Evolution Research Articles

Rmacrostrat : An R package for accessing and retrieving data from the Macrostrat geological database

The geological record is a vast archive of information that provides the only empirical data about the evolution of the Earth. In recent years, concentrated efforts have been made to compile macrostratigraphic data into the online centralized database Macrostrat. Macrostrat is a global stratigraphic database containing information regarding surface and subsurface rock units and their respective ages, lithologies, geographic extents, and various other associated metadata. However, these raw data are currently directly accessible only through the Macrostrat application programming interface, which is a barrier to potential users that are less familiar with such services. This data accessibility hurdle currently prevents full capitalization of the value offered by Macrostrat, particularly its potential to improve understanding of the geological and biological evolution of the Earth. Here, we introduce rmacrostrat, an R package that interfaces with the Macrostrat database to access and retrieve a variety of geological, paleontological, and economic data directly into the R programming environment. In this article, we provide details about how the package can be installed, its implementation, and potential use cases. For the latter, we showcase how rmacrostrat can be used to visualize regional stratigraphic columns, produce regional geologic outcrop maps, and investigate temporal trends in macrostratigraphic units. We hope that this package will make geological data more readily accessible and in turn will facilitate new research utilizing Earth system data.

Prevalence and genetic evolution analysis of porcine epidemic diarrhea virus and porcine circovirus type 2 in Sichuan Province, China, from 2023 to 2024.

Porcine circovirus type 2 (PCV2) and Porcine epidemic diarrhea virus (PEDV) are highly prevalent in Sichuan, significantly affecting the swine industry's development. PCV2, known for its immunosuppressive effects, can compromise pigs' immune systems, while PEDV typically causes diarrhea in piglets, leading to high mortality rates. Despite their impact, recent studies on the epidemiology and genetic diversity of PCV2 and PEDV within Sichuan Province remain limited. This study examines clinical samples from 352 diarrheal piglets across 63 pig farms in 17 regions of Sichuan Province, revealing positivity rates of 42.33% (149/352) for PCV2 and 50.28% (177/352) for PEDV, with a co-infection rate of 27.56% (97/352). Notably, the highest positivity rates were observed in Ziyang for PCV2 at 61.90% (13/21), and in Meishan for PEDV at 73.81% (31/42), both regions also reported the highest co-infection rates of 47.62%. Seasonal analysis indicated that PEDV infections peaked during winter, whereas PCV2 showed no significant seasonal trends. Phylogenetic analysis identified 14 PCV2 strains, categorizing 2 as PCV2b (14.29%), 10 as PCV2d (71.43%), and 2 as PCV2e (14.29%). Among the 16 PEDV strains, 2 were classified as G1a (12.5%) and 14 as G2a (87.5%), with PCV2d and PEDV G2a identified as the predominant strains in the region. The study also highlights a high mutation rate at the antigenic sites of both viruses, potentially affecting vaccine efficacy. These findings underscore the need for ongoing surveillance and vaccine development tailored to the prevalent strains to improve control measures within the province.

Generalized Multicategories: Change-of-Base, Embedding, and Descent

Via the adjunction -∗1⊣V(1,-):Span(V)→V-Mat\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$ - *\\mathbbm {1} \\dashv \\mathcal V(\\mathbbm {1},-) :\ extsf {Span}({\\mathcal {V}}) \\rightarrow {\\mathcal {V}} \ ext {-} \ extsf {Mat} $$\\end{document} and a cartesian monad T on an extensive category V\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$ {\\mathcal {V}} $$\\end{document} with finite limits, we construct an adjunction -∗1⊣V(1,-):Cat(T,V)→(T¯,V)-Cat\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$ - *\\mathbbm {1} \\dashv {\\mathcal {V}}(\\mathbbm {1},-) :\ extsf {Cat}(T,{\\mathcal {V}}) \\rightarrow ({\\overline{T}}, \\mathcal V)\ ext{- }\ extsf{Cat} $$\\end{document} between categories of generalized enriched multicategories and generalized internal multicategories, provided the monad T satisfies a suitable property, which holds for several examples. We verify, moreover, that the left adjoint is fully faithful, and preserves pullbacks, provided that the copower functor -∗1:Set→V\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$ - *\\mathbbm {1} :\ extsf {Set} \\rightarrow {\\mathcal {V}} $$\\end{document} is fully faithful. We also apply this result to study descent theory of generalized enriched multicategorical structures. These results are built upon the study of base-change for generalized multicategories, which, in turn, was carried out in the context of categories of horizontal lax algebras arising out of a monad in a suitable 2-category of pseudodouble categories.

