Evolution Research Articles

Eels’ individual migratory behavior stems from a complex syndrome involving cognition, behavior, physiology, and life history

Variability within species is key for adaptability and biological evolution. To understand individualities in the context of animal movement, we focused on one of the most remarkable migrations—the journey of the endangered European eel from their birthplace in the Sargasso Sea to freshwater environments. Laboratory observations unveiled a continuum of diverse phenotypes of migrating eels: Some displayed a heightened tendency to swim against a constant water flow, while others a greater propensity to climb obstacles. Looking for the biological underpinnings of this migratory diversity, we characterized the eels’ individual differences in traits of four key domains: life history, physiology, behavior, and cognition, among which we found significant variance and interconnectedness. Upon reducing this variance to its primary multivariate axes, we found that these predict the migratory types. Eels with 1) low exploration, high activity, low boldness, and high lateralization; 2) strong lateralization, enhanced quantitative abilities, short problem-solving time, high boldness, and low growth rates; or 3) enhanced problem-solving, reduced spatial learning, high cognitive flexibility, and shorter time to solve the cognitive tasks were more likely to display the climbing migratory type. Field sampling revealed how specific traits’ combinations seemed to influence the distribution of eels once they begin to settle in the freshwater environment. Our study underscores the impressive diversity of individuals during this critical migration, emphasizing an intrinsic connection to multidomain trait variance. Preserving this diversity becomes paramount, as it likely contributes to the resilience and adaptability of endangered migratory species.

A tale of two cultures: How L. Luca Cavalli-Sforza bridged the gap between science and the humanities

This article retraces the career of geneticist L. Luca Cavalli-Sforza, from his days as a student researcher to his tenure as a Stanford University professor, and beyond. We show how Cavalli-Sforza’s untiring curiosity, enthusiasm, and global knowledge led him to make incisive contributions to topics as diverse as bacterial genetics and human evolution, both biological and cultural. In an academic world where hyperspecialization is the norm, Cavalli-Sforza stood out as a scientist unafraid to promulgate and apply multidisciplinary approaches to complex issues of human origins and culture.

Bridging theory and data: A computational workflow for cultural evolution

Cultural evolution applies evolutionary concepts and tools to explain the change of culture over time. Despite advances in both theoretical and empirical methods, the connections between cultural evolutionary theory and evidence are often vague, limiting progress. Theoretical models influence empirical research but rarely guide data collection and analysis in logical and transparent ways. Theoretical models themselves are often too abstract to apply to specific empirical contexts and guide statistical inference. To help bridge this gap, we outline a quality-assurance computational workflow that starts from generative models of empirical phenomena and logically connects statistical estimates to both theory and real-world explanatory goals. We emphasize and demonstrate validation of the workflow using synthetic data. Using the interplay between conformity, migration, and cultural diversity as a case study, we present coded and repeatable examples of directed acyclic graphs, tailored agent-based simulations, a probabilistic transmission model for longitudinal data, and an approximate Bayesian computation model for cross-sectional data. We discuss the assumptions, opportunities, and pitfalls of different approaches to generative modeling and show how each can be used to improve data analysis depending on the structure of available data and the depth of theoretical understanding. Throughout, we highlight the significance of ethnography and of collecting basic cultural and demographic information about study populations and call for more emphasis on logical and theory-driven workflows as part of science reform.

Forward and backward modeling of cultural evolutionary processes

Modern cultural evolution theory adopts a variety of concepts and methods developed in mathematical biology, in particular population genetics theory. In addition to forward-looking approaches such as two-locus models, backward-looking approaches such as coalescent theory, which describe ancestral states of the current population, have played an important role in population genetics. Here, we show how forward and backward approaches can be applied to two examples in cultural evolution. The first example deals with the number of cultural traits, which can be analyzed by a backward approach. Cultural coalescent theory illustrates many unique aspects of cultural processes such as information transfer (i.e., social learning) from many donors (“cultural parents”), including or excluding the biological parents. Theory predicts that many cultural traits of intermediate (or higher) frequency (popularity) can exist that are surprisingly old. Many unsolved issues remain, however, such as how to incorporate social structure as well as natural and/or cultural selection, which we believe to be an urgent agenda. The second example is the punishment of sibling incest, a problem to which cultural coalescent theory cannot currently be usefully applied. By analyzing forward recursions, we show that punishment is ineffective in suppressing incest, unless the incestuous inclination is diminished by the presence of punishers. Based on these examples, we discuss the merits and demerits of forward and backward approaches.

