Interplay of Light and ABA signaling to modulate plant development

The exogenous light cues and the phytohormone Abscisic acid (ABA) regulate several aspects of plant growth and development. In recent years, the role of the crosstalk between the light and ABA signaling pathways in regulating different physiological processes has become increasingly evident. This includes the regulation of germination and early seedling development, control of stomatal development and conductance, growth and development of roots, buds, branches, and regulation of flowering. Light and ABA signaling cascades have various convergence points at both DNA and protein levels. The molecular crosstalk involves several light signaling factors like HY5, COP1, PIFs and BBXs that integrate with ABA signaling components like the PYL receptors and ABI5. Especially, ABI5 and PIF4 promoters serve as key "hotspots" for the integration of these two pathways. Plants acquired both light and ABA signaling pathways before they colonized land almost 500 million years ago. In this review, we discuss the recent advances in the interplay of light and ABA signaling regulating plant development and provide an overview of the evolution of these two pathways.

Analysis of the evolution of water culture and water security in the Weihe River Basin over a 100 year-period

The significance of water culture in addressing water crises and ensuring water security has garnered considerable attention, emerging as a focal point in global change and water science research. Water culture is a societal adaptation to changes in hydrological systems. However, this needs to be acknowledged within contemporary discourse on water security governance. This study utilized historical policy document data from many sources, including local municipal records from Shaanxi and Gansu, and water conservancy records. It aimed to identify the significant nodes and stages of policy transformation in the Weihe River Basin (WRB) during the last century (1949-2020). This study employed a content analysis method to elucidate the evolutionary patterns of water culture in the study region during the previous century. Drawing on the co-evolution framework, our investigation delved into the reciprocal relationship between changes in water culture and the evolution of water security in the WRB. Our findings indicated that water culture transformation in the WRB has undergone four significant stages: the Disaster-Resistant Hydraulic (1949-1966), Irrigation Hydraulic (1967-1998), Resources Hydraulic (1999-2010), and Ecological Hydraulic (2011-2020) phases. Water security assessment showed that policy attention varied across the different stages. The disaster-resistant hydraulic phase primarily addressed water-related disaster concerns, whereas the irrigation hydraulic phase emphasized the scarcity of water resources. The resource hydraulic phase focused on ensuring the security of the water environment, while the ecological hydraulic phase placed emphasis on safeguarding water sustainability. Moreover, we found that prevailing water policies prioritize resolving isolated issues; however, water security is a multifaceted systemic matter that requires a comprehensive approach. This study has the potential to offer policy makers a more comprehensive and systematic perspective, enabling them to enhance their understanding of the underlying nature of the problems. Additionally, this study can assist in developing future water security policies.

Strong mitonuclear discordance in the phylogeny of Neodermata and evolutionary rates of Polyopisthocotylea

The genomic evolution of Polyopisthocotylea remains poorly understood in comparison to the remaining three classes of Neodermata: Monopisthocotylea, Cestoda, and Trematoda. Moreover, the evolutionary sequence of major events in the phylogeny of Neodermata remains unresolved. Herein we sequenced the mitogenome and transcriptome of the polyopisthocotylean Diplorchis sp., and conducted comparative evolutionary analyses using nuclear (nDNA) and mitochondrial (mtDNA) genomic datasets of Neodermata. We found strong mitonuclear discordance in the phylogeny of Neodermata. Polyopisthocotylea exhibited striking mitonuclear discordance in relative evolutionary rates: the fastest-evolving mtDNA in Neodermata and a comparatively slowly-evolving nDNA genome. This was largely attributable to its very long stem branch in mtDNA topologies, not exhibited by the nDNA data. We found indications that the fast evolution of mitochondrial genomes of Polyopisthocotylea may be driven both by relaxed purifying selection pressures and elevated levels of directional selection. We identified mitochondria-associated genes encoded in the nuclear genome: they exhibited unique evolutionary rates, but not correlated with the evolutionary rate of mtDNA, and there is no evidence for compensatory evolution (they evolved slower than the rest of the genome). Finally, there appears to exist an exceptionally large (≈6.3 kb) nuclear mitochondrial DNA segment (numt) in the nuclear genome of newly sequenced Diplorchis sp. A 3'-end segment of the 16S rRNA gene encoded by the numt was expressed, suggesting that this gene acquired novel, regulatory functions after the transposition to the nuclear genome. In conclusion, Polyopisthocotylea appears to be the lineage with the fastest-evolving mtDNA sequences among all of Bilateria, but most of the substitutions were accumulated deep in the evolutionary history of this lineage. As the nuclear genome does not exhibit a similar pattern, the circumstances underpinning this evolutionary phenomenon remain a mystery.

Evolution of Transcript Abundance is Influenced by Indels in Protein Low Complexity Regions

Protein Protein low complexity regions (LCRs) are compositionally biased amino acid sequences, many of which have significant evolutionary impacts on the proteins which contain them. They are mutationally unstable experiencing higher rates of indels and substitutions than higher complexity regions. LCRs also impact the expression of their proteins, likely through multiple effects along the path from gene transcription, through translation, and eventual protein degradation. It has been observed that proteins which contain LCRs are associated with elevated transcript abundance (TAb), despite having lower protein abundance. We have gathered and integrated human data to investigate the co-evolution of TAb and LCRs through ancestral reconstructions and model inference using an approximate Bayesian calculation based method. We observe that on short evolutionary timescales TAb evolution is significantly impacted by changes in LCR length, with insertions driving TAb down. But in contrast, the observed data is best explained by indel rates in LCRs which are unaffected by shifts in TAb. Our work demonstrates a coupling between LCR and TAb evolution, and the utility of incorporating multiple responses into evolutionary analyses.

Phylogenetic congruence of Plasmodium spp. and wild ungulate hosts in the Peruvian Amazon

Malaria parasites are known to infect a variety of vertebrate hosts, including ungulates. However, ungulates of Amazonia have not been investigated. We report for the first time, the presence of parasite lineages closely related to Plasmodium odocoilei clade 1 and clade 2 in free-ranging South American red-brocket deer (Mazama americana; 44.4%, 4/9) and gray-brocket deer (Mazama nemorivaga; 50.0%, 1/2). We performed PCR-based analysis of blood samples from 47 ungulates of five different species collected during subsistence hunting by an indigenous community in the Peruvian Amazon. We detected Plasmodium malariae/brasilianum lineage in a sample from red-brocket deer. However, no parasite DNA was detected in collared peccary (Pecari tajacu; 0.0%, 0/10), white-lipped peccary (Tayassu pecari; 0.0%, 0/15), and tapir (Tapirus terrestris; 0.0%, 0/11). Concordant phylogenetic analyses suggested a possible co-evolutionary relationship between the Plasmodium lineages found in American deer and their hosts.

Severe zoonotic viruses carried by different species of bats and their regional distribution

BACKGROUND

Bats have garnered increased attention in the field of life sciences for their typical biological characteristics of carrying a variety of zoonotic viruses without disease, long lifespans, low tumorigenesis rates, and high metabolism. When it was found that bats can carry the rabies virus, over 60 years of research revealed that bats host over 4100 distinct viruses, including Ebola virus and SARS-CoV.

OBJECTIVES

This paper primarily reviews the profiles of zoonotic viruses carried by bats across various regions globally. The review aims to provide a foundation and reference for future research on monitoring zoonotic viruses in diverse global regions and bat species, exploring the coevolutionary relationship between bats and viruses, understanding the tolerance mechanisms of bat B cells, prevention, and treatment of zoonotic diseases caused by bats.

SOURCES

The search used 'bat', 'bats', 'rabies virus', 'Dengue virus', 'West Nile virus', 'Zika virus', 'St. Louis encephalitis virus', 'Japanese encephalitis virus', 'Hantavirus', 'Novel hantavirus', 'Rift Valley fever virus', 'Crimean Congo hemorrhagic fever virus', 'Paramyxovirus', 'Nipah virus', 'Hendra virus', 'Menangle virus', 'Tioman virus', 'Marburg Virus', 'Bombali virus', 'Ebola virus', 'Influenza A virus', 'coronavirus', 'Hepatitis B virus', and 'Hepatitis E virus' as text in PubMed.

CONTENT

A total of 147 references were obtained. Surveys on severe zoonotic virus carriage have been limited to only 83 bat species belonging to nine families, which are distributed all over the world. We also briefly describe the antibody responses and B-cell molecules in bats.

IMPLICATIONS

Several viruses have been found in different species of bats. This suggests that bats may be important hosts for future viral infectious diseases. Particularly in recent years, the close correlation between human infection pandemics caused by coronaviruses and bats highlights the pressing need to comprehend the species, tolerance, and coevolutionary mechanisms of zoonotic viruses carried by different bat species.