Teologi Islam dan Kosmologi: Penciptaan Alam Semesta Menurut Al-Qur'an, Konsep Multiverse, dan Hubungan Teori Evolusi dengan Ajaran Islam dalam Perspektif Sains Modern

The development of modern science, particularly in cosmology and evolutionary biology, raises questions about how Islamic theology can engage in dialogue with contemporary scientific theories such as the Big Bang theory, the multiverse concept, and the theory of evolution. The objective of this research is to explore Islamic theology and cosmology, focusing on the aspects of the Creation of the Universe according to the Qur'an, the Multiverse Concept, and the Relationship between Evolutionary Theory and Islamic Teachings from the perspective of modern science. The method used in this study is a Systematic Literature Review by analyzing previous relevant studies on Islamic theology and cosmology. The findings show a connection between Islamic theology and the science of the creation of the universe, the multiverse, and evolutionary theory. The Qur'an presents creation as the will of God, encompassing both physical and spiritual dimensions. The concept of the multiverse is acceptable as long as it does not contradict the oneness of God (tawhid), while the theory of evolution is understood as part of the divine plan. Dialogue between theology and science enriches our understanding of the cosmos and opens up opportunities for relevant interdisciplinary research.

DESAFIOS DO ENSINO DE PALEONTOLOGIA NA ESCOLA: CONCEPÇÕES DOS ALUNOS SOBRE A CIÊNCIA PALEONTOLÓGICA

ABSTRACT - Paleontology is one of the natural sciences that can provide students with an awareness of the environment in which they live and how the evolution of organisms provides the diversity seen today. Based on this assumption, this article presents results through the analysis of paleontological knowledge data obtained in a Reference School in High School with 43 students of the 2nd year. The methodology consisted of applying a qualitative and quantitative questionnaire to obtain data and diagnose the students' paleontological knowledge. It was seen that the students' knowledge about this science is very low, it was noted that when the subject is dinosaurs, a subject that tends to be always interesting for most students, they showed very little interest, demonstrating not knowing the species discovered in Brazil, but on the other hand, it was noted that they knew that paleontology helps to clarify and support evolutionary theory. Despite this, it is necessary to have pedagogical intervention projects to disseminate this science and awaken curiosity in students to become future researchers.

Resource-rational contractualism: A triple theory of moral cognition.

It is widely agreed upon that morality guides people with conflicting interests towards agreements of mutual benefit. We therefore might expect numerous proposals for organizing human moral cognition around the logic of bargaining, negotiation, and agreement. Yet, while "contractualist" ideas play an important role in moral philosophy, they are starkly underrepresented in the field of moral psychology. From a contractualist perspective, ideal moral judgments are those that would be agreed to by rational bargaining agents-an idea with wide-spread support in philosophy, psychology, economics, biology, and cultural evolution. As a practical matter, however, investing time and effort in negotiating every interpersonal interaction is unfeasible. Instead, we propose, people use abstractions and heuristics to efficiently identify mutually beneficial arrangements. We argue that many well-studied elements of our moral minds, such as reasoning about others' utilities ("consequentialist" reasoning) or evaluating intrinsic ethical properties of certain actions ("deontological" reasoning), can be naturally understood as resource-rational approximations of a contractualist ideal. Moreover, this view explains the flexibility of our moral minds-how our moral rules and standards get created, updated and overridden and how we deal with novel cases we have never seen before. Thus, the apparently fragmentary nature of our moral psychology-commonly described in terms of systems in conflict-can be largely unified around the principle of finding mutually beneficial agreements under resource constraint. Our resulting "triple theory" of moral cognition naturally integrates contractualist, consequentialist and deontological concerns.

