Coevolutionary Patterns Research Articles

Phylogeny of euophryine jumping spiders from ultra‐conserved elements, with evidence on the intersexual coevolution of genitalia (Araneae: Salticidae: Euophryini)

AbstractKnowledge of phylogeny is required to understand the evolution of highly diverse groups such as the euophryine jumping spiders, a lineage showing high species and morphological diversity. In this study, we applied a phylogenomic approach using ultra‐conserved elements (UCE) obtained from 145 taxa to infer the phylogeny of euophryine jumping spiders. The results provide a well‐supported phylogenetic framework for Euophryini, especially for the deeper relationships, in which the monophyly of Euophryini, as well as most clades corresponding to a genus or a group of closely related genera, are strongly supported. Additionally, the evolutionary patterns of male embolus length and female copulatory duct length of 117 euophryine species were investigated through ancestral character state reconstruction and phylogenetically independent contrast analyses using the UCE phylogenetic framework. The results suggest strongly that the evolution of the lengths of male embolus and female copulatory duct in Euophryini is positively correlated. The common ancestor of Euophryini likely had relatively short embolus and copulatory duct, followed by repeated lengthening or shortening of both structures in different lineages. Possible mechanisms that may have caused this intersexual coevolution pattern in Euophryini are discussed. This study advances our understandings of the phylogeny, systematics and genitalic evolution of euophryines, providing a solid foundation for future studies on the diversification and evolution of this jumping spider group.

Elevated Temperature Diminishes Reciprocal Selection in an Experimental Plant-Pollinator-Herbivore System.

The geographic mosaic of coevolution predicts reciprocal selection, the first step in coevolution, to vary with changing biotic and abiotic environmental conditions. Studying how temperature affects reciprocal selection is essential to connect effects of global warming on the microevolutionary patterns of coevolution to the ecological processes underlying them. In this study, we investigated whether temperature influenced reciprocal selection between a plant (Brassica rapa) and its pollinating butterfly herbivore (Pieris rapae). In two temperature environments (ambient and hot), we measured the phenotypes of plants and butterflies, their interactions and fitness, which we used to calculate reciprocal selection. We found a variety of traits involved in reciprocal selection in the ambient environment, but none in the hot environment. We provide experimental evidence that elevated temperature weakens reciprocal selection, which will help better predict the consequences of global warming for coevolution.

Industrial policy and complexity economics

Mainstream theory underlying industrial policy highlights the neoclassical and structuralist approaches. The discussion on structuralist theories readily segues to complexity economics where industrial policy foments structural transformation by creating reinforcing feedback loops, particularly among manufacturing, exports, and investment. Empirical evidence is provided by applying panel cointegration analysis to investigate coevolution patterns among the following variables: investment-GDP ratio, exports-GDP ratio and manufacturing-GDP ratio. Econometric estimates show that there is indeed a long-run relationship that is bidirectional among the three variables. However, this is only a necessary condition for reinforcing feedback loops to materialize. Idiosyncratic factors in each country determine whether industrial policy has led to growth-oriented feedback loops. In the Philippines, despite interventions to boost manufacturing, no growthoriented loop was established because of inadequate investment, particularly in infrastructure. Moreover, exports were hampered by the poor record in latching on to regional production networks. The Republic of Korea has had more success than Malaysia because it strengthened its innovation system. The missing link in Malaysia is own-technology creation.

Patterns of genotype-specific interactions in an obligate host-specific insect pathogenic fungus.

