The skeletome of the red coral Corallium rubrum indicates an independent evolution of biomineralization process in octocorals

Chromosome-level genome assembly of a cliff plant Taihangia rupestris var. ciliata provides insights into its adaptation and demographic history

BACKGROUND

Cliffs are recognized as one of the most challenging environments for plants, characterized by harsh conditions such as drought, infertile soil, and steep terrain. However, they surprisingly host ancient and diverse plant communities and play a crucial role in protecting biodiversity. The Taihang Mountains, which act as a natural boundary in eastern China, support a rich variety of plant species, including many unique to cliff habitats. However, it is little known how cliff plants adapt to harsh habitats and the demographic history in this region.

RESULTS

To better understand the demographic history and adaptation of cliff plants in this area, we analyzed the chromosome-level genome of a representative cliff plant, T. rupestris var. ciliata, which has a genome size of 769.5 Mb, with a scaffold N50 of 104.92 Mb. The rapid expansion of transposable elements may have contributed to the increasing genome and its ability to adapt to unique and challenging cliff habitats. Comparative analysis of the genome evolution between Taihangia and non-cliff plants in Rosaceae revealed a significant expansion of gene families associated with oxidative phosphorylation, which is likely a response to the abiotic stresses faced by cliff plants. This expansion may explain the long-term adaptation of Taihangia to harsh cliff environments. The effective population size of the two varieties has continuously decreased due to climatic fluctuations during the Quaternary period. Furthermore, significant differences in gene expression between the two varieties may explain the varied leaf phenotypes and adaptations to harsh conditions in different natural distributions.

CONCLUSION

Our study highlights the extraordinary adaptation of T. rupestris var. ciliata, shedding light on the evolution of cliff plants worldwide.

Genomic epidemiology of West Nile virus in Europe

West Nile virus is one of the most widespread mosquito-borne zoonotic viruses, with unique transmission dynamics in various parts of the world. Genomic surveillance has provided important insights in the global patterns of West Nile virus emergence and spread. In Europe, multiple West Nile virus lineages have been isolated, with lineage 1a and 2 being the main lineages responsible for human infections. In contrast to North America, where a single introduction of lineage 1a resulted in the virus establishing itself in a new continent, at least 13 introductions of lineages 1a and 2 have occurred into Europe, which is likely a vast underestimation of the true number of introductions. Historically, lineage 1a was the main lineage circulating in Europe, but since the emergence of lineage 2 in the early 2000s, the latter has become the predominant lineage. This shift in West Nile virus lineage prevalence has been broadly linked to the expansion of the virus into northerly temperate regions, where autochthonous cases in animals and humans have been reported in Germany and The Netherlands. Here, we discuss how genomic analysis has increased our understanding of the epidemiology of West Nile virus in Europe, and we present a global Nextstrain build consisting of publicly available West Nile virus genomes (https://nextstrain.org/community/grubaughlab/WNV-Global). Our results elucidate recent insights in West Nile virus lineage dynamics in Europe, and discuss how expanded programs can fill current genomic surveillance gaps.

The first mitogenomic phylogenetic framework of Dorcus sensu lato (Coleoptera: Lucanidae), with an emphasis on generic taxonomy in Eastern Asia

BACKGROUND

Dorcus stag beetles in broad sense are one of the most diverse group in Lucanidae and important saproxylic insects playing a crucial role in nutrient recycling and forest biomonitoring. However, the dazzling morphological differentiations have caused numerous systematic confusion within the big genus, especially the puzzlingly generic taxonomy. So far, there is lack of molecular phylogenetic study to address the chaotic situation. In this study, we undertook mitochondrial genome sequencing of 42 representative species including 18 newly-sequenced ones from Eastern Asia and reconstructed the phylogenetic framework of stag beetles in Dorcus sensu lato for the first time.

RESULTS

The mitogenome datasets of Dorcus species have indicated the variable mitogenomic lengths ranged from 15,785 to 19,813 bp. Each mitogenome contained 13 PCGs, 2 rRNAs, 22 tRNAs, and a control region, and all PCGs were under strong purifying selection (Ka/Ks < 1). Notably, we have identified the presence of a substantial intergenic spacer (IGS) between the trnAser (UCN) and NAD1 genes, with varying lengths ranging from 129 bp (in D. hansi) to 158 bp (in D. tityus). The mitogenomic phylogenetic analysis of 42 species showed that Eastern Asia Dorcus was monophyletic, and divided into eight clades with significant genetic distance. Four of them, Clade VIII, VII, VI and I are clustered by the representative species of Serrognathus Motschulsky, Kirchnerius Schenk, Falcicornis Séguy and Dorcus s.s. respectively, which supported their fully generic positions as the previous morphological study presented. The topology also showed the remaining clades were distinctly separated from the species of Dorcus sensu lato, which implied that each of them might demonstrate independent generic status. The Linnaeus nomenclatures were suggested as Eurydorcus Didier stat. res., Eurytrachellelus Didier stat. res., Hemisodorcus Thomson stat. res. and Velutinodorcus Maes stat. res. For Clade V, IV, III and II respectively.

CONCLUSION

This study recognized the monophyly of Dorcus stag beetles and provided a framework for the molecular phylogeny of this group for the first time. The newly generated mitogenomic data serves as a valuable resource for future investigations on lucanid beetles. The generic relationship would facilitate the systematics of Dorcus stag beetles and thus be useful for exploring their evolutionary, ecological, and conservation aspects.

From genes to ecosystems: Decoding plant tolerance mechanisms to arsenic stress

Arsenic (As), a metalloid of considerable toxicity, has become increasingly bioavailable through anthropogenic activities, raising As contamination levels in groundwater and agricultural soils worldwide. This bioavailability has profound implications for plant biology and farming systems. As can detrimentally affect crop yield and pose risks of bioaccumulation and subsequent entry into the food chain. Upon exposure to As, plants initiate a multifaceted molecular response involving crucial signaling pathways, such as those mediated by calcium, mitogen-activated protein kinases, and various phytohormones (e.g., auxin, methyl jasmonate, cytokinin). These pathways, in turn, activate enzymes within the antioxidant system, which combat the reactive oxygen/nitrogen species (ROS and RNS) generated by As-induced stress. Plants exhibit a sophisticated genomic response to As, involving the upregulation of genes associated with uptake, chelation, and sequestration. Specific gene families, such as those coding for aquaglyceroporins and ABC transporters, are key in mediating As uptake and translocation within plant tissues. Moreover, we explore the gene regulatory networks that orchestrate the synthesis of phytochelatins and metallothioneins, which are crucial for As chelation and detoxification. Transcription factors, particularly those belonging to the MYB, NAC, and WRKY families, emerge as central regulators in activating As-responsive genes. On a post-translational level, we examine how ubiquitination pathways modulate the stability and function of proteins involved in As metabolism. By integrating omics findings, this review provides a comprehensive overview of the complex genomic landscape that defines plant responses to As. Knowledge gained from these genomic and epigenetic insights is pivotal for developing biotechnological strategies to enhance crop As tolerance.