That's Not a Hybrid: How to Distinguish Patterns ofAdmixture and Isolation By Distance.

Describing naturally occurring genetic variation is a fundamental goal of molecular phylogeography and population genetics. Popular methods for this task include STRUCTURE, a model-based algorithm that assigns individuals to genetic clusters, and principal component analysis (PCA), a parameter-free method. The ability of STRUCTURE to infer mixed ancestry makes it popular for documenting natural hybridisation, which is of considerable interest to evolutionary biologists, given that such systems provide a window into the speciation process. Yet, STRUCTURE can produce misleading results when its underlying assumptions are violated, like when genetic variation is distributed continuously across geographic space. To test the ability of STRUCTURE and PCA to accurately distinguish admixture from continuous variation, we use forward-time simulations to generate population genetic data under three demographic scenarios: two involving admixture and one with isolation by distance (IBD). STRUCTURE and PCA alone cannot distinguish admixture from IBD, but complementing these analyses with triangle plots, which visualise hybrid index against interclass heterozygosity, provides more accurate inference of demographic history, especially in cases of recent admixture. We demonstrate that triangle plots are robust to missing data, while STRUCTURE and PCA are not, and show that setting a low allele frequency difference threshold for ancestry-informative marker (AIM) identification can accurately characterise the relationship between hybrid index and interclass heterozygosity across demographic histories of admixture and range expansion. While STRUCTURE and PCA provide useful summaries of genetic variation, results should be paired with triangle plots before admixture is inferred.

Unprecedented spread and genetic evolution of the Oropouche virus.

Unprecedented spread and genetic evolution of the Oropouche virus.

Evolutionary Pedagogy: Evolutionary Foundations of Certain Pedagogical Practices and Their Implications in Teaching Processes

Human evolution is the result of highly complex biological, psychological and cultural changes over millions of years. This process can be traced back to the evolution of modern humans, thanks to the ability of human ancestors to adapt to environmental conditions. The evolutionary process involves the development not only of physical characteristics, but also of mental capacities and social structures. It is therefore a natural consequence that evolution has fundamentally influenced human cultural and psychological traits. The main reason for the emergence of fields such as evolutionary psychology and evolutionary psychiatry in the light of recent studies is the search for the contributions of evolutionary processes to such fields. Evolutionary pedagogy is basically the result of such a search. It was shaped as a result of the search for the reflections of psychological and cultural situations affected by evolutionary processes on pedagogy. Therefore, evolutionary pedagogy is a synthesis and it seeks to explain how many pedagogical practices may have been shaped in the evolutionary process. To this end, it draws heavily on evolutionary psychology and directly on human biological evolution. Such a quest for grounding predicts that a more beneficial process can be realized in the teaching-learning process by reproducing evolutionary situations in the classroom environment. In other words, the learning process can become more effective if teachers use the features compatible with evolutionary processes in their teaching techniques, classroom management, and the development of skills for learning to learn, and if they include them in the classroom environment. This is the main starting point of the study. Throughout the study, some examples of the pedagogical practices in which can manifest itself are emphasized. In addition to the explanations and examples given in the study, other researchers may associate different pedagogical practices with evolutionary processes. Therefore, evolutionary pedagogy is not only a new field but also a field that is open to the interest of researchers as a field open to development.

Comparative analysis of complete chloroplast genomes of 14 Asteraceae species.