Host-pathogen infections and possible effects on co-evolutionary patterns depend on the genotypes of both host and pathogen. Obligate fungal pathogens of plants are often characterized by host-pathogen genotype-by-genotype (GxG) interactions, but whether these patterns exist in obligate insect fungal pathogens is unclear. We take advantage of the obligate insect pathogenic fungus Entomophthora muscae, where individual isolates are specific to different dipteran host species in nature but can cross-infect multiple fly species in the laboratory. We collected three new isolates of E. muscae from Drosophila species. Phylogenetic analysis showed that Drosophila-isolated E. muscae represents a distinct geographically widespread Drosophila lineage compared to the house fly (Musca domestica) or Delia species-isolated E. muscae. We used the three new E. muscae isolates from Drosophila spp. together with a genetically distinct E. muscae isolate from house flies and assessed their virulence in a cross-infection experiment using one house fly, three Drosophila suzukii, and two D. melanogaster genotypes as hosts. All fungal isolates successfully infected hosts, induced behavioural manipulation, sporulated in all fly hosts, and differed in virulence between host genotypes, revealing GxG interactions. While house flies were most susceptible to fungal infection with 99% mortality, we found a lower virulence of 49% and 25% mortality in D. melanogaster and D. suzukii genotypes, respectively. Furthermore, all isolates harboured a specific mycovirus (family Iflaviridae), but co-phylogenetic branching patterns did not support fungus-virus co-speciation. We show that the genetic makeup of both fungal pathogen and fly host influence E. muscae infectivity, confirming GxG interactions in obligate fly fungal pathogens.

Biogeography confounds the signal of cospeciation in Batesian mimicry

Since the inception of the field of evolution, mimicry has yielded insights into foundational evolutionary processes, including adaptive peak shifts, speciation, and the emergence and maintenance of phenotypic polymorphisms.1,2,3 In recent years, the coevolutionary processes generating mimicry have gained increasing attention from researchers. Despite significant advances in understanding Batesian and Müllerian mimicry in Lepidopteran systems, few other mimetic systems have received similar detailed research. Here, we present a Batesian mimicry complex involving flightless, armored Pachyrhynchus weevils and their winged Doliops longhorn beetle mimics and examine their coevolutionary patterns within the Philippine archipelagos. Pachyrhynchus weevils are primarily found in the Philippines, where distinct species radiations have occurred on different islands, each with unique color patterns serving as a warning to predators. This defensive trait and mimicry between unrelated species were first described by Wallace in 1889. Notably, the distantly related longhorn beetle Doliops, despite being soft-bodied and ostensibly palatable, mimics the heavily armored, flightless Pachyrhynchus. To address mimicry in this system, we reconstructed the phylogeny of Doliops using a probe set consisting of 38,000 ultraconserved elements. Our study examines the following questions central to understanding the Pachyrhynchus-Doliops mimicry system: (1) to what extent are coevolutionary interactions conserved (i.e., lineage-constrained) and (2) are the codiversification patterns primarily driven by biotic or abiotic factors?4,5,6 To assess color mimicry and cospeciation, we examined the evolution of nanostructure-based warning colors and the effect of island biogeography on cospeciation. Our findings demonstrate the beetle's ability to repeatedly evolve multiple solutions to similar evolutionary challenges, evolving similar color patterns using different types of photonic crystals with varying degrees of order. We revealed that the observed pattern of cospeciation is driven mainly by abiotic factors from their biogeographic history. Unlike the patterns of coevolution seen between angiosperms and insect lineages,7 most ecological interactions do not persist longer than a few million years, leading to patterns of modularity rather than ecological nestedness.4,6,7.

The mining of China's policies against COVID-19 based on a policy target and tool co-evolution framework

Mining all COVID-19 policies issued by China can provide valuable lessons for both China and other countries in future pandemic control efforts. In this paper, we introduce a novel framework for mining the co-evolution of policy targets and policy tools. We employ bibliometric methods, text mining, and network analysis to explore the entire evolution of China's COVID-19 policies. Examining 1154 central government policies, (a) we extract policy targets from each policy, uncovering their evolution across different stages of the pandemic; (b) propose to identify the policy tool used in each policy unit by integrating an automatic identification model and active learning. We also reveal the categorical structure of these tools; (c) characterize the co-evolution pattern between policy targets and policy tools, shedding light on their dynamic relationship. Our findings indicate that policy targets have shifted across various stages, revealing unique characteristics in China's COVID-19 prevention and control efforts. Notably, there is a self-paradox between prevention measures and economic development. We identify the inadequateness in the distribution and utilization of policy tools. Ensuring the alignment of policy targets with appropriate tools is crucial. This synchronization and co-evolution between policy targets and tools are essential for enhancing the functional approach to policy implementation. This paper is the first systematic mining and review about the COVID-19 policies issued by the Chinese government, and our policy target and tool co-evolution mining framework provides a new quantitative framework for policy mining, especially an improved large language model and active learning theory are integrated to identify the policy tools automatically.