Specificity and breadth of plant specialized metabolite-microbe interactions

Plant specialized metabolites shape plant interactions with the environment including plant-microbe interactions. While we often group compounds into generic classes, it is the precise structure of a compound that creates a specific role in plant-microbe or-pathogen interactions. Critically, the structure guides definitive targets in individual interactions, yet single compounds are not limited to singular mechanistic targets allowing them to influence interactions across broad ranges of attackers, from bacteria to fungi to animals. Further, the direction of the effect can be altered by counter evolution within the interacting organism leading to single compounds being both beneficial and detrimental. Thus, the benefit of a single compound to a host needs to be assessed by measuring the net benefit across all interactions while in each specific interaction. Factoring this complexity for single compounds in plant-microbe interactions with the massive expansion in our identification of specialized metabolite pathways means that we need systematic studies to classify the full breadth of activities. Only with this full biological knowledge we can develop mechanistic, ecological, and evolutionary models to understand how plant specialized metabolites fully influence plant-microbe and plant-biotic interactions more broadly.

The evolutionary trajectories of specialized metabolites towards antiviral defense system in plants

Viral infections in plants pose major challenges to agriculture and global food security in the twenty-first century. Plants have evolved a diverse range of specialized metabolites (PSMs) for defenses against pathogens. Although, PSMs-mediated plant-microorganism interactions have been widely discovered, these are mainly confined to plant-bacteria or plant-fungal interactions. PSM-mediated plant-virus interaction, however, is more complicated often due to the additional involvement of virus spreading vectors. Here, we review the major classes of PSMs and their emerging roles involved in antiviral resistances. In addition, evolutionary scenarios for PSM-mediated interactions between plant, virus and virus-transmitting vectors are presented. These advancements in comprehending the biochemical language of PSMs during plant-virus interactions not only lay the foundation for understanding potential co-evolution across life kingdoms, but also open a gateway to the fundamental principles of biological control strategies and beyond.

Co-phylogeny of a hyper-symbiotic system: Endosymbiotic bacteria (Gammaproteobacteria), chewing lice (Insecta: Phthiraptera) and birds (Passeriformes)

Chewing lice are hosts to endosymbiotic bacteria as well as themselves being permanent parasites. This offers a unique opportunity to examine the cophylogenetic relationships between three ecologically interconnected organismal groups: birds, chewing lice, and bacteria. Here, we examine the cophylogenetic relationships between lice in the genus Guimaraesiella Eichler, 1949, their endosymbiotic Sodalis-allied bacteria, and a range of bird species from across South China. Both event and distance-based cophylogenetic analyses were explored to compare phylogenies of the three organismal groups. Pair-wise comparisons between lice-endosymbionts and bird-endosymbionts indicated that their evolutionary histories are not independent. However, comparisons between lice and birds, showed mixed results; the distance-based method of ParaFit indicated that their evolutionary histories are not independent, while the event-based method of Jane indicated that their phylogenies were no more congruent than expected by chance. Notably, louse host-switching does not seem to have affected bacterial strains, as conspecific lice sampled from distantly related hosts share bacteria belonging to the same clade.

Seasonality and Strain Specificity Drive Rapid Co-evolution in an Ostreococcus-Virus System from the Western Baltic Sea

Marine viruses are a major driver of phytoplankton mortality and thereby influence biogeochemical cycling of carbon and other nutrients. Phytoplankton-targeting viruses are important components of ecosystem dynamics, but broad-scale experimental investigations of host-virus interactions remain scarce. Here, we investigated in detail a picophytoplankton (size 1 µm) host's responses to infections by species-specific viruses from distinct geographical regions and different sampling seasons. Specifically, we used Ostreococcus tauri and O. mediterraneus and their viruses (size ca. 100 nm). Ostreococcus sp. is globally distributed and, like other picoplankton species, play an important role in coastal ecosystems at certain times of the year. Further, Ostreococcus sp. is a model organism, and the Ostreococcus-virus system is well-known in marine biology. However, only few studies have researched its evolutionary biology and the implications thereof for ecosystem dynamics. The Ostreococcus strains used here stem from different regions of the Southwestern Baltic Sea that vary in salinity and temperature and were obtained during several cruises spanning different sampling seasons. Using an experimental cross-infection set-up, we explicitly confirm species and strain specificity in Ostreococcus sp. from the Baltic Sea. Moreover, we found that the timing of virus-host co-existence was a driver of infection patterns as well. In combination, these findings prove that host-virus co-evolution can be rapid in natural systems.

Mycobacteriaceae Phenome Atlas (MPA): A Standardized Atlas for the Mycobacteriaceae Phenome Based on Heterogeneous Sources

The bacterial family Mycobacteriaceae includes pathogenic and nonpathogenic bacteria, and systematic research on their genome and phenome can give comprehensive perspectives for exploring their disease mechanism. In this study, the phenotypes of Mycobacteriaceae were inferred from available phenomic data, and 82 microbial phenotypic traits were recruited as data elements of the microbial phenome. This Mycobacteriaceae phenome contains five categories and 20 subcategories of polyphasic phenotypes, and three categories and eight subcategories of functional phenotypes, all of which are complementary to the existing data standards of microbial phenotypes. The phenomic data of Mycobacteriaceae strains were compiled by literature mining, third-party database integration, and bioinformatics annotation. The phenotypes were searchable and comparable from the website of the Mycobacteriaceae Phenome Atlas (MPA, https://www.biosino.org/mpa/). A topological data analysis of MPA revealed the co-evolution between Mycobacterium tuberculosis and virulence factors, and uncovered potential pathogenicity-associated phenotypes. Two hundred and sixty potential pathogen-enriched pathways were found by Fisher's exact test. The application of MPA may provide novel insights into the pathogenicity mechanism and antimicrobial targets of Mycobacteriaceae.

Supplementary Information

The online version contains supplementary material available at 10.1007/s43657-023-00101-5.

Do adaptive policy adjustments deliver ecosystem-agriculture-economy co-benefits in land degradation neutrality efforts? Evidence from southeast coast of China

Ecosystem restoration projects (ERPs) facilitate land degradation neutrality (LDN). However, the response dynamics and interactions of sectors within ecosystem-agriculture-economy nexus (EAEN) have not been sufficiently explored, which constrains the coordinated efficacy of LDN efforts. To bridge the knowledge gaps, the present study selected a land restoration hotspot in southeastern China as a case to investigate the simultaneous responses of the EAEN sectors to ERPs from a novel social-ecological system (SES)-based LDN perspective. Various biophysical models and Manne-Kendall trend test as well as multi-source spatially explicit data and socioeconomic statistics were applied to quantify the co-evolution of natural and socioeconomic indicators. ERPs converting cropland to woodland and grassland promoted vegetation restoration, reduced soil erosion, and enhanced carbon sequestration. However, cropland loss initially resulted in a decline in grain productivity. Policy adjustments and improvements in ecosystem restoration efforts and agricultural production conditions improved food security and increased agricultural production capacity. Effective policymaking and favorable resident engagement accelerated the transformation from a grain-production-based agriculture to diversified industries and, by extension, economic output, income, and population. The success of socioeconomic development under the SES framework for LDN demonstrated that this strategy could achieve the desired environmental, agricultural, and economic targets. EAEN under the SES conceptual framework provides an inclusive, comprehensive LDN perspective and improves ERP efficacy. The findings of the present work might be applicable to other land restoration areas challenged by the complex interactions among multidimensional factors. Comparably successful implementation of these ERPs could be realized if individual environmental and socioeconomic conditions are thoroughly considered during the formulation of coordinated development policies.

Bringing resilience together: On the co-evolutionary capacities of boundary organizations during the COVID-19 pandemic in Rotterdam

For a city to maintain its vitality during a crisis like the COVID-19 pandemic, social resilience is pivotal. It is a manifestation of adaptive and transformative capacities in a city, through a multitude of interactions between initiatives and organizations, including local government. Resilience can take many forms: coping, adaptive, transformative; community-based, organizational, and institutional. Due to this hybridity and multiplicity, it remains to be seen how all forms of resilience interact and mutually benefit from one another in a city under crisis. Building further in the relational and dynamic dimensions of resilience, we conceptualize these mutual influences as co-evolution and hypothesise that for mutually beneficial co-evolution a city requires boundary organizations, i.e., organizations that facilitate collaboration and information-flow between differently organized societal domains. In our study of the activities of boundary organizations in the Dutch city Rotterdam during the COVID-19 pandemic, we found that boundary organizations were indeed supportive in building social and especially community resilience, but mainly coping and adaptive. Evidence for co-evolutions between various forms of resilience and institutional transformative resilience remained limited. Transformative potential seemed to get lost in procedural translations, was jeopardized by recentralization policies, and seemed only possible on the currents of already ongoing change.