Adaptive changes in BMAL2 with increased locomotion associated with the evolution of unihemispheric slow-wave sleep in mammals

Marine mammals, especially cetaceans, have evolved a very special form of sleep characterized by unihemispheric slow-wave sleep (USWS) and a negligible amount or complete absence of rapid-eye-movement sleep; however, the underlying genetic mechanisms remain unclear. Here, we detected unique, significant selection signatures in basic helix-loop-helix ARNT like 2 (BMAL2; also called ARNTL2), a key circadian regulator, in marine mammal lineages, and identified two nonsynonymous amino acid substitutions (K204E and K346Q) in the important PER-ARNT-SIM domain of cetacean BMAL2 via sequence comparison with other mammals. In vitro assays revealed that these cetacean-specific mutations specifically enhanced the response to E-box-like enhancer and consequently promoted the transcriptional activation of PER2, which is closely linked to sleep regulation. The increased PER2 expression, which was further confirmed both in vitro and in vivo, is beneficial for allowing cetaceans to maintain continuous movement and alertness during sleep. Concordantly, the locomotor activities of zebrafish overexpressing the cetacean-specific mutant bmal2 were significantly higher than the zebrafish overexpressing the wild-type gene. Subsequently, transcriptome analyses revealed that cetacean-specific mutations caused the upregulation of arousal-related genes and the downregulation of several sleep-promoting genes, which is consistent with the need to maintain hemispheric arousal during USWS. Our findings suggest a potential close relationship between adaptive changes in BMAL2 and the remarkable adaptation of USWS and may provide novel insights into the genetic basis of the evolution of animal sleep.

Sensing in the dark: Constructive evolution of the lateral line system in blind populations of Astyanax mexicanus

Cave-adapted animals evolve a suite of regressive and constructive traits that allow survival in the dark. Most studies aiming at understanding cave animal evolution have focused on the genetics and environmental underpinnings of regressive traits, with special emphasis on vision loss. Possibly as a result of vision loss, other non-visual sensory systems have expanded and compensated in cave species. For instance, in many cave-dwelling fish species, including the blind cavefish of the Mexican tetra, Astyanax mexicanus, a major non-visual mechanosensory system called the lateral line, compensated for vision loss through morphological expansions. While substantial work has shed light on constructive adaptation of this system, there are still many open questions regarding its developmental origin, synaptic plasticity, and overall adaptive value. This review provides a snapshot of the current state of knowledge of lateral line adaption in A. mexicanus, with an emphasis on anatomy, synaptic plasticity, and behavior. Multiple open avenues for future research in this system, and how these can be leveraged as tools for both evolutionary biology and evolutionary medicine, are discussed.

Fitness difference between two synonymous mutations of Phytophthora infestans ATP6 gene

BACKGROUND

Sequence variation produced by mutation provides the ultimate source of natural selection for species adaptation. Unlike nonsynonymous mutation, synonymous mutations are generally considered to be selectively neutral but accumulating evidence suggests they also contribute to species adaptation by regulating the flow of genetic information and the development of functional traits. In this study, we analysed sequence characteristics of ATP6, a housekeeping gene from 139 Phytophthora infestans isolates, and compared the fitness components including metabolic rate, temperature sensitivity, aggressiveness, and fungicide tolerance among synonymous mutations.

RESULTS

We found that the housekeeping gene exhibited low genetic variation and was represented by two major synonymous mutants at similar frequency (0.496 and 0.468, respectively). The two synonymous mutants were generated by a single nucleotide substitution but differed significantly in fitness as well as temperature-mediated spatial distribution and expression. The synonymous mutant ending in AT was more common in cold regions and was more expressed at lower experimental temperature than the synonymous mutant ending in GC and vice versa.

CONCLUSION

Our results are consistent with the argument that synonymous mutations can modulate the adaptive evolution of species including pathogens and have important implications for sustainable disease management, especially under climate change.

Twenty years on from Developmental Plasticity and Evolution: middle-range theories and how to test them

In Developmental Plasticity and Evolution, Mary-Jane West-Eberhard argued that the developmental mechanisms that enable organisms to respond to their environment are fundamental causes of adaptation and diversification. Twenty years after publication of this book, this once so highly controversial claim appears to have been assimilated by a wealth of studies on 'plasticity-led' evolution. However, we suggest that the role of development in explanations for adaptive evolution remains underappreciated in this body of work. By combining concepts of evolvability from evolutionary developmental biology and quantitative genetics, we outline a framework that is more appropriate to identify developmental causes of adaptive evolution. This framework demonstrates how experimental and comparative developmental biology and physiology can be leveraged to put the role of plasticity in evolution to the test.

Genetic diversity, spatial connectivity, and population structure of Asian silurid catfish Wallago attu (Bloch and Schneider, 1801) in the Ganga River System: insights from mitochondrial DNA analysis

BACKGROUND

The Ganga River System (GRS) is a biodiversity hotspot, its ecological richness is shaped by a complex geological history. In this study, we examined the genetic diversity, spatial connectivity, and population structure of the Asian Silurid catfish, Wallago attu, across seven tributaries of the GRS.

METHODS AND RESULTS

We employed three mitochondrial DNA (mtDNA) regions: cytochrome c oxidase subunit I (COXI), cytochrome b (Cyt b), and control region (CR). Our comprehensive dataset encompassed 2420 bp of mtDNA, derived from 176 W. attu individuals across 19 sampling sites within the seven rivers of GRS. Our findings revealed high gene diversity (Hd:0.99) within W. attu populations. Analysis of Molecular Variance (AMOVA) highlighted that maximum genetic variations were attributed within the populations, and the observed genetic differentiation among the seven populations of W. attu ranged from low to moderate. Network analysis uncovered the presence of three distinct genetic clades, showing no specific association with seven studied rivers. Bayesian skyline plots provided insights into the demographic history of W. attu, suggesting a recent population expansion estimated to have occurred approximately 0.04 million years ago (mya) during the Pleistocene epoch.

CONCLUSIONS

These results significantly enhance our understanding of the genetic diversity and spatial connectivity of W. attu, serving as a vital foundation for developing informed conservation strategies and the sustainable management of this economically valuable resource within the Ganga River System.