Impact of urbanization on water-energy-carbon nexus system: The case of Zhengzhou, China

Exploring the impact of urbanization on water-energy‑carbon nexus system is helpful to discover the inherent interaction mechanism and co-evolutionary pattern of water-energy‑carbon nexus in urban expansion. Based on the calculation of water-energy‑carbon of different land use types, the impact of urbanization on water-energy‑carbon nexus system in Zhengzhou was analyzed, and the future evolution of water-energy‑carbon nexus system under different urbanization scenarios was simulated. The results showed that land use change during urbanization was affected by the industrial pattern and the intensity of human activities, which further caused the increases in water and energy consumption and carbon emissions. There was a positive correlation between urbanization level and coupling coordination degree of water-energy‑carbon nexus system. Especially, the changes in water and energy consumption caused by land use change during urbanization largely determined the coupling coordination level of water-energy‑carbon nexus system. Additionally, different urbanization scenarios would lead to different growth rates of water and energy consumption and carbon emissions, in which the impact of land urbanization on urban water-energy‑carbon nexus system was greater than that of the economic and population urbanization. In the future, urban expansion control and land use regulation based on collaborative optimization of water-energy‑carbon should be adopted.

Meristic co-evolution and genomic co-localization of lateral line scales and vertebrae in Central American cichlid fishes.

Meristic traits are often treated as distinct phenotypes that can be used to differentiate and delineate recently diverged species. For instance, the number of lateral line scales and vertebrae, two traits that vary substantially among Neotropical Heroine cichlid species, have been previously suggested to co-evolve. These meristic traits could co-evolve due to shared adaptive, developmental, or genetic factors. If they were found to be genetically or developmentally non-independent, this might require a more general re-evaluation of their role in evolutionary or taxonomic studies. We expanded a previous analysis of correlated evolution of meristic traits (lateral line scales and vertebrae counts) in these fishes to include a range of phylogenetic reconstructions as well as the analyses of 13 Nicaraguan Midas cichlid species (Amphilophus spp.). Additionally, we performed qualitative traits locus (QTL) mapping in a F2 laboratory-reared hybrid population from two ecologically divergent Midas cichlid fish species to discover and evaluate whether genomic co-segregation might explain the observed patterns of meristic co-evolution. Meristic values for these traits were found to morphologically differentiate some species of the Midas cichlid adaptive radiation. Our QTL analysis pinpointed several genomic regions associated with divergence in these traits and highlighted the potential for genomic co-segregation of the lateral line and vertebrae numbers on two chromosomes. Further, our phylogenetic comparative analyses consistently recovered a significant positive evolutionary correlation between the counts of lateral line scale and vertebrae numbers in Neotropical cichlids. Hence, the findings of genomic co-segregation could partially explain the co-evolution of these two meristic traits in these species. Continuing to unravel the genetic architecture governing meristic divergence helps to better understand both trait correlations and the utility of meristic traits in taxonomic diagnoses and how traits in phenotypes might be expected to co-evolve.

The Impact of Environmental Governance and Quality of Life on Fertility Intentions

Objectives: Here, local environmental governance, quality of life, and fertility intention in 30 provinces, municipalities, and regions of China during 2004–2020 are also examined in terms of their co-evolution pattern. Methods: A detailed analytical method of evaluation is used by our team. It entails the determination of the environmental governance index, quality of life index and fertility intention index in order to examine their inter relacion with each other the variation and distribution within regions. Results: Our research is also demonstrated by the fact that as a whole the values of the environmental governance index and the quality of life index are increasing nationwide, which indicates that China is also experiencing certain positive changes for the better regarding environmental protection and the quality of life. Nonetheless, fertility intention index trend was characterized by increase then decrease, apparently indicating the underlying socioeconomic factors. Regional comparisons show that the East is the best place for environment governance and quality, and the fertility intention index of Northeast remains lower than other areas. Conclusions: China has become one of the advanced countries in environmental governance and improved quality of life, but the continuously decreasing level in fertility intention reflects the complex effect of changes in population policy and soci:economic factors.