Metal-based nanomaterials as antimicrobial agents: A novel driveway to accelerate the aggravation of antibiotic resistance

The consequences of antibiotic tolerance directly affect human health and result in socioeconomic loss. Nanomaterials as antimicrobial agents are considered a promising alternative to antibiotics and have been blended with various medical applications. However, with increasing evidence that metal-based nanomaterials may induce antibiotic tolerance, there is an urgent need to scrutinize how nanomaterial-induced microbial adaption affects the evolution and spread of antibiotic tolerance. Accordingly, within this investigation, we summarized the principal factors influencing the resistance development exposed to metal-based nanomaterials, including physicochemical properties, exposure scenario, as well as bacterial response. Furthermore, the mechanisms of metal-based nanomaterial-induced antibiotic resistance development were comprehensively elucidated from acquired resistance by horizontal transfer of antibiotic resistance genes (ARGs), intrinsic resistance by genetic mutation or upregulated resistance-related gene expression, and adaptive resistance by global evolution. Overall, our review raises concerns about the safety of nanomaterials as antimicrobial agents, which will facilitate assistance in the safe development of antibiotic-free antibacterial strategies.

Avoidance and attraction behaviour of slugs exposed to parasitic nematodes

Avoidance of pathogens and parasites is the first line of defense to survive. Several slug species avoid the parasitic nematode Phasmarhabditis hermaphrodita to reduce infection however, there is nothing known about whether slugs avoid other members of the Phasmarhabditis genus. I exposed two slug species (Deroceras invadens and Limax maculatus) to Phasmarhabditis californica and P. neopapillosa. D. invadens avoided P. californica but was strangely attracted to P. neopapillosa. L. maculatus did not avoid P. californica, but on day 1 and 3 significantly more slugs were found with P. neopapillosa. Reasons for host attraction to P. neopapillosa are discussed.

Achieving balance between socioeconomic development and ecosystem conservation via policy adjustments in Guangdong Province of southeastern China

Rapid urbanization improves socioeconomic development but challenges ecosystem sustainability. Meanwhile, the gradient responses of ecosystem services (ESs) to landscape structures and associated regime shifts of the agriculture-ecosystem-economy nexus (AEEN) have not been sufficiently addressed, preventing an effective balance between socioeconomic prosperity and ecosystem conservation. To bridge this knowledge gap, this study selected the Guangdong Province of southeastern China to explore landscape dynamics from 1985 to 2020 and their spatially heterogeneous impacts on ESs and the AEEN, based on Integrated Valuation of Ecosystem Services and Trade-offs approach and other biophysical models as well as statistical records about socioeconomic factors. AEEN elements, including ESs, responded directly to policy adjustments in terms of ecosystem restoration and landscape management and presented remarkable regime shifts (i.e., phase changes) and spatial heterogeneity. Aggressive agricultural reclamation before 1999 increased crop productivity but caused vegetation degradation and biomass decline. Accelerated urban expansion and ecosystem restoration efforts have improved economic and ecological benefits but have substantially reduced crop productivity and threatened food security. However, timely policy adjustments since 2009 reversed the declining trend and maintained the grain supply. Landscape composition presented patterns of gradual decline along the urban-rural gradient, which in turn determined ES gradient patterns. For instance, water yield and nitrogen export positively correlated with each other (p < 0.0001) but negatively correlated with other ESs. Our study enriches the understandings of social-ecological systems' response to man-made interventions from AEEN perspective allowing for spatial variabilities and regime shifts, which support policy formulation for coordinating ecological and economic benefits.

Genomic coevolution of papillomavirus and immune system in placental mammals indicates the role of IFN-γ in the emergence of new variants

Papillomaviruses (PVs) are causative agents for warts and cancers in different parts of the body in the mammalian lineage. Therefore, these viruses are proposed as model organisms to study host immune responses to pathogens causing chronic infections. The virus-associated cancer progression depends on two integral processes namely angiogenesis and immune response (AIR). The angiogenesis process aids in tumour progression through vessel formation and maturation but the host immune response, in contrast, makes every attempt to eliminate pathogens and thereby maintain healthy tissues. However, the evolutionary contribution of individual viral genes and host AIR genes in carcinogenesis is yet to be explored. Here, we applied the evolutionary genomics approach to find correlated evolution between six PV genes and 23 host AIR-related genes. We estimated that IFN-γ is the only host gene evolving in a correlated manner with all six PV genes under study. Furthermore, three papillomavirus genes, L2, E6, and E7, are found to interact with two third of host AIR-related genes. Moreover, a combined differential gene expression analysis and network analysis showed that inflammatory cytokine IFN-γ is the key regulator of hub genes in the PPI network of the differentially expressed genes. Functional enrichment of these hub genes is consistent with their established role in different cancers and viral infections. Overall, we conclude that IFN-γ maintains selective pressure on mammalian PV genes and seems to be a potential biomarker for PV-related cancers. This study demonstrates the evolutionary importance of IFN-γ in deciding the fate of carcinogenic PV variants.

Genetic diversity, phylogenetic position, and co-phylogenetic relationships of Karyolysus, a common blood parasite of lizards in the western Mediterranean

The genus Karyolysus was originally proposed to accommodate blood parasites of lacertid lizards in Western Europe. However, recent phylogenetic analyses suggested an inconclusive taxonomic position of these parasites of the order Adeleorina based on the available genetic information. Inconsistencies between molecular phylogeny, morphology, and/or life cycles can reflect lack of enough genetic information of the target group. We therefore surveyed 28 localities and collected blood samples from 828 lizards of 23 species including lacertids, skinks, and geckoes in the western Mediterranean, North Africa, and Macaronesia, where species of Karyolysus and other adeleorine parasites have been described. We combined molecular and microscopic methods to analyze the samples, including those from the host type species and the type locality of Karyolysus bicapsulatus. The phylogenetic relationship of these parasites was analyzed based on the 18S rRNA gene and the co-phylogenetic relationship with their vertebrate hosts was reconstructed. We molecularly detected adeleorine parasites in 37.9% of the blood samples and found 22 new parasite haplotypes. A phylogenetic reconstruction with 132 sequences indicated that 20 of the newly detected haplotypes clustered in a well-supported clade with another 18 sequences that included Karyolysus galloti and Karyolysus lacazei. Morphological evidence also supported that K. bicapsulatus clustered in this monophyletic clade. These results supported the taxonomic validity of the genus. In addition, we found some parasite haplotypes that infected different lizard host genera with ancient diverging histories, which suggested that Karyolysus is less host-specific than other blood parasites of lizards in the region. A co-phylogenetic analysis supported this interpretation because no significant co-speciation signal was shown between Karyolysus and lizard hosts.

Comparative analysis of the endophytic bacteria inhabiting the phyllosphere of aquatic fern Azolla species by high-throughput sequencing

BACKGROUND

Azolla is a small floating fern living in symbiosis with nitrogen-fixing cyanobacteria and provides a variety of important ecosystem benefits. Previous studies have presented that Azolla harbors diverse bacteria that may play a key role in host fitness and productivity. However, the characteristics of endophytic bacteria inhabiting the phyllosphere of different species of Azolla have not yet been fully understood.

RESULTS

In this study, the 16S ribosomal DNA (rDNA) V5-V7 region of bacteria was determined by Illumina high-throughput sequencing platform to study the diversity and richness of endophytic bacterial communities in the phyllosphere of five Azolla species collected from different countries. A total of 1150 operational taxonomic units (OTUs) were detected for the endophytic bacteria community. According to the α diversity indices, the diversity of bacteria was ordered as Azolla imbricata > A. pinnata > A. filiculoides > A. mexicana > A. caroliniana. The PCoA results displayed that the bacterial communities of A. mexicana and A. caroliniana shared the highest similarity, followed by the similarity between A. pinnata and A. imbricata, and they were significantly distinct from the community of A. filiculoides. The dominant bacteria of Azolla mainly belonged to the phylum of Proteobacteria, followed by Actinobacteria, Chlorobillobacteria, and Firmicutes. In detail, the relative abundance of Proteobacteria in A. imbricata was 52.23%, whereas it was more than 80.00% in the other four species of Azolla. Notably, Herbaspirillum (45.91%, 44.08%) and Methylophilus (29.97%, 37.96%) were the main genera inhabiting A. mexicana and A. caroliniana respectively. Ferrovibrio (18.54%) and Rhizobium (16.68%) were the dominant genera inhabiting A. filiculoides. The group of unidentified genera (41.63%, 44.92%) consisted most of the bacteria in A. imbricata and A. pinnata respectively. Further analysis suggested that the significant different bacteria identified in LDA Effect Size analysis existed Azolla species-specific patterns.

