Evolution Research Articles

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.

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.

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.

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.

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.

The origin of mutational epistasis.

The interconnected processes of protein folding, mutations, epistasis, and evolution have all been the subject of extensive analysis throughout the years due to their significance for structural and evolutionary biology. The origin (molecular basis) of epistasis-the non-additive interactions between mutations-is still, nonetheless, unknown. The existence of a new perspective on protein folding, a problem that needs to be conceived as an 'analytic whole', will enable us to shed light on the origin of mutational epistasis at the simplest level-within proteins-while also uncovering the reasons why the genetic background in which they occur, a key component of molecular evolution, could foster changes in epistasis effects. Additionally, because mutations are the source of epistasis, more research is needed to determine the impact of post-translational modifications, which can potentially increase the proteome's diversity by several orders of magnitude, on mutational epistasis and protein evolvability. Finally, a protein evolution thermodynamic-based analysis that does not consider specific mutational steps or epistasis effects will be briefly discussed. Our study explores the complex processes behind the evolution of proteins upon mutations, clearing up some previously unresolved issues, and providing direction for further research.

Voices without words: the spectrum of nonverbal vocalisations

ABSTRACT Nonverbal vocalisations are a fundamental part of human life. Here, we use Tinbergen’s ethological framework to examine the functions, ontogenetic trajectories, evolutionary history, and underlying mechanisms of five types of vocalisations: cries, laughter, moans, screams, and sighs. Integrating insights from evolutionary biology and social psychology, we demonstrate how biological functions and social factors shape vocalisations. Tracing the development of vocalisations from infancy to adulthood emphasises the role of innate tendencies, as well as delineating processes of social learning. For each vocalisation type, we map their distinct nature and communicative potential: cries are crucial for survival and caregiving responses; laughter fosters social bonding and group cohesion; moans convey a wide range of internal states from pleasure to discomfort; screams serve as urgent alarms in critical situations; and sighs regulate emotions and signal shifts in emotional states. We conclude that both biological and social factors must be considered to understand nonverbal vocalisations.

Factors contributing to organelle genomes size variation and the intracellular DNA transfer in Polygonaceae

The use of complete organelle genomes, including chloroplast and mitochondrial genomes, is a powerful molecular method for studying biological evolution and gene transfer. However, in the case of Polygonaceae, an important family with numerous edible, medicinal, and ornamental species, the mitochondrial genomes of only three species have been sequenced and analyzed. In this study, we present the mitochondrial and chloroplast genomes of two important Tibetan medicinal plants, Bistorta viviparum and B. macrophyllum. All the organelle genomes are assembled into a single circular structure and contain a common set of 32 protein-coding genes (PCGs). Some genes such as rps2 and ndhF were found to have high nucleotide polymorphism (Pi) in the chloroplast genomes, while cox1, mttB and rps12 showed pronounced Pi values in the mitochondrial genomes. Furthermore, our analysis revealed that most chloroplast genes and mitochondrial PCGs in Polygonaceae plants are under purifying selection. However, a few genes, including the chloroplast gene psaJ and the mitochondrial genes ccmFc, atp8 and nad4, showed positive selection in certain Polygonaceae plants, as indicated by a Ka/Ks ratio greater than one. Structural variation analysis revealed a wealth of differences between the mitochondrial genomes of five Polygonaceae species, with a particularly notable large-scale inversion observed between Reynoutria japonica and Fallopia aubertii. Furthermore, an analysis of the homologous sequences in the chloroplast and mitochondrial genomes revealed that the rps7 has been transferred from the chloroplast to the mitochondrial genome in all five Polygonaceae species. Finally, ecological niche models were constructed for B. viviparum and B. macrophyllum, indicating that mean annual temperature and altitude are the main climatic factors influencing the distribution of both species. Although the current distribution of B. viviparum is significantly wider than that of B. macrophyllum, projections suggest that the optimal growth ranges of both species will expand in the future, with B. macrophyllum potentially exceeding B. viviparum. This study not only contributes to the plastid genome database for Polygonaceae plants, but also provides theoretical insights into the adaptive evolution of these plants.

Phylogenetic Insights into H7Nx Influenza Viruses: Uncovering Reassortment Patterns and Geographic Variability

Influenza A viruses (IAVs), which belong to the Orthomyxoviridae family, are RNA viruses characterized by a segmented genome that allows them to evolve and adapt rapidly. These viruses are mainly transmitted by wild waterfowl. In this study, we investigated the evolutionary processes of H7Nx (H7N1, H7N2, H7N3, H7N4, H7N5, H7N6, H7N7, H7N8, H7N9) viruses, which pose a significant pandemic risk due to the known cases of human infection and their potential for rapid genetic evolution and reassortment. The complete genome sequences of H7Nx influenza viruses (n = 3239) were compared between each other to investigate their phylogenetic relationships and reassortment patterns. For the selected viruses, phylogenetic trees were constructed for eight genome segments (PB2, PB1, PA, HA, NP, NA, M, NS) to assess the genetic diversity and geographic distribution of these viruses. Distinct phylogenetic clades with remarkable geographic patterns were found for the different segments. While the viruses were consistently grouped by subtype based on the NA segment sequences, the phylogeny of the other segment sequences, with the exception of the NS segment, showed distinct grouping patterns based on geographic origin rather than formal subtype assignment. Reassortment events leading to complex phylogenetic relationships were frequently observed. In addition, multiple cases of previously undescribed reassortments between subtypes were detected, emphasizing the fluidity of H7Nx virus populations. These results indicate a high degree of genetic diversity and reassortment within H7Nx influenza viruses. In other words, H7Nx viruses exist as constantly changing combinations of gene pools rather than stable genetic lineages.