Fumarate reductase drives methane emissions in the genus Oryza through differential regulation of the rhizospheric ecosystem

The emergence of waterlogged Oryza species ∼15Mya (million years ago) supplied an anoxic warm bed for methane-producing microorganisms, and methane emissions have hence accompanied the entire evolutionary history of the genus Oryza. However, to date no study has addressed how methane emission has been altered during Oryza evolution. In this paper we used a diverse collection of wild and cultivated Oryza species to study the relation between Oryza evolution and methane emissions. Phylogenetic analyses and methane detection identified a co-evolutionary pattern between Oryza and methane emissions, mediated by the diversity of the rhizospheric ecosystems arising from different oxygen levels. Fumarate was identified as an oxygen substitute used to retain the electron transport/energy production in the anoxic rice root, and the contribution of fumarate reductase to Oryza evolution and methane emissions has also been assessed. We confirmed the between-species patterns using genetic dissection of the traits in a cross between a low and high methane-emitting species. Our findings provide novel insights on the evolutionary processes of rice paddy methane emissions: the evolution of wild rice produces different Oryza species with divergent rhizospheric ecosystem attributing to the different oxygen levels and fumarate reductase activities, methane emissions are comprehensively assessed by the rhizospheric environment of diversity Oryza species and result in a co-evolution pattern.

Mixed Wolbachia infections resolve rapidly during in vitro evolution.

The intracellular symbiont Wolbachia pipientis evolved after the divergence of arthropods and nematodes, but it reached high prevalence in many of these taxa through its abilities to infect new hosts and their germlines. Some strains exhibit long-term patterns of co-evolution with their hosts, while other strains are capable of switching hosts. This makes strain selection an important factor in symbiont-based biological control. However, little is known about the ecological and evolutionary interactions that occur when a promiscuous strain colonizes an infected host. Here, we study what occurs when two strains come into contact in host cells following horizontal transmission and infection. We focus on the faithful wMel strain from Drosophila melanogaster and the promiscuous wRi strain from Drosophila simulans using an in vitro cell culture system with multiple host cell types and combinatorial infection states. Mixing D. melanogaster cell lines stably infected with wMel and wRi revealed that wMel outcompetes wRi quickly and reproducibly. Furthermore, wMel was able to competitively exclude wRi even from minuscule starting quantities, indicating that this is a nearly deterministic outcome, independent of the starting infection frequency. This competitive advantage was not exclusive to wMel's native D. melanogaster cell background, as wMel also outgrew wRi in D. simulans cells. Overall, wRi is less adept at in vitro growth and survival than wMel and its in vivo state, revealing differences between the two strains in cellular and humoral regulation. These attributes may underlie the observed low rate of mixed infections in nature and the relatively rare rate of host-switching in most strains. Our in vitro experimental framework for estimating cellular growth dynamics of Wolbachia strains in different host species and cell types provides the first strategy for parameterizing endosymbiont and host cell biology at high resolution. This toolset will be crucial to our application of these bacteria as biological control agents in novel hosts and ecosystems.

Probing of plant transcriptomes reveals the hidden genetic diversity of the family Secoviridae.