CONCLUSIONS

In summary, all results suggested that the diversity and composition of the endophytic bacterial communities were different in Azolla species.

An integrated understanding of the evolutionary and structural features of the SARS-CoV-2 spike receptor binding domain (RBD)

Conventional drug development strategies typically use pocket in protein structures as drug-target sites. They overlook the plausible effects of protein evolvability and resistant mutations on protein structure which in turn may impair protein-drug interaction. In this study, we used an integrated evolution and structure guided strategy to develop potential evolutionary-escape resistant therapeutics using receptor binding domain (RBD) of SARS-CoV-2 spike-protein/S-protein as a model. Deploying an ensemble of sequence space exploratory tools including co-evolutionary analysis and deep mutational scans we provide a quantitative insight into the evolutionarily constrained subspace of the RBD sequence-space. Guided by molecular simulation and structure network analysis we highlight regions inside the RBD, which are critical for providing structural integrity and conformational flexibility. Using fuzzy C-means clustering we combined evolutionary and structural features of RBD and identified a critical region. Subsequently, we used computational drug screening using a library of 1615 small molecules and identified one lead molecule, which is expected to target the identified region, critical for evolvability and structural stability of RBD. This integrated evolution-structure guided strategy to develop evolutionary-escape resistant lead molecules have potential general applications beyond SARS-CoV-2.

Allopodocotyle palmi sp. nov. and Prosorhynchus maternus Bray & Justine, 2006 (Digenea: Opecoelidae & Bucephalidae) from the Orange-Spotted Grouper Epinephelus coioides (Hamilton, 1822) off Bali, Indonesia, Described Using Modern Techniques

Background

The most convincing species of Allopodocotyle Pritchard, 1966 (Digenea: Opecoelidae) are known overwhelmingly from groupers (Serranidae: Epinephelinae). Six species of Allopodocotyle have been reported, collectively, from species of Cromileptes Swainson, 1839, Epinephelus Bloch, 1793 and Plectropomus Oken, 1817. These are A. epinepheli (Yamaguti, 1942), A. heronensis Downie & Cribb, 2011, A. manteri (Saoud & Ramadan, 1984), A. mecopera (Manter, 1940), A. plectropomi (Manter, 1963) and A. serrani (Yamaguti, 1952). In addition, a not yet fully described and unnamed seventh species, morphologically and phylogenetically close to A. epinepheli, was isolated from the orange-spotted grouper Epinephelus coioides (Hamilton, 1822) off Bali, Indonesia in 2016. An eighth species, again from E. coioides off Bali is described herein.

Methods

Morphological and phylogenetic analyses justify the recognition of A. palmi sp. nov., which is also genetically different from the as yet unnamed congener from the same host and locality. For the first time, 3D confocal laser scanning microscopy was applied to study and distinguish Digenea taxonomically. We introduce the ‘Palm pattern’, a new simplified way to visualise morphometric differences of related digenean taxa.

Results

Allopodocotyle palmi sp. nov. is distinguished from its congeners that infect groupers by its elongate body with a size > 2.7 mm and diagonal testes. The ovary is located mainly, and the anterior testis completely, in the posterior half of the body; the uterine coils are in the fourth eighth of the body. The cirrus-sac is 0.75–1.4 (1.1) mm long, its posterior extremity is well separated from the anterior extent of the vitelline fields, just reaching the anterior border of uterine coils. In addition, Prosorhynchus maternus Bray & Justine, 2006 (Bucephalidae) was isolated from E. coioides, representing the first record in Indonesia and the third record for this fish species.

Conclusion

The biodiversity research in Indonesia is enhanced with a new species description based on modern and newly applied techniques.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11686-022-00581-x.

Evolution and co-evolution: insights into the divergence of plant heat shock factor genes

The Heat Shock Factor (Hsf) genes are widely distributed across the plant kingdom regulating the plant response to various abiotic stresses. In addition to natural selection, breeding and accelerated selection changed the structure and function of Hsf genes. 1076 Hsf genes from 30 genera from primitive algae to the most advanced plant species and major crop plants were used for phylogenetic analysis. The interspecific divergence was studied with 11 members of genus Oryza while intraspecific divergence was studied with sesame pan-genome adapted to diverse ecological niches. B2 genes in eudicots and monocots originated separately while A1 gave rise to the recently evolved Class-C genes and land colonization happened with evolution of A1 genes. An increase in the number of lineages in the Oryza clade with the evolution of AA genome indicated independent domestication and positive selection was observed in > 53% of loci whereas the highly conserved homologues were under purifying selection. The paralogous genes under positive selection exhibited more domain changes for diversified function and increased fitness. A significant co-evolving cluster involving amino acids Phenylalanine, Lysine and Valine played crucial role in maintaining hydrophobic core along with highly conserved Tryptophan residues. A mutation of Glutamic acid to Glutamine was observed in A8 genes of Lamiales affecting protein solvency. Breeding resulted in accumulation of mutations reducing the hydrophobicity of proteins and a further reduction in protein aggregation. This study identify genome duplications, non-neutral selection and co-evolving residues as causing drastic changes in the conserved domain of Hsf proteins.

Supplementary information

The online version contains supplementary material available at 10.1007/s12298-022-01183-7.

A spotlight on non-host resistance to plant viruses

Plant viruses encounter a range of host defenses including non-host resistance (NHR), leading to the arrest of virus replication and movement in plants. Viruses have limited host ranges, and adaptation to a new host is an atypical phenomenon. The entire genotypes of plant species which are imperceptive to every single isolate of a genetically variable virus species are described as non-hosts. NHR is the non-specific resistance manifested by an innately immune non-host due to pre-existing and inducible defense responses, which cannot be evaded by yet-to-be adapted plant viruses. NHR-to-plant viruses are widespread, but the phenotypic variation is often not detectable within plant species. Therefore, molecular and genetic mechanisms of NHR need to be systematically studied to enable exploitation in crop protection. This article comprehensively describes the possible mechanisms of NHR against plant viruses. Also, the previous definition of NHR to plant viruses is insufficient, and the main aim of this article is to sensitize plant pathologists to the existence of NHR to plant viruses and to highlight the need for immediate and elaborate research in this area.

Phylogenetic relationship between the endosymbiont "Candidatus Riesia pediculicola" and its human louse host

Background

The human louse (Pediculus humanus) is a haematophagous ectoparasite that is intimately related to its host. It has been of great public health concern throughout human history. This louse has been classified into six divergent mitochondrial clades (A, D, B, F, C and E). As with all haematophagous lice, P. humanus directly depends on the presence of a bacterial symbiont, known as “Candidatus Riesia pediculicola”, to complement their unbalanced diet. In this study, we evaluated the codivergence of human lice around the world and their endosymbiotic bacteria. Using molecular approaches, we targeted lice mitochondrial genes from the six diverged clades and Candidatus Riesia pediculicola housekeeping genes.

Methods

The mitochondrial cytochrome b gene (cytb) of lice was selected for molecular analysis, with the aim to identify louse clade. In parallel, we developed four PCR primer pairs targeting three housekeeping genes of Candidatus Riesia pediculicola: ftsZ, groEL and two regions of the rpoB gene (rpoB-1 and rpoB-2).

Results

The endosymbiont phylogeny perfectly mirrored the host insect phylogeny using the ftsZ and rpoB-2 genes, in addition to showing a significant co-phylogenetic congruence, suggesting a strict vertical transmission and a host–symbiont co-speciation following the evolutionary course of the human louse.

Conclusion

Our results unequivocally indicate that louse endosymbionts have experienced a similar co-evolutionary history and that the human louse clade can be determined by their endosymbiotic bacteria.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05203-z.