Biomineralization in a cold environment: Insights from shield compositions and transcriptomics of polar sternaspids (Sternaspidae, Polychaeta)

The survival and physiological functions of polar marine organisms are impacted by global climate changes. Investigation of the adaptation mechanisms underlying biomineralization in polar organisms at low temperatures is important for understanding mineralized organismal sensitivity to climate change. Here, we performed electron probe analysis on the shields of Antarctic polychaete Sternaspis sendalli and Arctic polychaete Sternaspis buzhinskajae (Sternaspidae), and sequenced the transcriptomes of the tissues surrounding shields to examine biomineral characteristics and adaptive mechanisms in persistently cold environments. Compared to the temperate relative species, the relative abundance of iron, phosphorus, calcium, magnesium, nitrogen, sulfur and silicon in two polar sternaspid shields was similar to Sternaspis chinensis. However, the diversity and expression levels of biomineralization-related shell matrix proteins differed between the polar and temperate species, suggesting distinct molecular mechanisms underlying shield formation in cold environments. Tubulin and cyclophilin were upregulated compared to the temperate species. Furthermore, 42 positively selected genes were identified in Antarctic S. sendalli, with functions in cytoskeletal structure, DNA repair, immunity, transcription, translation, protein synthesis, and lipid metabolism. Highly expressed genes in both polar species were associated with cytoskeleton, macromolecular complexes and cellular component biosynthesis. Overall, this study reveals conserved elemental composition yet distinct biomineralization processes in the shields of polar sternaspids. The unique expression of biomineralization related genes and other cold-adaptation related genes provide molecular insights into biomineralization in cold marine environments.

Complex dental wear analysis reveals dietary shift in Triassic placodonts (Sauropsida, Sauropterygia)

Placodonts were durophagous reptiles of the Triassic seas with robust skulls, jaws, and enlarged, flat, pebble-like teeth. During their evolution, they underwent gradual craniodental changes from the Early Anisian to the Rhaetian, such as a reduction in the number of teeth, an increase in the size of the posterior palatal teeth, an elongation of the premaxilla/rostrum, and a widening of the temporal region. These changes are presumably related to changes in dietary habits, which, we hypothesise, are due to changes in the type and quality of food they consumed. In the present study, the dental wear pattern of a total of nine European Middle to Late Triassic placodont species were investigated using 2D and 3D microwear analyses to demonstrate whether there could have been a dietary shift or grouping among the different species and, whether the possible changes could be correlated with environmental changes affecting their habitats. The 3D analysis shows overlap between species with high variance between values and there is no distinct separation. The 2D analysis has distinguished two main groups. The first is characterised by low number of wear features and high percentage of large pits. The other group have a high feature number, but low percentage of small pits. The 2D analysis showed a correlation between the wear data and the size of the enlarged posterior crushing teeth. Teeth with larger sizes showed less wear feature (with higher pit ratio) but larger individual features. In contrast, the dental wear facet of smaller crushing teeth shows more but smaller wear features (with higher scratch number). This observation may be related to the size of the food consumed, i.e., the wider the crown, the larger food it could crush, producing larger features. Comparison with marine mammals suggests that the dietary preference of Placochelys, Psephoderma and Paraplacodus was not exclusively hard, thick-shelled food. They may have had a more mixed diet, similar to that of modern sea otters. The diet of Henodus may have included plant food, similar to the modern herbivore marine mammals and lizards.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13358-024-00304-x.

Morphometric and genetic characterization of cultured and wild populations of tilapia, Oreochromis niloticus in India

To study genetic variation in Indian populations of tilapia, Oreochromis niloticus, both truss morphometrics and genetic characterization have been performed. In the present study, 88 individuals from two farm populations (GIFT and West Bengal) and one reservoir population (Gujarat) were selected to analyse variations at ten morphometric landmarks and eight microsatellite loci. Truss morphometric analysis showed PCI, PCII, and PCIII expressing 29.1%, 21.36%, and 15.48% of the variance, respectively. Results showed no clear shift in shape between the studied populations of O. niloticus, indicating low morphological variability among them. The number of microsatellite alleles ranged from 3 to 9, while expected heterozygosity (HE) and observed heterozygosity (HO) values ranged from 0.56 (WB) to 0.68 (Guj) and 0.59 (GIFT) to 0.72 (Guj), respectively. The Gujarat and West Bengal populations had the smallest pairwise distance (0.0123) between them, indicating that they were genetically closer. Individuals from GIFT, however, showed the largest distance from the other populations. DNA marker variations revealed the highest genetic variability in the Gujarat population and the lowest variability in the GIFT population. The results of this study will help establish a base population for genetic improvement program and conservation of wild populations.

Latitudinal variation in survival and immature development of Ceratitis capitata populations reared in two key overwintering hosts

Ceratitis capitata, a major agricultural pest, is currently expanding its geographic distribution to northern, temperate areas of Europe. Its seasonal biology and invasion success depend on temperature, humidity and host availability. In coastal warmer Mediterranean regions and cooler temperature areas, bitter oranges and apples serve as overwintering hosts during the larval stage. We assessed the overwintering capacity of C. capitata populations obtained from different areas of the northern hemisphere by studying the survival and development rates of immature stages in both fruits under laboratory conditions. Eggs from each population were artificially inserted in the flesh of the two hosts and kept at 15, 20, or 25 °C until pupation and adult emergence. Climatic analysis of the area of the population origin showed combined effects of latitude, host and macroclimatic variables on immature survival and development rates. Egg to adult survival rates and developmental duration were longer in apples than in bitter oranges. For populations originated from southern-warmer areas, egg to adult developmental duration was prolonged and adult emergence reduced at 15 °C compared to those populations obtained from northern regions. Our findings reveal varying plastic responses of medfly populations to different overwintering hosts and temperatures highlighting the differential overwintering potential as larvae within fruits. This study contributes towards better understanding the medfly invasion dynamics in temperate areas of Northern Europe and other parts of the globe with similar climates.

Small-scale metapopulation structure of a limnophilic fish species in a natural river system investigated using microsatellite genotyping by amplicon sequencing (SSR-GBAS)

Habitat niches of fish species can exert a strong influence on population structure, even on a small geographical scale. In this scope, Pelasgus thesproticus is a great model species to study connectivity in riverine environments owing to its naturally patchy habitat distribution. Furthermore, it is important to conduct such studies in near-natural systems to avoid the impact of human disturbances on the river, such as fragmentation, morphological changes and habitat degradation. In this sense, the Vjosa in Albania is an excellent study area. A total of 204 individuals were sampled from five locations in the lower Vjosa and two tributaries and genotyped with 33 newly designed microsatellites loci using high throughput sequencing. The application of microsatellite genotyping by sequencing revealed genetic structure and some differentiation, even at a small spatial scale (< 65 river km). A total of 500 alleles were found with an average of 0.93 private alleles among sites with rather low FST values (< 0.04). The extent of admixture observed in some populations indicate that the genetic structure is mainly influenced by upstream populations, either from the main river itself or from tributaries. In addition, the connection between a tributary and the other sites is disrupted by the flow regime, which is reflected in a high degree of divergence from the other populations. Our results indicate that hydrological conditions of the flowing river present strong barriers to gene flow, particularly in the upstream direction, but at the same time act as dispersal corridors in the downstream direction and exhibit source-sink dynamics in which upstream populations contribute disproportionately to downstream populations for this habitat specialist along the river. It is suggested that processes of colonization and reinforcement may play an important role in shaping the genetic structure of patchily distributed fish species in natural river systems. Future studies should increase the knowledge of dispersal factors, habitat heterogeneity, consequence of source-sink dynamics, and gene flow within the system, which will help to understand and maintain important processes related to metapopulation theory and the potential evolutionary consequences of habitat loss and fragmentation.