Secoviruses are single-stranded RNA viruses that infect plants. In the present study, we identified 61 putative novel secoviral genomes in various plant species by mining publicly available plant transcriptome data. These viral sequences represent the genomes of 13 monopartite and 48 bipartite secovirids. The genome sequences of 52 secovirids were coding-complete, and nine were partial. Except for small open reading frames (ORFs) determined in waikaviral genomes and RNA2 of torradoviruses, all of the recovered genomes/genome segments contained a large ORF encoding a polyprotein. Based on genome organization and phylogeny, all but three of the novel secoviruses were assigned to different genera. The genome organization of two identified waika-like viruses resembled that of the recently identified waika-like virus Triticum aestivum secovirus. Phylogenetic analysis revealed a pattern of host-virus co-evolution in a few waika- and waika-like viruses and increased phylogenetic diversity of nepoviruses. The study provides a basis for further investigation of the biological properties of these novel secoviruses.

Comparative genomics of the primary endosymbiont Buchnera aphidicola in aphid hosts and their coevolutionary relationships

BackgroundCoevolution between modern aphids and their primary obligate, bacterial endosymbiont, Buchnera aphidicola, has been previously reported at different classification levels based on molecular phylogenetic analyses. However, the Buchnera genome remains poorly understood within the Rhus gall aphids.ResultsWe assembled the complete genome of the endosymbiont Buchnera in 16 aphid samples, representing 13 species in all six genera of Rhus gall aphids by shotgun genome skimming method. We compared the newly assembled genomes with those from GenBank to comprehensively investigate patterns of coevolution between the bacteria Buchnera and their aphid hosts. Buchnera genomes were mostly collinear, and the pan-genome contained 684 genes, in which the core genome contained 256 genes with some lineages having large numbers of tandem gene duplications. There has been substantial gene-loss in each Buchnera lineage. We also reconstructed the phylogeny for Buchnera and their host aphids, respectively, using 72 complete genomes of Buchnera, along with the complete mitochondrial genomes and three nuclear genes of 31 corresponding host aphid accessions. The cophylogenetic test demonstrated significant coevolution between these two partner groups at individual, species, generic, and tribal levels.ConclusionsBuchnera exhibits very high levels of genomic sequence divergence but relative stability in gene order. The relationship between the symbionts Buchnera and its aphid hosts shows a significant coevolutionary pattern and supports complexity of the obligate symbiotic relationship.

Online rumors during the COVID-19 pandemic: co-evolution of themes and emotions.

During public health emergencies, online rumors spread widely on social media, causing public information anxiety and emotional fluctuations. Analyzing the co-evolution patterns of online rumor themes and emotions is essential for implementing proactive and precise governance of online rumors during such events. Rumor texts from mainstream fact-checking platforms during the COVID-19 pandemic were collected and analyzed in phases based on the crisis lifecycle theory. The LDA topic model was applied to analyze the distribution of rumor themes at different stages. The Baidu AI Sentiment Analysis API was used to study the emotional tendencies of rumors at different stages. Line graphs were utilized to analyze the co-evolution characteristics of rumor themes and emotions. During the COVID-19 pandemic, the themes of online rumors can be categorized into five types: epidemic prevention and control, panic-inducing, production and livelihood, virus dissemination, and social figures. These themes exhibited repetition and fluctuation at different stages of the pandemic. The emotions embedded in pandemic-related online rumors evolved with the progression of the pandemic. Panic-inducing rumors co-evolved with negative emotions, while epidemic prevention and control rumors co-evolved with positive emotions. The study results help to understand the public's focus and emotional tendencies at different stages of the COVID-19 pandemic, thereby enabling targeted public opinion guidance and crisis management.

Rhizobium hidalgonense and Rhizobium redzepovicii as faba bean (Vicia faba L.) microsymbionts in Mexican soils.