The Asteraceae family, the largest and one of the most diverse families of angiosperms, presents significant challenges in taxonomic classification and systematic research due to its vast species diversity and morphological complexity. A comprehensive understanding of the chloroplast genomes within this family is essential for refining taxonomic classifications and advancing phylogenetic studies. In this study, we sequenced the complete chloroplast genomes of 14 Asteraceae species and conducted a thorough bioinformatic analysis of their characteristics. The chloroplast genomes, ranging from 150,907bp to 152,858bp, exhibit a typical quadripartite structure: a large single-copy (LSC) region (83,044bp to 84,625bp), a small single-copy (SSC) region (18,223bp to 18,673bp), and a pair of inverted repeats (IRs) (24,806bp to 25,201bp). These genomes encode 87 to 89 protein-coding genes (PCGs), 36 to 37 tRNA genes, and 8 rRNA genes, with high conservation in size, structure, gene content, and order. Comparative analysis with other Asteraceae species' chloroplast genomes revealed notable similarities and structural variations, particularly in the IR regions. Nucleotide polymorphism analysis identified four genes-trnY-GUA, trnE-UUC, ycf1, and rrn23-with higher Pi values, suggesting potential hotspots for evolutionary studies. Phylogenetic analysis using maximum likelihood (ML) and Bayesian inference (BI) approaches provided new insights, proposing the reclassification of Himalaiella auriculata and Jacobaea raphanifolia as independent genera, distinct from Saussurea and Senecio. This study presents a comprehensive analysis of the chloroplast genome structures and phylogenetic relationships of 14 Asteraceae species, offering critical data for future molecular identification, evolutionary biology, and population genetics research. The findings hold significant implications for the ongoing refinement of Asteraceae taxonomic classifications and enhance our understanding of the evolutionary dynamics within this complex family.

An adaptive differential evolution algorithm driven by multiple probabilistic mutation strategies for influence maximization in social networks

Influence maximization is a critical research topic of social network analysis, particularly with the increasing involvement of individuals in the global networked society. The purpose of the problem is to identify k influential nodes from the social network and activate them initially to maximize the expected number of influenced nodes at the end of the spreading process. Although some meta-heuristics based on swarm intelligence or biological evolution have been proposed to tackle this intractable problem, further investigation is required to refine the exploration and exploitation operations based on the iterative information from the evolutionary process. In this paper, an adaptive differential evolution algorithm driven by multiple probabilistic mutation strategies is proposed for the influence maximization problem. In order to enhance the evolutionary capability of the later stages of the discrete differential evolution, the mutation in the framework, consisting of three policies, namely comprehensive learning particle swarm mutation strategy, differential mutation strategy, and perturbation strategy, is implied based on different probabilistic models. An adaptive local search strategy is presented to improve the local optimum results based on a potential alternative library consisting of structural hole nodes, which guides the differential evolution to find a more optimal solution. Experimental results on six real-world social networks demonstrate the competitive performance of the proposed algorithm in terms of both efficacy and efficiency compared to state-of-the-art algorithms.

The legacy and evolvability of Pere Alberch's ideas.

Pere Alberch played a pivotal role in shaping the field of evolutionary developmental biology during the 1980s and 1990s. Whereas initially his contributions were sidelined by the empirical advancements of the molecular revolution in developmental and evolutionary biology, his theoretical insights have left a lasting impact on the discipline. This article provides a comprehensive review of the legacy and evolvability of Alberch's ideas in contemporary evo-devo, which included the study of morphogenesis as the proper level of developmental causation, the interplay between developmental constraints and natural selection, the epistemic role of teratologies, the origin of evolutionary novelties and the concept of evolvability.

Enhanced flight performance and adaptive evolution of Mesozoic giant cicadas.