Dependence of genome size and copy number of rRNA gene on cell volume in dinoflagellates

Dinoflagellates are an ecologically important group of protists in aquatic environment and have evolved many unusual and enigmatic genomic features such as immense genome sizes, high repeated genes, and a large portion of hydroxymethyluracil in DNA. Although previous studies have observed positive correlations between the large subunit (LSU) rRNA gene copy number and genome size of a variety of eukaryotic organisms (e.g. higher plants and animals), or between cell volume and LSU rRNA gene copy number, and/or between genome size and cell size, which suggests a possible co-evolution among these three features in different lineages of life, it remains an open question regarding the relationships among these three parameters in dinoflagellates. For the first time, we estimated the copy numbers of the LSU rRNA gene, the genome sizes, and cell volumes within a broad range of dinoflagellates (covering 15 species of 11 genera) using single-cell qPCR-based assay (determining LSU rRNA gene copy number), FlowCAM (cell volume measurement), and ultraviolet spectrophotometry (genome size estimation). The measured copy number of LSU rRNA gene ranged from 398 ± 184 (Prorocentrum minimum) to 152,078 ± 33,555 copies•cell^-1 (Alexandrium pacificum), while the genome size and the cell volume ranged from 5.6 ± 0.2 (Karlodinium veneficum) to 853 ± 19.9 pg•cell^-1 (Pseliodinium pirum), and from 1,070 ± 225 (Kar. veneficum) to 168,474 ± 124,180 μm³ (Ps. pirum), respectively. Together with the three parameters measured in literature, there are significant positive linear correlations between LSU rRNA gene copy numbers and genome sizes, cell volumes and LSU rRNA gene copy numbers, and between genome sizes and cell volumes via comparisons of multi-model regression analyses, suggesting a dependence of genome size and rRNA gene copy number on the cell volumes of dinoflagellates. Validation of the measurement methods was conducted via comparisons between reported data in the literature and that predicted using the linear equations we obtained, and between genome size measured by flow cytometry (FCM) and ultraviolet spectrophotometry (Nanodrop). These results provide insightful understandings of dinoflagellate evolution in terms of the relationships among genomes, gene copy number, and cell volume, and of rRNA gene-based studies in intra-populational and intra-individual genetic diversity, taxonomy, and diversity assessment in the environment of dinoflagellates. The results also provide a dataset useful for reads calibration in environmental metabarcoding studies of dinoflagellates and selection of candidate species for whole genome sequencing.

Fantasy visions, informal urbanization, and local conflict: an evolutionary perspective on smart city governance in India

Smart city imaginaries have emerged in southern cities driven by neoliberal logics in the urban space. Scholarly work in India has continued to engage with sweeping accounts of cities as opposed to detailed empirical studies of local projects. This paper attempts to address this gap through an in-depth ethnographic inquiry of a slum redevelopment project in the city of Bhubaneswar, India. The key objective is to understand the ways in which informal residents adapted to and changed smart city policies in India in recent years. Using an evolutionary lens, and drawing on participant observation; document analysis; and semi-structured interviews, the paper puts forth a descriptive cases that advances the notion that smart cities imaginaries have resulted in abrupt changes in the institutional context while getting entangled itself within the legal system. The paper also demonstrates how smart cities discourses counter-intuitively result in emergent spaces of resistance in the form of counter-hegemonic practices, thus allowing spaces for the evolution of new actors and imaginaries from unfamiliar territories. The paper concludes by discussing that city planning and governance pathways in India risk creating complicated path dependencies and rigid governance future pathways that may amplify conflict.

Biotransformation ability of endophytic fungi: from species evolution to industrial applications

Abstract

Increased understanding of the interactions between endophytic fungi and plants has led to the discovery of a new generation of chemical compounds and processes between endophytic fungi and plants. Due to the long-term co-evolution between fungal endophytes and host plants, endophytes have evolved special biotransformation abilities, which can have critical consequences on plant metabolic processes and their composition. Biotransformation or bioconversion can impact the synthesis and decomposition of hormones, sugars, amino acids, vitamins, lipids, proteins, and various secondary metabolites, including flavonoids, polysaccharides, and terpenes. Endophytic fungi produce enzymes and various bioactive secondary metabolites with industrial value and can degrade or sequester inorganic and organic small molecules and macromolecules (e.g., toxins, pollutants, heavy metals). These fungi also have the ability to cause highly selective catalytic conversion of high-value compounds in an environmentally friendly manner, which can be important for the production/innovation of bioactive molecules, food and nutrition, agriculture, and environment. This work mainly summarized recent research progress in this field, providing a reference for further research and application of fungal endophytes.

Key points

•The industrial value of degradation of endophytes was summarized.

• The commercial value for the pharmaceutical industry is reviewed.

Graphical abstract

Exploring the ecological and evolutionary relationships between Rickettsia and hard ticks in the Neotropical region

This study addresses a meta-analysis of the distribution of Rickettsia spp. in the Neotropical region, as well as their associations with ticks and vertebrates. A total of 219 published reports on Rickettsia in ticks in the target region were compiled, providing 599 records of 31 species of Rickettsia recorded in 50 species of Ixodidae. The aim is to capture the phylogenetic relationships between rickettsiae and the ticks carrying them in the target region, with a focus on the co-speciation ticks-rickettsiae. We compared the phylogeny of ticks, the records of rickettsiae, the environmental gradients colonized by ticks and the effect of the phylogenetic composition of vertebrates feeding ticks on the detection of Rickettsia in ticks. Results show that differences in rickettsial composition in ticks do not depend on the vertebrate's blood-source. This is the first time this result is demonstrated. This study pinpoints that some Neotropical rickettsial organisms are associated with well-defined phylogenetical clusters of ticks. Secondarily, and probably only in a few cases, rickettsiae share species of phylogenetically distant ticks distributed along a gradient of environmental traits in which the ticks overlap (i.e., the different strains of Rickettsia parkeri sensu lato). We outline the importance of some ticks that share hosts and habitat: these ticks may act as "bridges" for the circulation of rickettsial species. There are also many species of Rickettsia that have been detected so far in only one tick species, pointing to a tight relationship or to the lack of data preventing conclusions about the detection of these bacteria in other ticks. Two species, namely Rickettsia amblyommatis and Rickettsia bellii have been recorded in the majority of ticks in the region (mainly Amblyomma spp.) and seem to be not associated with definite tick species because they may be an essential symbiont of the ticks. We conclude that an adequate analysis of rickettsiae-ticks-habitat is necessary to address the human health issues derived from the infections by rickettsiae.

Molecular evolution and regulation of DHN melanin-related gene clusters are closely related to adaptation of different melanin-producing fungi

Many genes responsible for melanin biosynthesis in fungi were physically linked together. The PKS gene clusters in most of the melanin-producing fungi were regulated by the Cmr1. It was found that a close rearrangement of the PKS gene clusters had evolved in most of the melanin-producing fungi and various functions of melanin in them were beneficial to their adaptation to the changing environments. The melanin-producing fungi had undergone at least five large-scale differentiations, making their PKS gene clusters be quickly evolved and the fungi be adapted to different harsh environments. The recent gene losses and expansion were remarkably frequent in the PKS gene clusters, leading to their rapid evolution and adaptation of their hosts to different environments. The PKS gene and the CMR1 gene in them were subject to a strong co-evolution, but the horizontal gene transfer events might have occurred in the genome-duplicated species, Aspergillus and Penicillium.

Domestication affects the composition, diversity, and co-occurrence of the cereal seed microbiota

Introduction

The seed-associated microbiome has a strong influence on plant ecology, fitness, and productivity. Plant microbiota could be exploited for a more responsible crop management in sustainable agriculture. However, the relationships between seed microbiota and hosts related to the changes from ancestor species to breeded crops still remain poor understood.

Objectives

Our aims were i) to understand the effect of cereal domestication on seed endophytes in terms of diversity, structure and co-occurrence, by comparing four cereal crops and the respective ancestor species; ii) to test the phylogenetic coherence between cereals and their seed microbiota (clue of co-evolution).

Methods

We investigated the seed microbiota of four cereal crops (Triticum aestivum, Triticum monococcum, Triticum durum, and Hordeum vulgare), along with their respective ancestors (Aegilops tauschii, Triticum baeoticum, Triticum dicoccoides, and Hordeum spontaneum, respectively) using 16S rRNA gene metabarcoding, Randomly Amplified Polymorphic DNA (RAPD) profiling of host plants and co-evolution analysis.

Results

The diversity of seed microbiota was generally higher in cultivated cereals than in wild ancestors, suggesting that domestication lead to a bacterial diversification. On the other hand, more microbe-microbe interactions were detected in wild species, indicating a better-structured, mature community. Typical human-associated taxa, such as Cutibacterium, dominated in cultivated cereals, suggesting an interkingdom transfers of microbes from human to plants during domestication. Co-evolution analysis revealed a significant phylogenetic congruence between seed endophytes and host plants, indicating clues of co-evolution between hosts and seed-associated microbes during domestication.

Conclusion

This study demonstrates a diversification of the seed microbiome as a consequence of domestication, and provides clues of co-evolution between cereals and their seed microbiota. This knowledge is useful to develop effective strategies of microbiome exploitation for sustainable agriculture.