As a legume crop widely cultured in the world, faba bean (Vicia faba L.) forms root nodules with diverse Rhizobium species in different regions. However, the symbionts associated with this plant in Mexico have not been studied. To investigate the diversity and species/symbiovar affiliations of rhizobia associated with faba bean in Mexico, rhizobia were isolated from this plant grown in two Mexican sites in the present study. Based upon the analysis of recA gene phylogeny, two genotypes were distinguished among a total of 35 isolates, and they were identified as Rhizobium hidalgonense and Rhizobium redzepovicii, respectively, by the whole genomic sequence analysis. Both the species harbored identical nod gene cluster and the same phylogenetic positions of nodC and nifH. So, all of them were identified into the symbiovar viciae. As a minor group, R. hidalgonense was only isolated from slightly acid soil and R. redzepovicii was the dominant group in both the acid and neutral soils. In addition, several genes related to resistance to metals (zinc, copper etc.) and metalloids (arsenic) were detected in genomes of the reference isolates, which might offer them some adaptation benefits. As conclusion, the community composition of faba bean rhizobia in Mexico was different from those reported in other regions. Furthermore, our study identified sv. viciae as the second symbiovar in the species R. redzepovicii. These results added novel evidence about the co-evolution, diversification and biogeographic patterns of rhizobia in association with their host legumes in distinct geographic regions.

Co-evolutionary digital twins: A multidimensional dynamic approach to digital engineering

Digital Engineering (DE) must be able to maximize efficiency and update dynamically in order to keep up with the wave of global interconnection. The evolution of the Digital Twin (DT) plays a significant role in DE as it enables autonomous optimization and an iterative cycle. However, the intricacy of real-world settings renders conventional evolutionary investigations of a solitary DT inadequate in tackling intricate systems at a comprehensive lifecycle magnitude. To address this, this paper presents the Co-evolutionary DTs (CoEDT), which has several key characteristics. (1) CoEDT study the evolutionary behavior of interconnected multi-DT. (2) CoEDT use a co-evolutionary distributed system architecture and is a DT technology that integrate MBSE. (3) CoEDT offers detailed dynamic models for the complex interactions and co-evolution among multi-DT throughout the lifecycle. It also supports real time measurement of multi-DT behavior to detect system anomalies. The significance of CoEDT lies in providing a more comprehensive insight for future product development by constructing a parallel world that simulates the lifecycle. In the CoEDT, we tackle the behavioral identification and structure of these evolving multi-DT throughout product lifecycle through the following approaches. Initially, drawing inspiration from biological cytology, we have conceived a concept of Collective DTs (CollDTs) to observing a collective behavioral of multi-DT. Subsequently, we further developed CoEDT to depict co-evolutionary behavior patterns and established a co-evolution architecture for all DT throughout the lifecycle by fusing Model-Based Systems Engineering (MBSE). Then, dynamic expressions and algorithm that can measure the co-evolution of every DT are inferred using information theory. Finally, the viability of the proposed CoEDT framework is demonstrated through the development of a solid rocket engine, which promotes the application of DT in the DE.

Binding Evolution of the Dengue Virus Envelope Against DC-SIGN: A Combined Approach of Phylogenetics and Molecular Dynamics Analyses Over 30 Years of Dengue Virus in Brazil

The Red Queen Hypothesis (RQH), derived from Lewis Carroll's “Through the Looking-Glass”, postulates that organisms must continually adapt in response to each other to maintain relative fitness. Within the context of host-pathogen interactions, the RQH implies an evolutionary arms race, wherein viruses evolve to exploit hosts and hosts evolve to resist viral invasion. This study delves into the dynamics of the RQH in the context of virus-cell interactions, specifically focusing on virus receptors and cell receptors. We observed multiple virus-host systems and noted patterns of co-evolution. As viruses evolved receptor-binding proteins to effectively engage with cell receptors, cells countered by altering their receptor genes. This ongoing mutual adaptation cycle has influenced the molecular intricacies of receptor-ligand interactions. Our data supports the RQH as a driving force behind the diversification and specialization of both viral and host cell receptors. Understanding this co-evolutionary dance offers insights into the unpredictability of emerging viral diseases and potential therapeutic interventions. Future research is crucial to dissect the nuanced molecular changes and the broader ecological consequences of this ever-evolving battle. Here, we combine phylogenetic inferences, structural modeling, and molecular dynamics analyses to describe the epidemiological characteristics of major Brazilian DENV strains that circulated from 1990 to 2022 from a combined perspective, thus providing us with a more detailed picture on the dynamics of such interactions over time.