Models of Fluctuating Selection Between Generations: A Solution for the Theoretical Inconsistency.

The theory of selection fluctuation between generations has been a topic with much activities in population genetics and molecular evolution in 1970's. Most studies suggested that, as the result of fluctuating selection between generations, the frequency of an (on average) neutral mutation may fluctuate around 0.5 during the long-term evolution before it was ultimately fixed or lost. However, this pattern can only be derived from a specific type Wright-Fisher additive model, coined by the Nei-Yokoyama puzzle. In this commentary, I revisited this issue and figured out a theoretical assumption that has never been claimed explicitly, the notion of reference phenotype. Consider one locus with two-alleles: A is the wildtype allele and A' is the mutation. The fluctuating selection model actually requires a constraint that one of three genotypes (AA, AA', or A'A') must maintain a constant fitness without fluctuating between generations. It appears that the balancing selection at a frequency of 0.5 emerges only when the heterozygote (AA') is the reference genotype. Because it is difficult to determine which genotype could be the reference genotype in a real population, a desirable population genetics model should take all three possibilities into account. To this end, I propose a mixture model, where each genotype has a certain chance to be the reference genotype. My analysis showed that the emergence of balancing selection depends on the relative proportions of three different reference genotypes.

The clinical impact of EGFR alterations in elderly glioblastoma patients: results from a real-life cohort.

The incidence of glioblastoma in the elderly population is increasing as the worldwide population ages. The differential and poorer survival in the elderly population compared to younger patients is partially explained. The present study aimed to investigate the clinical impact of epidermal growth factor receptor EGFR-altered glioblastoma in a real-life elderly glioblastoma population. A bicentric and retrospective study was conducted. Patients were 70years or older and suffering from histomolecularly confirmed glioblastoma. Single nucleotide variants (SNV), amplification, or chromosome 7 polysomy were sought. The primary endpoint was the comparison of overall survival (OS) in patients with or without EGFR alteration. Secondary objectives were to determine other clinical parameters correlated with EGFR alteration status. Seventy-three patients were analyzed: 41.1% had at least one EGFR alteration. The presence of EGFR alteration did not impact overall survival: HR 0.97 [0.6-1.57], p = 0.9; the median overall survival was 6.5months [5.3-9.3] in the EGFR-altered group versus 7months [4.5-10] in the EGFR wild-type group, p = 0.75. In multivariate analysis, tumor resection was associated with a significant overall survival improvement: the median OS in the resected group (n = 20) was 11months [95% CI 7.8-22] versus a median OS of 5.5months [4.6-7.8] in the unresected group (n = 53), without correlation to EGFR alteration status. In the modern era of molecular characterization and improved treatment modalities, the presence of at least one EGFR alteration did not influence survival outcomes in an elderly population of glioblastoma patients.

Propagation Dynamics in Time‐Periodic Reaction–Diffusion Systems with Network Structures

ABSTRACTThe main purpose of this paper is to study the propagation dynamics for a class of time‐periodic reaction–diffusion systems with network structures. In the first part, by using the persistence theory, we obtain threshold results for the extinction and uniform persistence of the corresponding periodic ordinary differential system. The second part is concerned with the asymptotic speed of spread and traveling wave solutions. The uniform boundedness of solutions is proved by employing the refined high‐dimensional local ‐estimate and abstract periodic evolution theories and the spreading properties of the corresponding solutions are established. We also prove the existence of the critical periodic traveling wave with wave speed by using a delicate limitation argument. Finally, these results are applied to a multistage epidemiological model.