Binary Yellow Supergiants in the Magellanic Clouds. I. Photometric Candidate Identification

Recent works have constrained the binary fraction of evolved populations of massive stars in local galaxies such as red supergiants and Wolf–Rayet stars, but the binary fraction of yellow supergiants (YSGs) in the Hertzsprung gap remains unconstrained. Binary evolution theory predicts that the Hertzsprung gap is home to multiple populations of binary systems with varied evolutionary histories. In this paper, we develop a method to distinguish single YSGs from YSG plus O- or B-type main-sequence binaries using optical and ultraviolet photometry, and then apply this method to identify candidate YSG binaries in the Magellanic Clouds. After constructing a set of combined stellar atmosphere models, we find that optical photometry is, given typical measurement and reddening uncertainties, sufficient to discern single YSGs from YSG+OB binaries if the OB-star is at least ∼5M ⊙ for T eff,YSG ∼ 4000 K, but requires a ∼20M ⊙ OB star for YSGs up to T eff,YSG ∼ 9000 K. For these hotter YSG temperatures, ultraviolet photometry allows binaries with OB companions as small as ∼7M ⊙ to be identified. We use color–color spaces developed from these models to search for evidence of excess blue or ultraviolet light in a set of ∼1000 YSG candidates in the Magellanic Clouds. We identify hundreds of candidate YSG binary systems and report a preliminary fraction of YSGs that show a blue/UV color excess of 20%–60%. Spectroscopic follow-up is now required to confirm the true nature of this population.

Aberrant Mitochondrial tRNA Genes Appear Frequently in Animal Evolution.

Mitochondrial tRNAs have acquired a diverse portfolio of aberrant structures throughout metazoan evolution. With the availability of more than 12,500 mitogenome sequences, it is essential to compile a comprehensive overview of the pattern changes with regard to mt-tRNA repertoire and structural variations. This, of course, requires reanalysis of the sequence data of more than 250,000 mt-tRNAs with a uniform workflow. Here, we report our results on the complete reannotation of all mitogenomes available in the RefSeq database by September 2022 using mitos2. Based on the individual cases of mt-tRNA variants reported throughout the literature, our data pinpoint the respective hotspots of change, i.e. Acanthocephala (Lophotrochozoa), Nematoda, Acariformes and Araneae (Arthropoda). Less dramatic deviations of mt-tRNAs from the norm are observed throughout many other clades. Loss of arms in animal mt-tRNA clearly is a phenomenon that occurred independently many times, not limited to a small number of specific clades. The summary data here provide a starting point for systematic investigations into the detailed evolutionary processes of structural reduction and and loss of mt-tRNAs as well as a resource for further improvements of annotation workflows for mt-tRNA annotation.

Mitochondrial genome insights into the spatio-temporal distribution and genetic diversity of Dendrobium hancockii Rolfe (Orchidaceae)

IntroductionWith its distinctive evolutionary rate and inheritance patterns separate from the nuclear genome, mitochondrial genome analysis has become a prominent focus of current research. Dendrobium hancockii Rolfe, a species of orchid with both medicinal and horticultural value, will benefit from the application of the fully assembled and annotated mitochondrial genome. This will aid in elucidating its phylogenetic relationships, comparative genomics, and population genetic diversity.MethodsBased on sequencing results from Illumina combined with PacBio and Nanopore, the mitochondrial genome map of D. hancockii was constructed. Comparative analysis was conducted from the perspectives of phylogeny across multiple species, selection pressure on protein-coding genes, and homologous segments. The population diversity of D. hancockii was analyzed using single nucleotide polymorphism (SNP) data from the mitochondrial genome and single-copy nuclear genes.Results and discussionThis research constructed a circular mitochondrial map for D. hancockii, spanning 523,952 bp, containing 40 unique protein-coding genes, 37 transfer RNA genes, and 4 ribosomal RNA genes. Comparative analysis of mitochondrial genes from 26 land plants revealed a conserved gene cluster, "rpl16-ccmFn-rps3-rps19," particularly within the Dendrobium genus. The mitochondrial genome of D. hancockii exhibits a lower point mutation rate but significant structural variation. Analysis of 103 resequencing samples identified 19,101 SNP sites, dividing D. hancockii into two major groups with limited gene flow between them, as supported by population diversity, genetic structure analysis, principal component analysis, and phylogenetic trees. The geographical distribution and genetic differentiation of D. hancockii into two major groups suggest a clear phytogeographical division, likely driven by ancient geological or climatic events. The close alignment of mitochondrial data with nuclear gene data highlights the potential of the mitochondrial genome for future studies on genetic evolution in this species.