Phylogenomic analysis of Stylops reveals the evolutionary history of a Holarctic Strepsiptera radiation parasitizing wild bees

Holarctic Stylops is the largest genus of the enigmatic insect order Strepsiptera, twisted winged parasites. Members of Stylops are obligate endoparasites of Andrena mining bees and exhibit extreme sexual dimorphism typical of Strepsiptera. So far, molecular studies on Stylops have focused on questions on species delimitation. Here, we utilize the power of whole genome sequencing to infer the phylogeny of this morphologically challenging genus from thousands of loci. We use a species tree method, concatenated maximum likelihood analysis and Bayesian analysis with a relaxed clock model to reconstruct the phylogeny of 46 Stylops species, estimate divergence times, evaluate topological consistency across methods and infer the root position. Furthermore, the biogeographical history and coevolutionary patterns with host species are assessed. All methods recovered a well resolved topology with close to all nodes maximally supported and only a handful of minor topological variations. Based on the result, we find that included species can be divided into 12 species groups, seven of them including only Palaearctic species, three Nearctic and two were geographically mixed. We find a strongly supported root position between a clade formed by the spreta, thwaitesi and gwynanae species groups and the remaining species and that the sister group of Stylops is Eurystylops or Eurystylops + Kinzelbachus. Our results indicate that Stylops originated in the Western Palaearctic or Western Palaearctic and Nearctic in the early Neogene or late Paleogene, with four independent dispersal events to the Nearctic. Cophylogenetic analyses indicate that the diversification of Stylops has been shaped by both significant coevolution with the mining bee hosts and host-shifting. The well resolved and strongly supported phylogeny will provide a valuable phylogenetic basis for further studies into the fascinating world of Strepsipterans.

PyCoM: a python library for large-scale analysis of residue-residue coevolution data.

Computational methods to detect correlated amino acid positions in proteins have become a valuable tool to predict intra- and inter-residue protein contacts, protein structures, and effects of mutation on protein stability and function. While there are many tools and webservers to compute coevolution scoring matrices, there is no central repository of alignments and coevolution matrices for large-scale studies and pattern detection leveraging on biological and structural annotations already available in UniProt. We present a Python library, PyCoM, which enables users to query and analyze coevolution matrices and sequence alignments of 457622 proteins, selected from UniProtKB/Swiss-Prot database (length ≤ 500 residues), from a precompiled coevolution matrix database (PyCoMdb). PyCoM facilitates the development of statistical analyses of residue coevolution patterns using filters on biological and structural annotations from UniProtKB/Swiss-Prot, with simple access to PyCoMdb for both novice and advanced users, supporting Jupyter Notebooks, Python scripts, and a web API access. The resource is open source and will help in generating data-driven computational models and methods to study and understand protein structures, stability, function, and design. PyCoM code is freely available from https://github.com/scdantu/pycom and PyCoMdb and the Jupyter Notebook tutorials are freely available from https://pycom.brunel.ac.uk.

Patterns of co-evolution: analyzing fashion brand and sewing contractor company dynamics

The purpose of this study is to identify the entry conditions that could form a co-evolutionary relationship between a sewing contractor company and a fashion brand, and reveal the outcome of such a relationship. In the Republic of Korea, many fashion brands and sewing companies coexist, and the situation in the fashion industry changes with the rapid development of the country, so it is a suitable environment for investigating their co-evolution strategies. A qualitative research methodology was used to examine the co-evolution process of the fashion brand and the sewing industry. In addition, an objective evaluation was conducted by using interviews with sewing contractor companies and fashion brands that have business relationships with the sewing contractor companies. The results indicated that sewing contractor companies evolve into either mass production or small production systems. In the co-evolutionary process, relational resources and business-to-business transaction suitability are the main entry conditions for sewing contractor companies to coevolve with fashion brands. Knowledge exchange, experience optimization, off-season ordering, and investment in trading companies were observed among sewing contractor companies that formed a co-evolutionary relationship with their fashion brand partners. This study identified and conceptualized factors that played a major role in the process of co-evolution and proved suitable for each production system of sewing contractor companies.