at most) single-residue indels or have introduced artifacts such as the existence of indivisible "fragments." We compare our algorithm to these previous methods by applying it to the structural homology dataset HOMSTRAD, evaluating the accuracy of (1) alignments and (2) evolutionary time estimates. With our method, it is possible (for the first time) to integrate probabilistic sequence alignment, with reliability indicators and arbitrary gap penalties, in the same framework as phylogenetic reconstruction. Our alignment algorithm requires that we evaluate the likelihood of any specific path of mutation events in a continuous-time Markov model, with the event times integrated out. To this effect, we introduce a "trajectory likelihood" algorithm (Appendix A). We anticipate that this algorithm will be useful in more general contexts, such as Markov Chain Monte Carlo simulations.

Algorithms↗

PubMed2002

Evolutionary dynamics and population control during in vitro selection and amplification with multiple targets.

Iterative cycles of in vitro selection and amplification allow rare functional nucleic acid molecules, aptamers, to be isolated from large sequence pools. Here we present an analysis of the progression of a selection experiment that simultaneously yielded two families of RNA aptamers against two disparate targets: the intended target protein (B52/SRp55) and the partitioning matrix. We tracked the sequence abundance and binding activity to reveal the enrichment of the aptamers through successive generations of selected pools. The two aptamer families showed distinct trajectories of evolution, as did members within a single family. We also developed a method to control the relative abundance of an aptamer family in selected pools. This method, involving specific ribonuclease digestion, can be used to reduce the background selection for aptamers that bind the matrix. Additionally, it can be used to isolate a full spectrum of aptamers in a sequential and exhaustive manner for all the different targets in a mixture.

Base Sequence↗

PubMed2006

Echolocating bats use a nearly time-optimal strategy to intercept prey.

Acquisition of food in many animal species depends on the pursuit and capture of moving prey. Among modern humans, the pursuit and interception of moving targets plays a central role in a variety of sports, such as tennis, football, Frisbee, and baseball. Studies of target pursuit in animals, ranging from dragonflies to fish and dogs to humans, have suggested that they all use a constant bearing (CB) strategy to pursue prey or other moving targets. CB is best known as the interception strategy employed by baseball outfielders to catch ballistic fly balls. CB is a time-optimal solution to catch targets moving along a straight line, or in a predictable fashion--such as a ballistic baseball, or a piece of food sinking in water. Many animals, however, have to capture prey that may make evasive and unpredictable maneuvers. Is CB an optimum solution to pursuing erratically moving targets? Do animals faced with such erratic prey also use CB? In this paper, we address these questions by studying prey capture in an insectivorous echolocating bat. Echolocating bats rely on sonar to pursue and capture flying insects. The bat's prey may emerge from foliage for a brief time, fly in erratic three-dimensional paths before returning to cover. Bats typically take less than one second to detect, localize and capture such insects. We used high speed stereo infra-red videography to study the three dimensional flight paths of the big brown bat, Eptesicus fuscus, as it chased erratically moving insects in a dark laboratory flight room. We quantified the bat's complex pursuit trajectories using a simple delay differential equation. Our analysis of the pursuit trajectories suggests that bats use a constant absolute target direction strategy during pursuit. We show mathematically that, unlike CB, this approach minimizes the time it takes for a pursuer to intercept an unpredictably moving target. Interestingly, the bat's behavior is similar to the interception strategy implemented in some guided missiles. We suggest that the time-optimal strategy adopted by the bat is in response to the evolutionary pressures of having to capture erratic and fast moving insects.

Animals↗

PubMedDate not supplied

Somatic versus reproductive energy allocation in Papua New Guinea: life history theory and public health policy.

A fundamental evolutionary problem faced by organisms is how to allocate energy to somatic and reproductive functions in ways that optimize fitness. Given that energy is limited in all environments, energy allocation necessarily involves physiological tradeoffs between such factors as growth and reproduction, reproduction and condition, and current reproduction and future survival. Ultimately, the "decisions" that are made about energy allocation among growth, survival, and reproduction determine life history patterns and trajectories of organisms. For humans, knowing how energy allocation to reproduction will likely impact other aspects of the somatic well-being of individuals may also have practical implications for public health policy. This article reviews the evidence for energy tradeoffs between somatic and reproductive functioning in a range of human societies. It also seeks to corroborate the results of earlier work in Papua New Guinea on lactation-related maternal energy depletion using an independent measure of maternal energy reserves, tetrapolar bioelectrical impedance analysis. The current analysis shows that maternal energy reserves decline over the course of lactation and that a cumulative parity-specific decline in maternal energy reserves also exists. A longitudinal follow-up of five women over 11 years shows the decline to amount to about 3 mm of subcutaneous fat per round of pregnancy and lactation. The results corroborate predictions from life history theory and have applied public health implications. In particular, It is suggested that policies such as lactation advocacy that encourage enhanced energy allocation to reproduction in order to promote child health may have the unintended result of compromising maternal well-being, particularly in nations of the developing world. Consequently, it is recommended that nutritional support of mothers be implemented in concert with lactation promotion.

Body Composition↗

PubMed1995

Heritability of nestling growth in cross-fostered European Starlings Sturnus vulgaris.