Genomic Architecture Underlying the Striking Colour Variation in the Presence of Gene Flow for the Guinan Toad-Headed Lizard.

How divergence occurs between closely related organisms in the absence of geographic barriers to gene flow stands as one of the long-standing questions in evolutionary biology. Previous studies suggested that the interplay between selection, gene flow and recombination strongly affected the process of divergence with gene flow. However, the extent to which these forces interact to drive divergence remains largely ambiguous. Guinan toad-headed lizards (Phrynocephalus guinanensis) in the Mugetan Desert exhibit striking colour differences from lizards outside the desert and provide an excellent model to address this question. Through extensive sampling and whole genome sequencing, we obtained genotypes for 191 samples from 14 populations inside and outside the desert. Despite the colour differences, continuous and asymmetric gene flow was detected across the desert border. More importantly, 273 highly diverged regions (HDRs) were identified between them, accounting only for 0.47% of the genome but widely distributed across 20 (out of the total 24) chromosomes. Strong signatures of selection were identified in HDRs, and local recombination rates were repressed. Furthermore, five HDRs exhibited significantly higher divergence, which contained key genes associated with crucial functions in animal coloration, including pteridine and melanocyte pigmentation. Genes related to retinal cells and steroid hormones were identified in other HDRs, which might have also contributed to the formation of colour variation in the presence of gene flow. This study provided novel insights into the understanding of the evolutionary mechanisms of genetic divergence in the presence of gene flow.

Phylogenetic Trees Defined by at Most Three Characters

In evolutionary biology, phylogenetic trees are commonly inferred from a set of characters (partitions) of a collection of biological entities (e.g., species or individuals in a population). Such characters naturally arise from molecular sequences or morphological data. Interestingly, it has been known for some time that any binary phylogenetic tree can be (convexly) defined by a set of at most four characters, and that there are binary phylogenetic trees for which three characters are not enough. Thus, it is of interest to characterise those phylogenetic trees that are defined by a set of at most three characters. In this paper, we provide such a characterisation, in particular proving that a binary phylogenetic tree $T$ is defined by a set of at most three dcharacters precisely if $T$ has no internal subtree isomorphic to a certain tree.

The Collector Hypothesis : Who Benefits More from Art, the Artist or the Collector?

Human fascination with art has deep evolutionary roots, yet its role remains a puzzle for evolutionary theory. Although its widespread presence across cultures suggests a potential adaptive function, determining its evolutionary origins requires more comprehensive evidence beyond mere universality or assumed survival benefits. This paper introduces and tests the Collector Hypothesis, which suggests that artworks serve as indicators of collectors' surplus wealth and social status, offering greater benefits to collectors than to artists in mating and reproductive contexts. Our study among Indigenous Papuan communities provides preliminary support for the Collector Hypothesis, indicating that, compared to artists, collectors are perceived as having higher social status and greater attractiveness to women. These findings provide unique insights into Papuan communities and contribute to the ongoing discussion about art's adaptive significance of art by suggesting that artistic capacities may benefit not only creators but also those who accumulate and display art. Further research in diverse cultural contexts is needed for a comprehensive understanding of this interplay.

A conserved sequence that sparked the field of evo-devo.

The discovery that homeotic genes in Drosophila are conserved and utilized for embryonic development throughout the animal kingdom, including humans, revolutionized the fields of developmental biology and evolutionary developmental biology (evo-devo). In a pair of back-to-back papers published in Cell in 1984, researchers at the Biozentrum in Basel, Switzerland, showed that the homeobox - previously identified as a sequence shared by homeotic genes in Drosophila - was also present in the genome of diverse animals. The first paper (McGinnis et al., 1984a) showed that genomes of both invertebrates and vertebrates contain sequences that cross-hybridized with Drosophila homeobox probes. The second paper (Carrasco et al., 1984) identified a cross-hybridizing sequence in the model system Xenopus laevis. They then isolated the first vertebrate homeobox-containing gene by cloning and sequencing of the corresponding genomic region. Finally, they showed that this gene (AC1, later renamed HoxC6) was expressed during embryonic development, the first evidence that developmentally expressed Drosophila genes could be used to isolate regulators of vertebrate embryonic development. These findings led to a flurry of activity in the evo-devo field, initially focused on isolating Hox genes across diverse species, and then expanding to isolation of other gene families based on Drosophila orthologs, an approach that continues today. This led to the notion of a conserved genetic toolkit for embryonic development, currently accepted, but unexpected at the time of its discovery. We attempt to provide some context for the sea-change in thinking that these discoveries brought about by referring to Jean Piaget's theories about the sequential acquisition of scientific knowledge.