Unraveling the potential of environmental DNA for deciphering recent advances in plant-animal interactions: a systematic review

MAIN CONCLUSION

Environmental DNA-based monitoring provides critical insights for enhancing our understanding of plant-animal interactions in the context of worldwide biodiversity decrease for developing a global framework for effective plant biodiversity conservation. To understand the ecology and evolutionary patterns of plant-animal interactions (PAI) and their pivotal roles in ecosystem functioning advances in molecular ecology tools such as Environmental DNA (eDNA) provide unprecedented research avenues. These methods being non-destructive in comparison to traditional biodiversity monitoring methods, enhance the discernment of ecosystem health, integrity, and complex interactions. This review intends to offer a systematic and critical appraisal of the prospective of eDNA for investigating PAI. The review thoroughly discusses and analyzes the recent reports (2015-2022) employing preferred reporting items for systematic reviews and meta-analyses (PRISMA) to outline the recent progression in eDNA approaches for elucidating PAI. The current review envisages that eDNA has a significant potential to monitor both plants and associated cohort of prospective pollinators (avian species and flowering plants, bees and plants, arthropods and plants, bats and plants, etc.). Furthermore, a brief description of the factors that influence the utility and interpretation of PAI eDNA is also presented. The review establishes that factors such as biotic and abiotic, primer selection and taxonomic resolution, and indeterminate spatio-temporal scales impact the availability and longevity of eDNA. The study also identified the limitations that influence PAI detection and suggested possible solutions for better execution of these molecular approaches. Overcoming these research caveats will augment the assortment of PAI analysis through eDNA that could be vital for ecosystem health and integrity. This review forms a critical guide and offers prominent insights for ecologists, environmental managers and researchers to assess and evaluate plant-animal interaction through environmental DNA.

Genome and transcriptome analyses reveal genes involved in the formation of fine ridges on petal epidermal cells in Hibiscus trionum

Hibiscus trionum, commonly known as the 'Flower of an Hour', is an easily cultivated plant in the Malvaceae family that is widespread in tropical and temperate regions, including drylands. The purple base part of its petal exhibits structural colour due to the fine ridges on the epidermal cell surface, and the molecular mechanism of ridge formation has been actively investigated. We performed genome sequencing of H. trionum using a long-read sequencing technology with transcriptome and pathway analyses to identify candidate genes for fine structure formation. The ortholog of AtSHINE1, which is involved in the biosynthesis of cuticular wax in Arabidopsis thaliana, was significantly overexpressed in the iridescent tissue. In addition, orthologs of AtCUS2 and AtCYP77A, which contribute to cutin synthesis, were also overexpressed. Our results provide important insights into the formation of fine ridges on epidermal cells in plants using H. trionum as a model.

The Coral Triangle and Strait of Malacca are two distinct hotspots of mangrove biodiversity

Knowledge of the biogeography of marine taxa has lagged significantly behind terrestrial ecosystems. A hotspot of marine biodiversity associated with coral reefs is known in the Coral Triangle of the Indo-West Pacific, but until now there was little data with which to evaluate broad patterns of species richness in the coastal fauna of ecosystems other than coral reefs. This data is critically needed for fauna with low functional redundancy like that of mangroves, that are vulnerable to habitat loss and rising sea levels. Here we show that the diversity of mangrove fauna is characterized by two distinct hotspots in the Indo-West Pacific, associated with two habitat types: fringe mangroves in the Coral Triangle, and riverine mangroves in the Strait of Malacca, between the west coast of Peninsular Malaysia and Sumatra. This finding, based on a family of slugs of which the systematics has been completely revised, illustrates an unexpected biogeographic pattern that emerged only after this taxon was studied intensively. Most organisms that live in the mangrove forests of Southeast Asia remain poorly known both taxonomically and ecologically, and the hotspot of diversity of onchidiid slugs in the riverine mangroves of the Strait of Malacca indicates that further biodiversity studies are needed to support effective conservation of mangrove biodiversity.

Genetic mapping of craniofacial traits in the Mexican tetra reveals loci associated with bite differences between cave and surface fish

BACKGROUND

The Mexican tetra, Astyanax mexicanus, includes interfertile surface-dwelling and cave-dwelling morphs, enabling powerful studies aimed at uncovering genes involved in the evolution of cave-associated traits. Compared to surface fish, cavefish harbor several extreme traits within their skull, such as a protruding lower jaw, a wider gape, and an increase in tooth number. These features are highly variable between individual cavefish and even across different cavefish populations.

RESULTS

To investigate these traits, we created a novel feeding behavior assay wherein bite impressions could be obtained. We determined that fish with an underbite leave larger bite impressions with an increase in the number of tooth marks. Capitalizing on the ability to produce hybrids from surface and cavefish crosses, we investigated genes underlying these segregating orofacial traits by performing Quantitative Trait Loci (QTL) analysis with F2 hybrids. We discovered significant QTL for bite (underbite vs. overbite) that mapped to a single region of the Astyanax genome. Within this genomic region, multiple genes exhibit coding region mutations, some with known roles in bone development. Further, we determined that there is evidence that this genomic region is under natural selection.

CONCLUSIONS

This work highlights cavefish as a valuable genetic model for orofacial patterning and will provide insight into the genetic regulators of jaw and tooth development.

Reappraising the evolutionary history of the largest known gecko, the presumably extinct Hoplodactylus delcourti, via high-throughput sequencing of archival DNA

Hoplodactylus delcourti is a presumably extinct species of diplodactylid gecko known only from a single specimen of unknown provenance. It is by far the largest known gekkotan, approximately 50% longer than the next largest-known species. It has been considered a member of the New Zealand endemic genus Hoplodactylus based on external morphological features including shared toe pad structure. We obtained DNA from a bone sample of the only known specimen to generate high-throughput sequence data suitable for phylogenetic analysis of its evolutionary history. Complementary sequence data were obtained from a broad sample of diplodactylid geckos. Our results indicate that the species is not most closely related to extant Hoplodactylus or any other New Zealand gecko. Instead, it is a member of a clade whose living species are endemic to New Caledonia. Phylogenetic comparative analyses indicate that the New Caledonian diplodactylid clade has evolved significantly more disparate body sizes than either the Australian or New Zealand clades. Toe pad structure has changed repeatedly across diplodactylids, including multiple times in the New Caledonia clade, partially explaining the convergence in form between H. delcourti and New Zealand Hoplodactylus. Based on the phylogenetic results, we place H. delcourti in a new genus.