In altricial birds, growth rates and nestling morphology vary between broods. For natural selection to produce evolutionary change in these variables, ther must exist heritable variation. Since nestling traits are not any longer presents in parents, traditional offspring-parent regressions cannot estimate heritabilities of these. In this study, a partial cross-fostering experiment was performed, where nestlings of the European Starling (Sturnus vulgaris) were reciprocally exchanged between nests. The experiment demonstrated a significant heritability of nestling tarsus length and body mass, but not of the growth trajectories followed by individual nestlings. the heritability estimate for tarsus length obtained in the cross-fostering experiment using full-sib analysis was lower than those obtained by offspring-parent regressions. This is likely due to a genotype-by-environment effect on tarsus length, with nestlings destined to become large but in poor condition having a low probability of appearing as parents. The main reason for the low heritability of growth was probably the large within-brood variation in growth pattern due to the initial size hierarchy of nestlings. Nestlings demonstrated targeted growth, where small-sized nestlings that initially grew slower than their siblings, managed to catch up.

Aging↗

PubMed2026

Genotype-structure-phenotype correlations define divergent natural history in early-onset spastic paraplegia type 4.

Hereditary spastic paraplegia type 4 (SPG4), caused by variants in SPAST, is the most common form of HSP and exhibits a remarkable phenotypic heterogeneity ranging from late-onset pure presentations to severe, early-onset complex disease. Robust genotype-phenotype correlations and detailed natural history data are lacking, limiting clinical trial readiness. We analyzed 206 patients with genetically confirmed SPG4 enrolled across seven international centers, complemented by high-quality literature-derived cases. Deep phenotyping included standardized motor scales, spasticity ratings, developmental milestones, and patient-reported outcomes. We developed an extended essentiality-mapping framework to classify SPAST missense variants by integrating in silico pathogenicity predictions, evolutionary constraint, physicochemical residue connectivity, and variant enrichment within the human spastin hexamer structure. Plasma neurofilament light chain (pNfL) using was quantified using Simoa in 26 patients and 101 controls. We identified 136 distinct SPAST variants, including 10 novel variants. Variant class segregated strongly by inheritance, with de novo cases enriched for missense variants and inherited cases showing a variety of variant classes with enrichment for truncating variants. Longitudinal analysis revealed two latent trajectories: a rapidly progressive severe subgroup enriched for de novo missense variants, and a biphasic moderate subgroup enriched for inherited truncating variants. Patient stratification integrating spastin essentiality mapping (missense variants affecting essential, neutral, or context-dependent residues) with established genetic modifiers (biallelic pathogenic variants or modifier variants in trans) classified patients into predicted severe and moderate subgroups with divergent age at onset and clinical disease progression. The severe subgroup showed early developmental delays, rapid loss of ambulation, and declining quality of life, while the moderate subgroup displayed delayed but accelerating disease progression. pNfL levels were elevated in both subgroups, most pronounced in severe early disease. This study provides the most detailed natural history of SPG4 to date and introduces a biologically informed stratification framework that links variant class and location to divergent clinical trajectories. These data establish clinically meaningful benchmarks and offer a genotype-based framework to improve anticipatory care and optimize trial design for SPG4.

SPAST↗

PubMed2003

Extremely short lifespan in the annual fish Nothobranchius furzeri.

Evolutionary theories of senescence postulate that lifespan is determined by the age-dependent decrease in the effects of natural selection. Factors that influence survival and reproduction at early life stages have a larger impact on fitness than factors that influence later life stages. According to these views, selection for rapid sexual maturation and a steep age-dependent decrease in fitness drive the evolution of short lifespans. Here, we report on the survival trajectory of Nothobranchius furzeri (Pisces: Ciprinodontidae): a member of a group of annual species found in temporary bodies of water whose life expectancy in the wild is limited to a few months. We find that maximum survival of N. furzeri in the laboratory is less than 12 weeks. The temporal trajectory of survival shows an age-dependent increase in the mortality rate that is typical of organisms with defined lifespans. The lifespan of N. furzeri is exceptionally short for a vertebrate: owing to its small size and the possibility of propagation in captivity, N. furzeri could be used as a convenient model for ageing research.

Adaptation, Biological↗

PubMed1996

Reproducible nonlinear population dynamics and critical points during replicative competitions of RNA virus quasispecies.

RNA virus evolution is generally considered to be highly unpredictable, but tests of determinism in the evolution of competing populations during viral infections have not been performed. Here we study the fate of two closely related evolving quasispecies of vesicular stomatitis virus, by determining the relative concentration of a wild-type clone and a surrogate marked virus subclone (MARM-C) upon extensive competitive replication in a constant cell culture environment. A highly predictable nonlinear behaviour of the two competing populations was found. In addition, the presence of critical points, which are defined as points from which viral competitions may follow different trajectories, has been documented. Critical points were reached after nearly constant periods of time. The dynamics of relative fitness values for both competing populations were calculated during the replication passages. Concomitant with expected fitness gain of both competing viral populations (which follow the Red Queen hypothesis) a tendency for the MARM-C to gain less fitness than the wild-type was observed. Although fitness variations were noisy, this tendency was seen in all evolutionary replicas. Thus, despite the stochastic process of mutation that leads to a continuous generation of mutant genomes during RNA virus replication, a nonlinear, nearly deterministic evolutionary behaviour has been observed. It is proposed that such a behaviour is mediated by a low-pass filter (averaging of mutational noise signals) due to competitive selection among variants.

Analysis of Variance↗