Insects have evolved diverse ecological flight behaviors and adaptations that played a key role in their large-scale evolutionary patterns. However, the evolution of their flight performance is poorly understood because reconstructing flight abilities of extinct insects is highly challenging. Here, we propose an integrated approach to reveal the evolution of flight performance of Palaeontinidae (giant cicadas), a Mesozoic arboreal insect clade with large bodies and wings. Our analyses unveil a faunal turnover from early to late Palaeontinidae during the latest Jurassic-earliest Cretaceous, accompanied by a morphological adaptive shift and remarkable improvement in flight abilities including increased flight speed and enhanced maneuverability. The adaptive aerodynamic evolution of Palaeontinidae may have been stimulated by the rise of early birds, supporting the hypothesis of an aerial evolutionary arms race (Air Race) between Palaeontinidae and birds. Our results provide a potential example of predator-induced morphological and behavioral macroevolution and contribute to our understanding of how powered flight has shaped animal evolution.

Selective expansion of motor cortical projections in the evolution of vocal novelty.

Deciphering how cortical architecture evolves to drive behavioral innovations is a long-standing challenge in neuroscience and evolutionary biology. Here, we leverage a striking behavioral novelty in the Alston's singing mouse ( Scotinomys teguina ), compared to the laboratory mouse ( Mus musculus ), to quantitatively test models of motor cortical evolution. We used bulk tracing, serial two-photon tomography, and high-throughput DNA sequencing of over 76,000 barcoded neurons to discover a specific and substantial expansion ( ∼ 200%) of orofacial motor cortical (OMC) projections to the auditory cortical region (AudR) and the midbrain periaqueductal gray (PAG), both implicated in vocal behaviors. Moreover, analysis of individual OMC neurons' projection motifs revealed preferential expansion of exclusive projections to AudR. Our results imply that selective expansion of ancestral motor cortical projections can underlie behavioral divergence over short evolutionary timescales, suggesting potential mechanisms for the evolution of enhanced cortical control over vocalizations-a crucial preadaptation for human language.

An Edge-on Regular Disk Galaxy at z = 5.289

While rotation-supported gas disks are known to exist as early as at z ≈ 7, it is still a general belief that stellar disks form late in the Universe. This picture is now being challenged by the observations from the James Webb Space Telescope (JWST), which have revealed a large number of disk-like galaxies that could be at z > 3, with some being candidates at z > 7. As an early formation of stellar disks will greatly impact our theory of galaxy formation and evolution, it is important to determine when such systems first emerged. Here we present D-CEERS-RUBIES-z5289 at z = 5.289 ± 0.001, the second confirmed stellar disk at z > 5, discovered using the archival JWST NIRCam imaging and NIRSpec spectroscopic data. This galaxy has a highly regular edge-on disk morphology, extends to ∼6.2 kpc along its major axis, and has an effective radius of ∼1.3–1.4 kpc. Such a large stellar disk is yet to be produced in numerical simulations. By analyzing its 10-band spectral energy distribution using four different tools, we find that it has a high stellar mass of 109.5–10.0 M ⊙. Its age is in the range of 330–510 Myr, and it has a mild star formation rate of 10–30 M ⊙ yr−1. While the current spectroscopic data do not allow the derivation of its rotation curve, the width of its Hα line from the partial slit coverage on one side of the disk reaches ∼345 km s−1, which suggests that it could have a significant contribution from rotation.

A JWST Pure-Parallel Search for the First Galaxies With PANORAMIC

The James Webb Space Telescope offers unparalleled capabilities for observing the most distant objects in the universe, allowing us to study the first galaxies to form. In this work, the Lyman-break technique and spectral energy distribution fitting were used to analyse the JWST PANORAMIC survey and identify 26 robust galaxy candidates at redshifts greater than 9.5, including three around redshift 14.5. These candidates will make excellent targets for follow-up spectroscopy. The derived UV luminosity function at z = 14.5 is consistent with literature determinations at similar redshifts and implies a modest evolution in the number density of galaxies from z ∼ 14 to z ∼ 11. Future research based on this work could determine when the first galaxies formed, confirming or challenging current theories of cosmic evolution.

Genomes of Microtus rodents highlight the importance of olfactory and immune systems in their fast radiation.