Thyroid hormone membrane receptor binding and transcriptional regulation in the sea urchin Strongylocentrotus purpuratus

Thyroid hormones (THs) are small amino acid derived signaling molecules with broad physiological and developmental functions in animals. Specifically, their function in metamorphic development, ion regulation, angiogenesis and many others have been studied in detail in mammals and some other vertebrates. Despite extensive reports showing pharmacological responses of invertebrate species to THs, little is known about TH signaling mechanisms outside of vertebrates. Previous work in sea urchins suggests that non-genomic mechanisms are activated by TH ligands. Here we show that several THs bind to sea urchin (Strongylocentrotus purpuratus) cell membrane extracts and are displaced by ligands of RGD-binding integrins. A transcriptional analysis across sea urchin developmental stages shows activation of genomic and non-genomic pathways in response to TH exposure, suggesting that both pathways are activated by THs in sea urchin embryos and larvae. We also provide evidence associating TH regulation of gene expression with TH response elements in the genome. In ontogeny, we found more differentially expressed genes in older larvae compared to gastrula stages. In contrast to gastrula stages, the acceleration of skeletogenesis by thyroxine in older larvae is not fully inhibited by competitive ligands or inhibitors of the integrin membrane receptor pathway, suggesting that THs likely activate multiple pathways. Our data confirms a signaling function of THs in sea urchin development and suggests that both genomic and non-genomic mechanisms play a role, with genomic signaling being more prominent during later stages of larval development.

Shark mandible evolution reveals patterns of trophic and habitat-mediated diversification

Environmental controls of species diversity represent a central research focus in evolutionary biology. In the marine realm, sharks are widely distributed, occupying mainly higher trophic levels and varied dietary preferences, mirrored by several morphological traits and behaviours. Recent comparative phylogenetic studies revealed that sharks present a fairly uneven diversification across habitats, from reefs to deep-water. We show preliminary evidence that morphological diversification (disparity) in the feeding system (mandibles) follows these patterns, and we tested hypotheses linking these patterns to morphological specialisation. We conducted a 3D geometric morphometric analysis and phylogenetic comparative methods on 145 specimens representing 90 extant shark species using computed tomography models. We explored how rates of morphological evolution in the jaw correlate with habitat, size, diet, trophic level, and taxonomic order. Our findings show a relationship between disparity and environment, with higher rates of morphological evolution in reef and deep-water habitats. Deep-water species display highly divergent morphologies compared to other sharks. Strikingly, evolutionary rates of jaw disparity are associated with diversification in deep water, but not in reefs. The environmental heterogeneity of the offshore water column exposes the importance of this parameter as a driver of diversification at least in the early part of clade history.

Responses of Aroma Related Metabolic Attributes of Opisthopappus longilobus Flowers to Environmental Changes

Opisthopappus longilobus (Opisthopappus) and its descendant species, Opisthopappus taihangensis, commonly thrive on the Taihang Mountains of China. Being typical cliff plants, both O. longilobus and O. taihangensis release unique aromatics. To determine the potential differentiation and environmental response patterns, comparative metabolic analysis was performed on O. longilobus wild flower (CLW), O. longilobus transplant flower (CLT), and O. taihangensis wild flower (TH) groups. Significant differences in the metabolic profiles were found, not within O. longilobus, but between O. longilobus and O. taihangensis flowers. Within these metabolites, twenty-eight substances related to the scents were obtained (one alkene, two aldehydes, three esters, eight phenols, three acids, three ketones, three alcohols, and five flavonoids), of which eugenol and chlorogenic were the primary aromatic molecules and enriched in the phenylpropane pathway. Network analysis showed that close relationships occurred among identified aromatic substances. The variation coefficient (CV) of aromatic metabolites in O. longilobus was lower than O. taihangensis. The aromatic related compounds were significantly correlated with the lowest temperatures in October and in December of the sampled sites. The results indicated that phenylpropane, particularly eugenol and chlorogenic, played important roles in the responses of O. longilobus species to environmental changes.

Digital holographic approaches to the detection and characterization of microplastics in water environments

Microplastic (MP) pollution is seriously threatening the environmental health of the world, which has accelerated the development of new identification and characterization methods. Digital holography (DH) is one of the emerging tools to detect MPs in a high-throughput flow. Here, we review advances in MP screening by DH. We examine the problem from both the hardware and software viewpoints. Automatic analysis based on smart DH processing is reported by highlighting the role played by artificial intelligence for classification and regression tasks. In this framework, the continuous development and availability in recent years of field-portable holographic flow cytometers for water monitoring also is discussed.

The complete mitochondrial genome of Pethia padamya (Actinopteri, Cyprinidae)

Pethia padamya (Kullander and Britz, 2008) is a freshwater fish distributed in the Mekong River basin of Thailand. It has beautiful colors and can be used as an ornamental fish. The complete mitochondrial genome of P. padamya was determined using next-generation sequencing technology and its characteristics were analyzed. The mitochondrial genome is a closed circular molecule comprising 16,792 bp, including 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a major non-coding region. The overall base composition of the mitochondrial genome is 32.47% A, 25.39% C, 26.08% T, and 16.06% G, with a high A + T bias of 58.55%. Phylogenetic analysis revealed P. padamya as a sister group of Pethia conchonius+(Pethia ticto+Pethia cumingii) and Pethia gelius with maximal support, providing support for the monophyly of the genus Pethia based on concatenated nucleotide sequences. The results of this study proved the monophyly of the genus Pethia. These data for the first time provide information on the complete mitochondrial genome of P. padamya and can contribute to further studies on the biodiversity and management of P. padamya.

Seasonal dynamics of a complex cheilostome bryozoan symbiosis: vertical transfer challenged

Symbiotic associations are dynamic systems influenced by both intrinsic and extrinsic factors. Here we describe for the first time the developmental and seasonal changes of the funicular bodies in the bryozoan Dendrobeania fruticosa, which are unique temporary organs of cheilostome bryozoans containing prokaryotic symbionts. Histological and ultrastructural studies showed that these organs undergo strong seasonal modification in the White Sea during the ice-free period. Initially (in June) they play a trophic function and support the development of a large population of bacteria. From June to September, both funicular bodies and bacteria show signs of degradation accompanied by development of presumed virus-like particles (VLPs); these self-organize to hollow spheres inside bacteria and are also detected outside of them. Although the destruction of bacteria coincides with the development of VLPs and spheres, the general picture differs considerably from the known instances of bacteriophagy in bryozoans. We broadly discuss potential routes of bacterial infection in Bryozoa and question the hypothesis of vertical transfer, which, although widely accepted in the literature, is contradicted by molecular, morphological and ecological evidence.