Fossils, DNA, and Nothing: evidence of evolutionary biology university students find compelling

Fossils, DNA, and Nothing: evidence of evolutionary biology university students find compelling

On the Correctness of Maximum Parsimony for Data with Few Substitutions in the NNI Neighborhood of Phylogenetic Trees

AbstractEstimating phylogenetic trees, which depict the relationships between different species, from aligned sequence data (such as DNA, RNA, or proteins) is one of the main aims of evolutionary biology. However, tree reconstruction criteria like maximum parsimony do not necessarily lead to unique trees and in some cases even fail to recognize the “correct” tree (i.e., the tree on which the data was generated). On the other hand, a recent study has shown that for an alignment containing precisely those binary characters (sites) which require up to two substitutions on a given tree, this tree will be the unique maximum parsimony tree. It is the aim of the present paper to generalize this recent result in the following sense: We show that for a tree T with n leaves, as long as $$k<\frac{n}{8}+\frac{11}{9}-\frac{1}{18}\sqrt{9\cdot \left( \frac{n}{4}\right) ^2+16}$$ k < n 8 + 11 9 - 1 18 9 · n 4 2 + 16 (or, equivalently, $$n>9k-11+\sqrt{9k^2-22k+17}$$ n > 9 k - 11 + 9 k 2 - 22 k + 17 , which in particular holds for all $$n\ge 12k$$ n ≥ 12 k ), the maximum parsimony tree for the alignment containing all binary characters which require (up to or precisely) k substitutions on T will be unique in the NNI neighborhood of T and it will coincide with T, too. In other words, within the NNI neighborhood of T, T is the unique most parsimonious tree for the said alignment. This partially answers a recently published conjecture affirmatively. Additionally, we show that for $$n\ge 8$$ n ≥ 8 and for k being in the order of $$\frac{n}{2}$$ n 2 , there is always a pair of phylogenetic trees T and $$T'$$ T ′ which are NNI neighbors, but for which the alignment of characters requiring precisely k substitutions each on T in total requires fewer substitutions on $$T'$$ T ′ .

Phylogenomic analyses of hamsters (Cricetinae) inferred from GBS data and mitochondrial genomes.

Accurate species delimitation and identification is crucial for species conservation, providing a foundation for studies on evolutionary biology, ecology, and essentially all biological disciplines. The subfamily Cricetinae (Cricetidae, Rodentia), known as hamsters, is widely distributed in the Palearctic region. At present, there are nine genera and 18 species of hamsters are recognized worldwide, although the taxonomic status of certain taxa remains unclear. In this study, we collected 146 hamster specimens representing 14 species and generated new mitochondrial genomes and nuclear genome-wide single nucleotide polymorphisms (SNPs) to explore their relationships among these hamsters using multiple species delimitation approaches. Results showed: (1) strong phylogenetic support for the classification of Urocricetus, Nothocricetulus, and Cansumys as separate genera; (2) Urocricetus contained two separate species, U. kamensis and U. lama, with U. alticola and U. tibetanus considered synonyms of U. lama; (3) U. kamensis and U. lama are separated by the Nujiang River, with the matching divergence time suggesting that the formation of the river was the primary evolutionary factor driving the species differentiation, and (4) genetic differentiation occurred within the Tscherskia genus, which included two cryptic species.