The characterization of genes and biological functions underlying functional diversification and the formation of species is a major goal of evolutionary biology. In this study, we investigated the fast radiation of Microtus voles, one of the most speciose group of mammals, which shows strong genetic divergence despite few readily observable morphological differences. We produced an annotated reference genome for the common vole, Microtus arvalis, and resequenced the genomes of 10 different species and evolutionary lineages spanning the Microtus speciation continuum. Our full genome sequences illustrate the recent and fast diversification of this group, and we identified genes in highly divergent genomic windows that have likely particular roles in their radiation. We found three biological functions enriched for highly divergent genes in most Microtus species and lineages: olfaction, immunity and metabolism. In particular, olfaction-related genes (mostly olfactory receptors and vomeronasal receptors) are fast evolving in all Microtus species indicating the exceptional importance of the olfactory system in the evolution of these rodents. Of note is e.g. the shared signature among vole species on Olfr1019 which has been associated with fear responses against predator odours in rodents. Our analyses provide a genome-wide basis for the further characterization of the ecological factors and processes of natural and sexual selection that have contributed to the fast radiation of Microtus voles.

Identification of positions in human aldolase a that are neutral for apparent KM

According to evolutionary theory, many naturally-occurring amino acid substitutions are expected to be neutral or near-neutral, with little effect on protein structure or function. Accordingly, most changes observed in human exomes are also expected to be neutral. As such, accurate algorithms for identifying medically-relevant changes must discriminate rare, non-neutral substitutions against a background of neutral substitutions. However, due to historical biases in biochemical experiments, the data available to train and validate prediction algorithms mostly contains non-neutral substitutions, with few examples of neutral substitutions. Thus, available training sets have the opposite composition of the desired test sets. Towards improving a dataset of these critical negative controls, we have concentrated on identifying neutral positions – those positions for which most of the possible 19 amino acid substitutions have little effect on protein structure or function. Here, we used a strategy based on multiple sequence alignments to identify putative neutral positions in human aldolase A, followed by biochemical assays for 147 aldolase substitutions. Results showed that most variants had little effect on either the apparent Michaelis constant for substrate fructose-1,6-bisphosphate or its apparent cooperativity. Thus, these data are useful for training and validating prediction algorithms. In addition, we created a database of these and other biochemically characterized aldolase variants along with aldolase sequences and characteristics derived from sequence and structure analyses. This database is publicly available at https://github.com/liskinsk/Aldolase-variant-and-sequence-database.

Evolusi Lanskap Budaya Tamansari Yogyakarta

Kota Yogyakarta, known for its cultural richness and sovereignty, displays its cultural heritage characteristics through Keraton Yogyakarta's heritage object. Tamansari is Keraton Yogyakarta's cultural complex built for the royal family's leisure. For 258 years, Tamansari Complex's cultural landscape has been undergoing transformation. The transformations trigger the evolutional process of the Tamansari Complex’s cultural landscape identity. This thesis investigates the evolutional process of Tamansari Complex's cultural landscape in 1765 - 2023. Cultural Landscape Evolution theory acts as the analysis method of this thesis research. The research time spans from January - August 2023. This research is the first attempt to view the Tamansari Complex from the perspective of cultural landscape focusing on the evolutional process of the Tamansari Complex’s cultural landscape identity.

Metopism and Its Clinical Relevance: A Persistent Suture.

Metopic suture is a dense fibrous joint extending from nasion to bregma. Normally, closure of this suture takes place between 1-8 years of age. Failure of this closure beyond 8 years leads to persistent metopic suture. Persistent metopic suture may mimic skull fracture. To differentiate metopism from frontal bone fracture. 54 dry skull of adult humans in were studied. These skulls were observed for the presence (complete or incomplete suture) or absence of metopic suture. Metopic suture was found in 3.7% skulls. Both complete and incomplete metopic suture were found in 1.85% of the dry skulls. Neurosurgeons, radiologists, otorhinolaryngologists, physicians, anatomists, forensic specialists, anthropologists and evolutionary biologists should have knowledge of this anatomical variation. This case series focusses on the importance of metopism. Metopism is a topic, which has not been much studied.