ACES: A co-evolution simulator generates co-varying protein and nucleic acid sequences

Sequence-specific and consequential interactions within or between proteins and/or RNAs can be predicted by identifying co-evolution of residues in these molecules. Different algorithms have been used to detect co-evolution, often using biological data to benchmark a methods ability to discriminate against indirect co-evolution. Such a benchmark is problematic, because not all the interactions and evolutionary constraints underlying real data can be known a priori. Instead, sequences generated in silico to simulate co-evolution would be preferable, and can be obtained using aCES, the software tool presented here. Conservation and co-evolution constraints can be specified for any residue across a number of molecules, allowing the user to capture a complex, realistic set of interactions. Resulting alignments were used to benchmark several co-evolution detection tools for their ability to separate signal from background as well as discriminating direct from indirect signals. This approach can aid in refinement of these algorithms. In addition, systematic tuning of these constraints sheds new light on how they drive co-evolution between residues. Better understanding how to detect co-evolution and the residue interactions they predict can lead to a wide range of insights important for synthetic biologists interested in engineering new, orthogonal interactions between two macromolecules.

Foundations of Erobotics

Technology is giving rise to artificial erotic agents, which we call erobots (erôs + bot). Erobots, such as virtual or augmented partners, erotic chatbots, and sex robots, increasingly expose humans to the possibility of intimacy and sexuality with artificial agents. Their advent has sparked academic and public debates: some denounce their risks (e.g., promotion of harmful sociosexual norms), while others defend their potential benefits (e.g., health, education, and research applications). Yet, the scientific study of human-machine erotic interaction is limited; no comprehensive theoretical models have been proposed and the empirical literature remains scarce. The current research programs investigating erotic technologies tend to focus on the risks and benefits of erobots, rather than providing solutions to resolve the former and enhance the latter. Moreover, we feel that these programs underestimate how humans and machines unpredictably interact and co-evolve, as well as the influence of sociocultural processes on technological development and meaning attribution. To comprehensively explore human-machine erotic interaction and co-evolution, we argue that we need a new unified transdisciplinary field of research-grounded in sexuality and technology positive frameworks-focusing on human-erobot interaction and co-evolution as well as guiding the development of beneficial erotic machines. We call this field Erobotics. As a first contribution to this new discipline, this article defines Erobotics and its related concepts; proposes a model of human-erobot interaction and co-evolution; and suggests a path to design beneficial erotic machines that could mitigate risks and enhance human well-being.

Experimental determination and data-driven prediction of homotypic transmembrane domain interfaces

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Homotypic TMD interfaces identified by different techniques share strong similarities.

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The GxxxG motif is the feature most strongly associated with interfaces.

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Other features include conservation, polarity, coevolution, and depth in the membrane

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The role of each of each feature strongly depends on the individual protein.

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Machine-learning helps predict interfaces from evolutionary sequence data

Interactions between their transmembrane domains (TMDs) frequently support the assembly of single-pass membrane proteins to non-covalent complexes. Yet, the TMD-TMD interactome remains largely uncharted. With a view to predicting homotypic TMD-TMD interfaces from primary structure, we performed a systematic analysis of their physical and evolutionary properties. To this end, we generated a dataset of 50 self-interacting TMDs. This dataset contains interfaces of nine TMDs from bitopic human proteins (Ire1, Armcx6, Tie1, ATP1B1, PTPRO, PTPRU, PTPRG, DDR1, and Siglec7) that were experimentally identified here and combined with literature data. We show that interfacial residues of these homotypic TMD-TMD interfaces tend to be more conserved, coevolved and polar than non-interfacial residues. Further, we suggest for the first time that interface positions are deficient in β-branched residues, and likely to be located deep in the hydrophobic core of the membrane. Overrepresentation of the GxxxG motif at interfaces is strong, but that of (small)xxx(small) motifs is weak. The multiplicity of these features and the individual character of TMD-TMD interfaces, as uncovered here, prompted us to train a machine learning algorithm. The resulting prediction method, THOIPA (www.thoipa.org), excels in the prediction of key interface residues from evolutionary sequence data.

Oil gland and oil pores in billfishes: in search of a function

Billfishes are well known for their distinctive elongated rostra, i.e. bills. The functional significance of billfish rostra has been frequently discussed and the recent discovery of an oil gland (glandula oleofera) at the base of the rostrum in swordfish, Xiphias gladius, has added an interesting facet to this discussion regarding the potential co-evolution of gland and rostra. Here, we investigated the oil gland and oil pores (through which the oil is brought to the skin surface) of four billfish species - swordfish, Atlantic blue marlin (Makaira nigricans), Indo-Pacific sailfish (Istiophorus platypterus) and striped marlin (Kajikia audax) - and provide detailed evidence for the presence of an oil gland in the last three. All four species had a high density of oil pores on the forehead which is consistent with the hypothesis of hydrodynamic benefits of the oil. The extension of the pores onto the front half of the rostrum in sailfish and striped marlin, but not in swordfish or blue marlin, suggests that the oil may have additional functions. One such function could be linked to the antibacterial and anti-inflammatory properties of the oil. However, the available evidence on predatory rostrum use (and hence the likelihood of tissue damage) is only partly consistent with the extension of pores on rostra across species. We conclude that the oil gland probably serves multiple, non-mutually exclusive functions. More detailed information on rostrum use in blue marlin and swordfish is needed to better link behavioural and morphological data with the aim of accomplishing a full comparative analysis.

Engineering lytic polysaccharide monooxygenases (LPMOs)

Lytic polysaccharide monooxygenases (LPMOs) are mono-copper enzymes that catalyze the hydroxylation of glycosidic bonds found in the most abundant and recalcitrant polysaccharides on Earth. Since their discovery in 2010, these enzymes have received extensive attention in both fundamental and applied research due to their remarkable oxidative power and synergistic interplay with hydrolytic enzymes. The harsh and unnatural conditions used in industrial enzymatic saccharification processes and the sensitivity of LPMOs for damage induced by reactive oxygen species call for enzyme engineering to develop LPMOs to become robust industrial biocatalysts. Other engineering targets include improved catalytic activity, adjusted substrate specificity and the introduction of completely new activities. Reaching these targets not only requires appropriate methods for measuring enzyme activity, but also requires in-depth knowledge of the active site and the reaction mechanism, which is yet to be achieved in the LPMO field. Here we describe what has been done in the LPMO engineering field so far. Furthermore, we address the difficulties involved in properly assessing LPMO functionality, which are due to common side reactions taking place in LPMO reactions and which complicate screening methods.

Correlated evolution of leaf and root anatomic traits in Dendrobium (Orchidaceae)

The whole-plant economic spectrum concept predicts that leaf and root traits evolve in coordination to cope with environmental stresses. However, this hypothesis is difficult to test in many species because their leaves and roots are exposed to different environments, above- and below-ground. In epiphytes, both leaves and roots are exposed to the atmosphere. Thus, we suspect there are consistent water conservation strategies in leaf and root traits of epiphytes due to similar selection pressures. Here, we measured the functional traits of 21 species in the genus Dendrobium, which is one of the largest epiphytic taxa in the family Orchidaceae, and used phylogenetically independent contrasts to test the relationships among traits, and between traits and the environment. Our results demonstrate that species with a thicker velamen tended to have thicker roots, a thicker root cortex and vascular cylinder, and a larger number of vessels in the root. Correspondingly, these species also had higher leaf mass per area, and thicker leaf lower cuticles. Leaf and root traits associated with water conservation showed significantly positive relationships. The number of velamen layers, leaf density and the ratio of vascular cylinder radius to root radius were significantly affected by the species' differing environments. Thus, traits related to water conservation and transport may play an important role in helping Dendrobium cope with the cool and dry conditions found at high elevations. These findings confirmed the hypothesis that leaf and root traits have evolved in coordination, and also provide insights into trait evolution and ecological adaptation in epiphytic orchids.

Detecting fitness epistasis in recently admixed populations with genome-wide data

BACKGROUND

Fitness epistasis, the interaction effect of genes at different loci on fitness, makes an important contribution to adaptive evolution. Although fitness interaction evidence has been observed in model organisms, it is more difficult to detect and remains poorly understood in human populations as a result of limited statistical power and experimental constraints. Fitness epistasis is inferred from non-independence between unlinked loci. We previously observed ancestral block correlation between chromosomes 4 and 6 in African Americans. The same approach fails when examining ancestral blocks on the same chromosome due to the strong confounding effect observed in a recently admixed population.

RESULTS

We developed a novel approach to eliminate the bias caused by admixture linkage disequilibrium when searching for fitness epistasis on the same chromosome. We applied this approach in 16,252 unrelated African Americans and identified significant ancestral correlations in two pairs of genomic regions (P-value< 8.11 × 10- 7) on chromosomes 1 and 10. The ancestral correlations were not explained by population admixture. Historical African-European crossover events are reduced between pairs of epistatic regions. We observed multiple pairs of co-expressed genes shared by the two regions on each chromosome, including ADAR being co-expressed with IFI44 in almost all tissues and DARC being co-expressed with VCAM1, S1PR1 and ELTD1 in multiple tissues in the Genotype-Tissue Expression (GTEx) data. Moreover, the co-expressed gene pairs are associated with the same diseases/traits in the GWAS Catalog, such as white blood cell count, blood pressure, lung function, inflammatory bowel disease and educational attainment.