Participatory science and course-based undergraduate research experience to improve research-informed teaching of evolution and palaeontology

AbstractThis study introduces a participatory science-inspired approach to teaching and curriculum design, involving undergraduate students directly in active research. Using a case study on dinosaur eye size, integrated into a first-year undergraduate course in Geology and Palaeontology at a UK university, this study presents the advantages and disadvantages of this approach for both teachers and learners. As part of the study, 22 undergraduate students were involved in data collection, analysis, and the subsequent publication processes, emphasizing active student participation in research. A subsequent survey demonstrated high student engagement and perceived relevance of this participatory science-style teaching approach. Results indicate that students found the approach appealing, engaging, and beneficial for understanding scientific concepts and methods. The case study shows that a participatory science approach through a course-based research experience can enhance student engagement and learning by providing meaningful, hands-on research experiences. This approach allowed students to apply theoretical knowledge in a realistic context, fostering their understanding of evolutionary theory through active data collection and analysis. However, care should be taken concerning data accuracy and ethical aspects, such as exploitation of labour and the recognition of knowledge creators and participants. Despite these challenges, the benefits of integrating such approaches into higher education curricula can be substantial, offering a valuable model for teaching evolutionary theory and related topics.

Genetic study of intrahepatic cholestasis of pregnancy in Chinese women unveils East Asian etiology linked to historic HBV epidemic.

Intrahepatic cholestasis of pregnancy (ICP) is the most common and high-risk liver disorder during pregnancy, with varying prevalence across populations. Our understanding of the mechanisms underlying ICP and its population difference remains limited. This study delves into the genetic etiology of ICP in East Asians, drawing comparisons with Europeans to comprehend ICP etiology in the context of genetic background and evolution. We conducted the hitherto largest-scale genome-wide association studies (GWAS) on fasting total serum bile acids (TBA) and ICP in 98,269 Chinese pregnancies. The findings were replicated in three cohorts and compared with European populations. Additionally, phenome-wide association and spatio-temporal evolution analyses were employed to investigate the function and evolutionary patterns of ICP-associated loci. We identified eight loci for fasting TBA and four for ICP, including ten novel loci. Notably, we discovered an East-Asian-specific locus within a 0.4Mbp region at 14q24.1, which increases fasting TBA by 6.12 μmol/L and ICP risk by 16.56-fold per risk allele (95% CI: 16.43 to 16.69, P = 7.06×10-381). Phenome-wide association and spatial-temporal evolution analyses revealed that this 14q24.1 ICP risk locus confers resistance to hepatitis B and has become prevalent in East and Southeast Asia within the last 3,000 years. We uncovered a distinct genetic etiology of ICP in East Asians, likely linked to a historic HBV epidemic in East and Southeast Asia within the last 3,000 years. These findings enhance our understanding of ICP pathophysiology and offer potential for more precise detection, assessment, and treatment of the disorder. This study provides novel insights into the genetic basis of intrahepatic cholestasis of pregnancy (ICP) in East Asian populations, where little was previously known. The identification of the East-Asian-specific 14q24.1 locus, associated with both fasting TBA and ICP, and its connection to a historical hepatitis B epidemic emphasize the importance of incorporating population-specific history into disease research. These findings are crucial for researchers studying pregnancy-related liver disorders and clinicians providing care to pregnant women, enabling more accurate screening, risk assessment, and targeted interventions for ICP.

Investigation of the interference between organic and mineral matter in coal and carbonaceous shale using FTIR spectroscopy