The first complete chloroplast genome in Engelhardia sensu stricto, Engelhardia hainanensis Chen: genome characterization and its phylogenetic relationships within the family Juglandaceae

Trees of Engelhardia are important components of subtropical and tropical forests in South-eastern Asia with great ecological and economic values. However, phylogenetic relationships within Engelhardioideae (Juglandaceae) remains obscure. In this study, we report the first complete chloroplast genome sequences of Engelhardia sensu stricto, Engelhardia hainanensis Chen, a rare species endemic in southern China. Its complete chloroplast genome is 161,574 bp in length, with a typical quadripartite structure that includes a large single-copy region of 91,158 bp, a small single-copy region of 18,790 bp, and its GC content is 35.8%. A total of 128 genes were identified, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Furthermore, a phylogenetic tree of Juglandaceae was constructed based the complete chloroplast genome sequence, which strongly support the three-subfamily classification system in Juglandaceae, and E. hainanensis was resolved sister to two Alfaropsis species. This study provides valuable genomic information for the species identification and phylogenetic study of Juglandaceae.

Perioral secretions enable complex social signaling in African mole-rats (genus Fukomys)

Subterranean common mole-rats of the genus Fukomys (family Bathyergidae) live in large, cooperatively-breeding families. Odor cues have been hypothesized to play an important role in mediating social behaviors in the underground ecotope, but only little is known about the role of olfactory signaling in burrowing mammals. Here we characterize the so far neglected perioral glands of Fukomys and other African mole-rats as an important source of olfactory social information. Histology demonstrates these structures to be derived sebaceous glands that are developed regardless of sex and reproductive status. However, gland activity is higher in Fukomys males, leading to sexually dimorphic patterns of stain and clotting of the facial pelage. Behavioral assays revealed that conspecifics prefer male but not female perioral swabs over scent samples from the back fur and that male sebum causes similar attraction as anogenital scent, a known source of social information in Fukomys. Finally, we assessed volatile compounds in the perioral sebum of the giant mole-rat (Fukomys mechowii) via GCxGC-MS-based metabolomic profiling. Volatiles display pronounced sex-specific signatures but also allow to differentiate between intrasexual reproductive status groups. These different lines of evidence suggest that mole-rat perioral glands provide complex odor signals which play a crucial role in social communication.

Comparative analysis of mitochondrial genomes reveals marine adaptation in seagrasses

BACKGROUND

Seagrasses are higher marine flowering plants that evolved from terrestrial plants, but returned to the sea during the early evolution of monocotyledons through several separate lineages. Thus, they become a good model for studying the adaptation of plants to the marine environment. Sequencing of the mitochondrial (mt) genome of seagrasses is essential for understanding their evolutionary characteristics.

RESULTS

In this study, we sequenced the mt genome of two endangered seagrasses (Zostera japonica and Phyllospadix iwatensis). These data and data on previously sequenced mt genomes from monocotyledons provide new evolutionary evidence of genome size reduction, gene loss, and adaptive evolution in seagrasses. The mt genomes of Z. japonica and P. iwatensis are circular. The sizes of the three seagrasses (including Zostera marine) that have been sequenced to date are smaller than that of other monocotyledons. Additionally, we found a large number of repeat sequences in seagrasses. The most abundant long repeat sequences were 31-40 bp repeats. Our study also found that seagrass species lost extensive ribosomal protein genes during evolution. The rps7 gene and the rpl16 gene of P. iwatensis are exceptions to this trend. The phylogenetic analysis based on the mt genome strongly supports the previous results. Furthermore, we identified five positive selection genes (atp8, nad3, nad6, ccmFn, and matR) in seagrasses that may be associated with their adaptation to the marine environment.

CONCLUSIONS

In this study, we sequenced and annotated the mt genomes of Z. japonica and P. iwatensis and compared them with the genome of other monocotyledons. The results of this study will enhance our understanding of seagrass adaptation to the marine environment and can inform further investigations of the seagrass mt genome.

Molecular identification of a new species of Rhigonema (Nematoda: Rhigonematidae) and phylogenetic relationships within the infraorder Rhigonematomorpha

Background

The infraorder Rhigonematomorpha comprises a group of obligate parasitic nematodes of millipedes (Arthropoda: Diplopoda). The current species identification of Rhigonematomorpha nematodes remains mainly based on morphological features, with molecular-based identification still in its infancy. Also, current knowledge of the phylogeny of Rhigonematomorpha is far from comprehensive.

Methods

The morphology of Rhigonematomorpha nematodes belonging to the genus Rhigonema, collected from the millipede Spirobolus bungii Brandt (Diplopoda: Spirobolida) in China, was studied in detail using light and scanning electron microscopy. Five different genetic markers, including the nuclear small ribosomal subunit (18S), internal transcribed spacer (ITS) and large ribosomal subunit (28S) regions and the mitochondrial cox1 and cox2 genes of these Rhigonematomorpha nematodes collected from China and Rhigonema naylae collected from Japan were sequenced and analyzed using Bayesian inference (BI) and Assemble Species by Automatic Partitioning (ASAP) methods. Phylogenetic analyses that included the most comprehensive taxa sampling of Rhigonematomorpha to date were also performed based on the 18S + 28S genes using maximum likelihood (ML) and BI methods.

Results

The specimens of Rhigonema collected from S. bungii in China were identified as a new species, Rhigonema sinense n. sp. Striking variability in tail morphology was observed among individuals of R. sinense n. sp. ASAP analyses based on the 28S, ITS, cox1 and cox2 sequences supported the species partition of R. sinense n. sp. and R. naylae, but showed no evidence that the different morphotypes of R. sinense n. sp. represent distinct genetic lineages. BI analyses also indicated that R. sinense n. sp. represents a separated species from R. naylae based on the cox1 and cox2 genes, but showed that R. naylae nested in samples of R. sinense n. sp. based on the ITS and 28S data. Phylogenetic results showed that the representatives of Rhigonematomorpha formed two large clades. The monophyly of the families Carnoyidae and Ichthyocephalidae and the genus Rhigonema was rejected. The representatives of the family Ransomnematidae clustered together with the family Hethidae with strong support.

Conclusions

A new species of Rhigonematomorpha, R. sinense n. sp. is described based on morphological and molecular evidence. ASAP analyses using 28S, ITS, cox1 and cox2 data indicate the striking variability in tail morphology of R. sinense n. sp. as intraspecific variation, and also suggest that partial 28S, ITS, cox1 and cox2 markers are effective for molecular identification of Rhigonematomorpha nematodes. The phylogenetic results support the traditional classification of Rhigonematomorpha into the two superfamilies Rhigonematoidea and Ransomnematoidea, and indicate that the families Carnoyidae and Ichthyocephalidae and the genus Rhigonema are non-monophyletic. The present phylogeny strongly supports resurrection of the family Brumptaemiliidae, and also indicates that the family Ransomnematidae is sister to the family Hethidae.