CONCLUSIONS

Our analyses revealed two instances of fitness epistasis on chromosomes 1 and 10, and the findings suggest a potential approach to improving our understanding of adaptive evolution.

Evolution of mutualistic behaviour between Chlorella sorokiniana and Saccharomyces cerevisiae within a synthetic environment

Yeast and microalgae are microorganisms with widely diverging physiological and biotechnological properties. Accordingly, their fields of applications diverge: yeasts are primarily applied in processes related to fermentation, while microalgae are used for the production of high-value metabolites and green technologies such as carbon capture. Heterotrophic-autotrophic systems and synthetic ecology approaches have been proposed as tools to achieve stable combinations of such evolutionarily unrelated species. We describe an entirely novel synthetic ecology-based approach to evolve co-operative behaviour between winery wastewater isolates of the yeast Saccharomyces cerevisiae and microalga Chlorella sorokiniana. The data show that biomass production and mutualistic growth improved when co-evolved yeast and microalgae strains were paired together. Combinations of co-evolved strains displayed a range of phenotypes, including differences in amino acid profiles. Taken together, the results demonstrate that biotic selection pressures can lead to improved mutualistic growth phenotypes over relatively short time periods.

Co-evolution in the Jungle: From Leafcutter Ant Colonies to Chromosomal Ends

Biological entities are multicomponent systems where each part is directly or indirectly dependent on the others. In effect, a change in a single component might have a consequence on the functioning of its partners, thus affecting the fitness of the entire system. In this article, we provide a few examples of such complex biological systems, ranging from ant colonies to a population of amino acids within a single-polypeptide chain. Based on these examples, we discuss one of the central and still challenging questions in biology: how do such multicomponent consortia co-evolve? More specifically, we ask how telomeres, nucleo-protein complexes protecting the integrity of linear DNA chromosomes, originated from the ancestral organisms having circular genomes and thus not dealing with end-replication and end-protection problems. Using the examples of rapidly evolving topologies of mitochondrial genomes in eukaryotic microorganisms, we show what means of co-evolution were employed to accommodate various types of telomere-maintenance mechanisms in mitochondria. We also describe an unprecedented runaway evolution of telomeric repeats in nuclei of ascomycetous yeasts accompanied by co-evolution of telomere-associated proteins. We propose several scenarios derived from research on telomeres and supported by other studies from various fields of biology, while emphasizing that the relevant answers are still not in sight. It is this uncertainty and a lack of a detailed roadmap that makes the journey through the jungle of biological systems still exciting and worth undertaking.

Association between louse abundance and MHC II supertypes in Galápagos mockingbirds

Major histocompatibility complex class II (MHC II) is an essential molecule triggering the adaptive immune response by the presentation of pathogens to helper T cells. The association between individual MHC II variants and various parasites has become a frequent finding in studies of vertebrate populations. However, although bird ectoparasites have a significant effect on their host's fitness, and the host's immune system can regulate ectoparasitic infections, no study has yet investigated the association between MHC II polymorphism and ectoparasite infection in the populations of free-living birds. Here, we test whether an association exists between the abundance of a chewing louse (Myrsidea nesomimi) and MHC II polymorphism of its hosts, the Galápagos mockingbirds (Mimus). We have found that the presence of two MHC II supertypes (functionally differentiated clusters) was significantly associated with louse abundance. This pattern supports the theory that a co-evolutionary interaction stands behind the maintenance of MHC polymorphism. Moreover, we have found a positive correlation between louse abundance and heterophil/lymphocyte ratio (an indicator of immunological stress) that serves as an additional piece of evidence that ectoparasite burden is affected by immunological state of Galápagos mockingbirds.

The evolutionary arms race between transposable elements and piRNAs in Drosophila melanogaster

BACKGROUND

The piwi-interacting RNAs (piRNAs) are small non-coding RNAs that specifically repress transposable elements (TEs) in the germline of Drosophila. Despite our expanding understanding of TE:piRNA interaction, whether there is an evolutionary arms race between TEs and piRNAs was unclear.

RESULTS

Here, we studied the population genomics of TEs and piRNAs in the worldwide strains of D. melanogaster. By conducting a correlation analysis between TE contents and the abundance of piRNAs from ovaries of representative strains of D. melanogaster, we find positive correlations between TEs and piRNAs in six TE families. Our simulations further highlight that TE activities and the strength of purifying selection against TEs are important factors shaping the interactions between TEs and piRNAs. Our studies also suggest that the de novo generation of piRNAs is an important mechanism to repress the newly invaded TEs.

CONCLUSIONS

Our results revealed the existence of an evolutionary arms race between the copy numbers of TEs and the abundance of antisense piRNAs at the population level. Although the interactions between TEs and piRNAs are complex and many factors should be considered to impact their interaction dynamics, our results suggest the emergence, repression specificity and strength of piRNAs on TEs should be considered in studying the landscapes of TE insertions in Drosophila. These results deepen our understanding of the interactions between piRNAs and TEs, and also provide novel insights into the nature of genomic conflicts of other forms.

Prediction and targeting of GPCR oligomer interfaces

GPCR oligomerization has emerged as a hot topic in the GPCR field in the last years. Receptors that are part of these oligomers can influence each other's function, although it is not yet entirely understood how these interactions work. The existence of such a highly complex network of interactions between GPCRs generates the possibility of alternative targets for new therapeutic approaches. However, challenges still exist in the characterization of these complexes, especially at the interface level. Different experimental approaches, such as FRET or BRET, are usually combined to study GPCR oligomer interactions. Computational methods have been applied as a useful tool for retrieving information from GPCR sequences and the few X-ray-resolved oligomeric structures that are accessible, as well as for predicting new and trustworthy GPCR oligomeric interfaces. Machine-learning (ML) approaches have recently helped with some hindrances of other methods. By joining and evaluating multiple structure-, sequence- and co-evolution-based features on the same algorithm, it is possible to dilute the issues of particular structures and residues that arise from the experimental methodology into all-encompassing algorithms capable of accurately predict GPCR-GPCR interfaces. All these methods used as a single or a combined approach provide useful information about GPCR oligomerization and its role in GPCR function and dynamics. Altogether, we present experimental, computational and machine-learning methods used to study oligomers interfaces, as well as strategies that have been used to target these dynamic complexes.

Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales

Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed the identification, detection and classification of both hosts and pathogens, allowing a greater resolution that helps decipher their underlying dynamics and provides novel insights into their environmental context. Nevertheless, many challenges to a general understanding of host-pathogen interactions remain, in particular in the synthesis and integration of concepts and findings across a variety of systems and different spatiotemporal and ecological scales. In this perspective we aim to highlight some of the commonalities and complexities across diverse studies of host-pathogen interactions, with a focus on ecological, spatiotemporal variation, and the choice of genomic methods used. We performed a quantitative review of recent literature to investigate links, patterns and potential tradeoffs between the complexity of genomic, ecological and spatiotemporal scales undertaken in individual host-pathogen studies. We found that the majority of studies used whole genome resolution to address their research objectives across a broad range of ecological scales, especially when focusing on the pathogen side of the interaction. Nevertheless, genomic studies conducted in a complex spatiotemporal context are currently rare in the literature. Because processes of host-pathogen interactions can be understood at multiple scales, from molecular-, cellular-, and physiological-scales to the levels of populations and ecosystems, we conclude that a major obstacle for synthesis across diverse host-pathogen systems is that data are collected on widely diverging scales with different degrees of resolution. This disparity not only hampers effective infrastructural organization of the data but also data granularity and accessibility. Comprehensive metadata deposited in association with genomic data in easily accessible databases will allow greater inference across systems in the future, especially when combined with open data standards and practices. The standardization and comparability of such data will facilitate early detection of emerging infectious diseases as well as studies of the impact of anthropogenic stressors, such as climate change, on disease dynamics in humans and wildlife.

ProteinNet: a standardized data set for machine learning of protein structure

Background

Rapid progress in deep learning has spurred its application to bioinformatics problems including protein structure prediction and design. In classic machine learning problems like computer vision, progress has been driven by standardized data sets that facilitate fair assessment of new methods and lower the barrier to entry for non-domain experts. While data sets of protein sequence and structure exist, they lack certain components critical for machine learning, including high-quality multiple sequence alignments and insulated training/validation splits that account for deep but only weakly detectable homology across protein space.