ABSTRACT Thirty-two coal (lignite-bituminous in rank) and carbonaceous shale samples, ranging from immature to overmature, were collected from the various coal-bearing basins (Saurashtra Basin, Bikaner Nagaur Basin, Damodar Basin, Mahanadi Basin, and Foreland Basin) in India and characterized petrographically (vitrinite reflectance and maceral composition), geochemically (total organic carbon and total sulfur) and chemically (Fourier Transform Infrared spectroscopy, FTIR). This paper explores utilization of FTIR study on bulk non-demineralized carbonaceous shale and coal to examine the interference between mineral and organic matter visible on FTIR spectra and application of such techniques to assess organic matter chemistry based on FTIR signal. Mineral matter is considerably affecting the organic matter FTIR signal in the region between 1700–1350 and 900–700 cm−1, while the 3100–2800 cm−1 region is unaffected. The general trends of organic matter evolution with thermal maturity, i.e. a decrease of aliphatic and oxygen-bearing groups and increase in aromatic signal, are visible in bulk non-demineralized samples; however, the interpretation of the signal is problematic due to the dilution-related signal weakening and region-specific overlapping. The quality of the FTIR signal is lower than the signal from demineralized kerogens or targeted specific maceral grains via combination of FTIR with microscopy. The spectra can still be useful for more qualitative aspects of FTIR, like assessment of organic functional groups, study of coal impurities, or as a complementary method in conjunction with other analytical techniques such as X-ray for mineral matter characterization.

A Natural Serotonin Stimulant for Appetite Suppression and Targeted Eating as an Alternative to Conventional Obesity Treatments

Recent advances in obesity management reflect the integration of pharmacological, surgical, and behavioral interventions, yet sustainable long-term outcomes remain elusive due to high attrition rates, the complexity of protocol compliance – and for some, costs, risks, and serious side effects. This research combined a patented nutraceutical designed to naturally stimulate serotonin, a biologic hunger agonist, to thereby aid in appetite control and facilitate weight loss through ‘Targeted Eating,’ a single, unrestricted daily meal protocol. Initial results from this ‘real world’ user study indicate promising weight management outcomes and compliance with this eating strategy. By exploring the evolutionary biology of perceived hunger and the anatomy associated with episodic versus circadian consumption, the study thus proposes a paradigm shift in obesity treatment and suggests further approaches to provide innovative solutions to the global obesity crisis.

Molecular epidemiology and pathogenicity of Wesselsbron virus circulating in Africa.

Wesselsbron is a neglected, mosquito-borne zoonotic disease transmitted by several species of virus-infected Aedes mosquitoes endemic to tropical regions in Africa. It affects primarily domestic livestock species with teratogenic effects, but can jump to humans. Herein, we investigated the molecular epidemiology of Wesselsbron virus in Africa using whole genome sequencing and structural analysis, and assessed its pathogenicity and tropism through in vivo experiments. A total of twenty-five isolates collected from three countries were successfully characterized. Our study is noteworthy by identifying, for the first time, inter-clade recombination events on the genome of Wesselsbron virus. However, more investigations on the precise molecular mechanisms conducting the occurrence of recombination on the genome of Wesselsbron virus, are warranted. The identification of polymorphisms on motifs of virulence and selection pressures on major proteins showed evidence of genetic evolution for Wesselsbron virus. The clade 1 was more pathogenic and neurotropic in suckling mice and the intramuscular route was found to be the best transmission mode. Our findings also provide new insights in the pathogenicity and tropism of Wesselsbron virus, which could be useful for prevention, preparedness and future outbreak response. Considering its high prevalence in mosquito populations and the increasing number of sporadic human cases, Wesselsbron virus merits more attention in terms of prevention and preparedness, as its mosquito vectors continue to globally expand and there is no vaccine.

Structural variations in livestock genomes and their associations with phenotypic traits: a review

Genomic structural variation (SV) refers to differences in gene sequences between individuals on a genomic scale. It is widely distributed in the genome, primarily in the form of insertions, deletions, duplications, inversions, and translocations. Due to its characterization by long segments and large coverage, SVs significantly impact the genetic characteristics and production performance of livestock, playing a crucial role in studying breed diversity, biological evolution, and disease correlation. Research on SVs contributes to an enhanced understanding of chromosome function and genetic characteristics and is important for understanding hereditary diseases mechanisms. In this article, we review the concept, classification, main formation mechanisms, detection methods, and advancement of research on SVs in the genomes of cattle, buffalo, equine, sheep, and goats, aiming to reveal the genetic basis of differences in phenotypic traits and adaptive genetic mechanisms through genomic research, which will provide a theoretical basis for better understanding and utilizing the genetic resources of herbivorous livestock.