Graphical Abstract

Evolution of cross-tolerance in Drosophila melanogaster as a result of increased resistance to cold stress

Cold stress is a critical environmental challenge that affects an organism's fitness-related traits. In Drosophila, increased resistance to specific environmental stress may lead to increased resistance to other kinds of stress. In the present study, we aimed to understand whether increased cold stress resistance in Drosophila melanogaster can facilitate their ability to tolerate other environmental stresses. For the current study, we used successfully selected replicate populations of D. melanogaster against cold shock and their control population. These selected populations have evolved several reproductive traits, including increased egg viability, mating frequency, male mating ability, ability to sire progenies, and faster recovery for mating latency under cold shock conditions. In the present work, we investigated egg viability and mating frequency with and without heat and cold shock conditions in the selected and their control populations. We also examined resistance to cold shock, heat shock, desiccation, starvation, and survival post-challenge with Staphylococcus succinus subsp. succinus PK-1 in the selected and their control populations. After cold-shock treatment, we found a 1.25 times increase in egg viability and a 1.57 times increase in mating frequency in the selected populations compared to control populations. Moreover, more males (0.87 times) and females (1.66 times) of the selected populations survived under cold shock conditions relative to their controls. After being subjected to heat shock, the selected population's egg viability and mating frequency increased by 0.30 times and 0.57 times, respectively, compared to control populations. Additionally, more selected males (0.31 times) and females (0.98 times) survived under heat shock conditions compared to the control populations. Desiccation resistance slightly increased in the females of the selected populations relative to their control, but we observed no change in the case of males. Starvation resistance decreased in males and females of the selected populations compared to their controls. Our findings suggest that the increased resistance to cold shock correlates with increased tolerance to heat stress, but this evolved resistance comes at a cost, with decreased tolerance to starvation.

Secondary contact rather than coexistence-Erebia butterflies in the Alps

Secondary contact zones are ideal systems to study the processes that govern the evolution of reproductive barriers, especially at advanced stages of the speciation process. An increase in reproductive isolation resulting from selection against maladaptive hybrids is thought to contribute to reproductive barrier buildup in secondary contact zones. Although such processes have been invoked for many systems, it remains unclear to which extent they influence contact zone dynamics in nature. Here, we study a very narrow contact zone between the butterfly species Erebia cassioides and Erebia tyndarus in the Swiss Alps. We quantified phenotypic traits related to wing shape and reproduction as well as ecology to compare the degree of intra- and interspecific differentiation. Even though only very few first-generation hybrids occur, we find no strong indications for current reinforcing selection, suggesting that if reinforcement occurred in our system, it likely operated in the past. Additionally, we show that both species differ less in their ecological niche at the contact zone than elsewhere, which could explain why coexistence between these butterflies may currently not be possible.

Chill coma recovery of Ceratitis capitata adults across the Northern Hemisphere

The Mediterranean fruit fly, Ceratitis capitata (Diptera: Tephritidae), is an invasive pest, that is currently expanding its geographic distribution from the Mediterranean coasts to more temperate areas of Europe. Given that low temperature is a primary determinant of insect species' range boundaries especially in the Northern Hemisphere with pronounced seasonality, we used chill coma recovery time for assessing latitudinal clines in basal chill tolerance of C. capitata adults. We selected six populations obtained from areas with broad climatic variability based on the main bioclimatic variables of temperature and precipitation, spanning a latitudinal range of about 19° from Middle East to Central Europe. Adults were exposed to 0 °C for 4 h, and time to regain the typical standing position of a fly at 25 °C were recorded. The post-stress survival after a period of 8 days was also recorded. Results revealed that adults from Israel and Austria were less chill tolerant than those from Greece, resulting in curvilinear trends with latitude. Analysis of macroclimatic conditions revealed combined effects of latitude (as a proxy of photoperiod) and macroclimatic conditions on chill coma recovery time. Nonetheless, there was not a deleterious effect on post-recovery survival, except for flies obtained from the northern most point (Vienna, Austria). Overall, it seems that evolutionary patterns of basal chill coma recovery time of C. capitata adults are driven mainly by local climatic variability.

Forest-Based Networks

In evolutionary studies, it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has occurred in the past, a tree may not provide a complete picture of their history. In such cases, tree-based phylogenetic networks can provide a useful, more refined representation of the species’ evolution. Such a network is essentially a phylogenetic tree with some arcs added between the tree’s edges so as to represent reticulate events such as gene transfer, hybridization and recombination. Even so, this model does not permit the direct representation of evolutionary scenarios where reticulate events have taken place between different subfamilies or lineages of species. To represent such scenarios, in this paper we introduce the notion of a forest-based network, that is, a collection of leaf-disjoint phylogenetic trees on a set of species with arcs added between the edges of distinct trees within the collection. Forest-based networks include the recently introduced class of overlaid species forests which can be used to model introgression. As we shall see, even though the definition of forest-based networks is closely related to that of tree-based networks, they lead to new mathematical theory which complements that of tree-based networks. As well as studying the relationship of forest-based networks with other classes of phylogenetic networks, such as tree-child networks and universal tree-based networks, we present some characterizations of some special classes of forest-based networks. We expect that our results will be useful for developing new models and algorithms to understand reticulate evolution, such as introgression and gene transfer between species.

One's trash is someone else's treasure: sequence read archives from Lepidoptera genomes provide material for genome reconstruction of their endosymbionts

BACKGROUND

Maternally inherited bacterial symbionts are extremely widespread in insects. They owe their success to their ability to promote their own transmission through various manipulations of their hosts' life-histories. Many symbionts however very often go undetected. Consequently, we have only a restricted idea of the true symbiont diversity in insects, which may hinder our understanding of even bigger questions in the field such as the evolution or establishment of symbiosis.

RESULTS

In this study, we screened publicly available Lepidoptera genomic material for two of the most common insect endosymbionts, namely Wolbachia and Spiroplasma, in 1904 entries, encompassing 106 distinct species. We compared the performance of two screening software, Kraken2 and MetaPhlAn2, to identify the bacterial infections and using a baiting approach we reconstruct endosymbiont genome assemblies. Of the 106 species screened, 20 (19%) and nine (8.5%) were found to be infected with either Wolbachia or Spiroplasma, respectively. Construction of partial symbiotic genomes and phylogenetic analyses suggested the Wolbachia strains from the supergroup B were the most prevalent type of symbionts, while Spiroplasma infections were scarce in the Lepidoptera species screened here.