Results

We created the ProteinNet series of data sets to provide a standardized mechanism for training and assessing data-driven models of protein sequence-structure relationships. ProteinNet integrates sequence, structure, and evolutionary information in programmatically accessible file formats tailored for machine learning frameworks. Multiple sequence alignments of all structurally characterized proteins were created using substantial high-performance computing resources. Standardized data splits were also generated to emulate the difficulty of past CASP (Critical Assessment of protein Structure Prediction) experiments by resetting protein sequence and structure space to the historical states that preceded six prior CASPs. Utilizing sensitive evolution-based distance metrics to segregate distantly related proteins, we have additionally created validation sets distinct from the official CASP sets that faithfully mimic their difficulty.

Conclusion

ProteinNet represents a comprehensive and accessible resource for training and assessing machine-learned models of protein structure.

A reduction in ecological niche for Trypanosoma cruzi-infected triatomine bugs

Background

Theory predicts that parasites can affect and thus drive their hosts’ niche. Testing this prediction is key, especially for vector-borne diseases including Chagas disease. Here, we examined the niche use of seven triatomine species that occur in Mexico, based on whether they are infected or not with Trypanosoma cruzi, the vectors and causative parasites of Chagas disease, respectively. Presence data for seven species of triatomines (Triatoma barberi, T. dimidiata, T. longipennis, T. mazzottii, T. pallidipennis, T. phyllosoma and T. picturata) were used and divided into populations infected and not infected by T. cruzi. Species distribution models were generated with Maxent 3.3.3k. Using distribution models, niche analysis tests of amplitude and distance to centroids were carried out for infected vs non-infected populations within species.

Results

Infected populations of bugs of six out of the seven triatomine species showed a reduced ecological space compared to non-infected populations. In all but one case (T. pallidipennis), the niche used by infected populations was close to the niche centroid of its insect host.

Conclusions

Trypanosoma cruzi may have selected for a restricted niche amplitude in triatomines, although we are unaware of the underlying reasons. Possibly the fact that T. cruzi infection bears a fitness cost for triatomines is what narrows the niche breadth of the insects. Our results imply that Chagas control programmes should consider whether bugs are infected in models of triatomine distribution.

Electronic supplementary material

The online version of this article (10.1186/s13071-019-3489-5) contains supplementary material, which is available to authorized users.

An intertidal fish shows thermal acclimation despite living in a rapidly fluctuating environment

The co-evolution of acclimation capacity and thermal performance breadth has been a contentious issue for decades, and little is known regarding the extent to which acclimation alters the shape of acute thermal performance curves. Current acclimation theory suggests that when daily variation is large and unpredictable ectotherms should not acclimate but should evolve wide performance breadths, allowing maintenance of performance across a wide thermal range. The subtropical intertidal zone, however, experiences a large amount of daily thermal variation, but daily means and ranges shift in predictable ways with season, where daily and seasonal variation is roughly equal. We predicted that animals in this habitat would maintain their capacity to acclimate and that performance breadth would not be altered by acclimation to maintain function with rapidly fluctuating daily temperatures. We tested our prediction using a subtropical goby, Bathygobius cocosensis, which lives in tide pools that vary widely, over days and seasons. We exposed B. cocosensis to winter (12-17 °C) and summer (30-35 °C) thermal conditions for six weeks and then measured the thermal dependence of burst swimming speed, routine and maximum metabolic rate, and ventilation rate between 12 and 36 °C. B. cocosensis exhibited an acclimation response for burst swimming speed, maximum metabolic rate and metabolic scope, but acclimation did not alter the shape of acute thermal performance curves. These results indicate that thermal acclimation can occur when short-term thermal variability is large and equal to seasonal variation, and wide performance breadths can be maintained with acclimation in heterogeneous environments.

The way forward: Can connectivity be useful to design better measuring and modelling schemes for water and sediment dynamics?

For many years, scientists have tried to understand, describe and quantify water and sediment fluxes, with associated substances like pollutants, at multiple scales. In the past two decades, a new concept called connectivity has been used by Earth Scientists as a means to describe and quantify the influences on the fluxes of water and sediment on different scales: aggregate, pedon, location on the slope, slope, watershed, and basin. A better understanding of connectivity can enhance our comprehension of landscape processes and provide a basis for the development of better measurement and modelling approaches, further leading to a better potential for implementing this concept as a management tool. This paper provides a short review of the State-of-the-Art of the connectivity concept, from which we conclude that scientists have been struggling to find a way to quantify connectivity so far. We adapt the knowledge of connectivity to better understand and quantify water and sediment transfers in catchment systems. First, we introduce a new approach to the concept of connectivity to study water and sediment transfers and the associated substances. In this approach water and sediment dynamics are divided in two parts: the system consists of phases and fluxes, each being separately measurable. This approach enables us to: i) better conceptualize our understanding of system dynamics at different timescales, including long timescales; ii) identify the main parameters driving system dynamics, and devise monitoring strategies which capture them; and, iii) build models with a holistic approach to simulate system dynamics without excessive complexity. Secondly, we discuss the role of system boundaries in designing measurement schemes and models. Natural systems have boundaries within which sediment connectivity varies between phases; in (semi-)arid regions these boundaries can be far apart in time due to extreme events. External disturbances (eg. climate change, changed land management) can change these boundaries. It is therefore important to consider the system state as a whole, including its boundaries and internal dynamics, when designing and implementing comprehensive monitoring and modelling approaches. Connectivity is a useful tool concept for scientists that must be expanded to stakeholder and policymakers.

Induction of domoic acid production in diatoms-Types of grazers and diatoms are important

Grazers can induce toxin (domoic acid, DA) production in diatoms. The toxic response has been observed in two species of Pseudo-nitzschia and was induced by Calanus copepods. In this study, interactions between diatoms and copepods were further explored using different species of diatoms and copepods. All herbivorous copepods induced toxin production, whereas exposure to carnivorous copepods did not. In line with this, increasing the number of herbivorous copepods resulted in even higher toxin production. The induced response is thus only elicited by copepods that pose a real threat to the responding cells, which supports that the induced toxin production in diatoms evolved as an inducible defense. The cellular toxin content in Pseudo-nitzschia was positively correlated to the concentration of a group of specific polar lipids called copepodamides that are excreted by the copepods. This suggests that copepodamides are the chemical cues responsible for triggering the toxin production. Carnivorous copepods were found to produce less or no copepodamides. Among the diatoms exposed to grazing herbivorous copepods, only two of six species of Pseudo-nitzschia and none of the Nitzschia or Fragilariopsis strains responded by producing DA, indicating that not all Pseudo-nitzschia species/strains are able to produce DA, and that different diatom species might have different strategies for coping with grazing pressure. Growth rate was negatively correlated to cellular domoic acid content indicating an allocation cost associated with toxin production. Long-term grazing experiments showed higher mortality rates of grazers fed toxic diatoms, supporting the hypothesis that DA production is an induced defense mechanism.

Possibilities for rationally exploiting co-evolution in addressing resistance to insecticides, and beyond

Certain biorational chemical agents used against insect pests impact essential stages or processes in insect life cycles when applied for pest management. Development of resistance to these agents, while involving maintenance of the natural role of the chemical agent, frequently requires the evolution of a new chemical structure by the resistant organism. When considering the process of resistance development, one could theoretically consider biorational structural determination rather than the less predictable or feasible generation of a novel replacement insecticide. At first consideration, this process might exclude toxicants such as typical pest control agents and rather be a phenomenon reserved principally for signalling processes such as are fulfilled by pheromones and other semiochemicals. However, because there is a unique co-evolutionary relationship between chemical defence and the physiology of the antagonistic organism, this process can be further explored for potential to overcome resistance to toxins. Given further consideration, newly evolved chemical defences may rationally provide options for new resistance-defeating chemistry. This review therefore discusses the potential for overcoming insecticide resistance through targeted application of this approach. Potential for use of a similar approach to counteract fungicide and herbicide resistance is also considered. Furthermore, the possible applications of this approach to address drug or pharmaceutic resistance are also considered.

Interplay between sequence, structure and linear motifs in the adenovirus E1A hub protein

E1A is the main transforming protein in mastadenoviruses. This work uses bioinformatics to extrapolate experimental knowledge from Human adenovirus serotype 5 and 12 E1A proteins to all known serotypes. A conserved domain architecture with a high degree of intrinsic disorder acts as a scaffold for multiple linear motifs with variable occurrence mediating the interaction with over fifty host proteins. While linear motifs contribute strongly to sequence conservation within intrinsically disordered E1A regions, motif repertoires can deviate significantly from those found in prototypical serotypes. Close to one hundred predicted residue-residue contacts suggest the presence of stable structure in the CR3 domain and of specific conformational ensembles involving both short- and long-range intramolecular interactions. Our computational results suggest that E1A sequence conservation and co-evolution reflect the evolutionary pressure to maintain a mainly disordered, yet non-random conformation harboring a high number of binding motifs that mediate viral hijacking of the cell machinery.