CONCLUSIONS

Our results indicate that many of the host-symbiont associations remain largely unexplored, with the majority of associations we identify never being recorded before. This highlights the usefulness of public databases to explore the hidden diversity of symbiotic entities, allowing the development of hypotheses regarding host-symbiont associations. The ever-expanding genomic databases provide a diverse databank from which one can characterize and explore the true diversity of symbiotic entities.

Synchrotron µ-XRF mapping analysis of trace elements in in-situ cultured Japanese red coral, Corallium japonicum

Precious corals belong to the family Coralliidae (Cnidaria, Octocorallia), and their axis, which consists of high magnesian calcium carbonate, has long been used in jewelry. With its low growth rate and long lifespan, precious coral is a representative taxon of the vulnerable marine ecosystem. Due to years of overfishing, coral fishery has become a controversial issue. To estimate the growth rate and clarify the uptake process of trace elements in relation to the growth of the carbonate axis, Japanese red coral (Corallium japonicum) was cultured at a depth of 135 m off Takeshima Island, Kagoshima, Japan for 98 months and analyzed by microscopic X-ray fluorescence/soft X-ray photoabsorption (µ-XRF/XAS) speciation mapping. The growth rate was estimated to be 0.37 mm/year in diameter, and 10-11 growth rings were observed in a cross section of the axis. This estimated growth-rate value is the first ever to be obtained from the in-situ culture of Japanese precious coral. The fluctuation in water temperature near the in-situ-culture site was recorded for part of the culture period and then compared with the changes in the growth ring and the distribution of trace elements in a cross section of the coral axis during the same period. When the water temperature was increasing, the growth ring was light in color, sulfur and phosphorus concentrations were low, and magnesium was high. Conversely, a dark band in the growth ring, high sulfur and phosphorus, and low magnesium concentrations were observed when the water temperature was decreasing. In a cross section of the coral axis, the distribution of sulfur and magnesium from the center to the surface corresponded, respectively, to dark and light bands in the annual growth ring. Sulfur concentration was high in the dark band and low in the light band, while magnesium was negatively correlated with sulfur.

Embedding gene trees into phylogenetic networks by conflict resolution algorithms

BACKGROUND

Phylogenetic networks are mathematical models of evolutionary processes involving reticulate events such as hybridization, recombination, or horizontal gene transfer. One of the crucial notions in phylogenetic network modelling is displayed tree, which is obtained from a network by removing a set of reticulation edges. Displayed trees may represent an evolutionary history of a gene family if the evolution is shaped by reticulation events.

RESULTS

We address the problem of inferring an optimal tree displayed by a network, given a gene tree G and a tree-child network N, under the deep coalescence and duplication costs. We propose an O(mn)-time dynamic programming algorithm (DP) to compute a lower bound of the optimal displayed tree cost, where m and n are the sizes of G and N, respectively. In addition, our algorithm can verify whether the solution is exact. Moreover, it provides a set of reticulation edges corresponding to the obtained cost. If the cost is exact, the set induces an optimal displayed tree. Otherwise, the set contains pairs of conflicting edges, i.e., edges sharing a reticulation node. Next, we show a conflict resolution algorithm that requires [Formula: see text] invocations of DP in the worst case, where r is the number of reticulations. We propose a similar [Formula: see text]-time algorithm for level-k tree-child networks and a branch and bound solution to compute lower and upper bounds of optimal costs. We also extend the algorithms to a broader class of phylogenetic networks. Based on simulated data, the average runtime is [Formula: see text] under the deep-coalescence cost and [Formula: see text] under the duplication cost.

CONCLUSIONS

Despite exponential complexity in the worst case, our algorithms perform significantly well on empirical and simulated datasets, due to the strategy of resolving internal dissimilarities between gene trees and networks. Therefore, the algorithms are efficient alternatives to enumeration strategies commonly proposed in the literature and enable analyses of complex networks with dozens of reticulations.

Reply to: "Research on agroforestry systems and biodiversity conservation: what can we conclude so far and what should we improve?" by Boinot et al. 2022

In our article ‘European agroforestry has no unequivocal effect on biodiversity: a time-cumulative meta-analysis’ (BMC Ecology and Evolution, 2021) we synthesize the effect of agroforestry on biodiversity. Boinot et al. (BMC Ecology and Evolution, 2022) criticise our approach arguing that our definitions of agroforestry and biodiversity are too narrow; that we use inappropriate control sites for primary studies lacking distance to the treatment sites; that there are too few studies for a meta-analysis in silvoarable systems; and that local practice should be emphasized. We agree on the importance of local practices and that more studies would improve the robustness of our meta-analytical results. However, our conclusions are robust to removing studies criticised for inappropriate controls. We also recognize the problem of different definitions of agroforestry and using species richness as sole proxy for biodiversity. We appreciate being given the opportunity to clarify our results and to trigger future discussions about definitions and the interpretation of results from meta-analysis.

Photoreceptor distributions, visual pigments and the opsin repertoire of Atlantic halibut (Hippoglossus hippoglossus)

Fishes often have cone photoreceptors organized in lattice-like mosaic formations. In flatfishes, these lattices undergo dramatic changes during metamorphosis whereby a honeycomb mosaic of single cones in the larva is replaced by a square mosaic of single and double cones in the adult. The spatio-temporal dynamics of this transition are not well understood. Here, we describe the photoreceptors and mosaic formations that occur during the larva to juvenile transition of Atlantic halibut from the beginning of eye migration to its completion. To gauge the possibility of colour vision, visual pigments in juveniles were measured by microspectrophotometry and the opsin repertoire explored using bioinformatics. At the start of eye migration, the larva had a heterogeneous retina with honeycomb mosaic in the dorsonasal and ventrotemporal quadrants and a square mosaic in the ventronasal and dorsotemporal quadrants. By the end of metamorphosis, the square mosaic was present throughout the retina except in a centrodorsotemporal area where single, double and triple cones occurred randomly. Six cone visual pigments were found with maximum absorbance (λ_max, in nm) in the short [S(431) and S(457)], middle [M(500), M(514) and M(527)], and long [L(550)] wavelengths, and a rod visual pigment with λ_max at 491 nm. These pigments only partially matched the opsin repertoire detected by query of the Atlantic halibut genome. We conclude that the Atlantic halibut undergoes a complex re-organization of photoreceptors at metamorphosis resulting in a multi-mosaic retina adapted for a demersal life style.

What you sample is what you get: ecomorphological variation in Trithemis (Odonata, Libellulidae) dragonfly wings reconsidered

Background

The phylogenetic ecology of the Afro-Asian dragonfly genus Trithemis has been investigated previously by Damm et al. (in Mol Phylogenet Evol 54:870–882, 2010) and wing ecomorphology by Outomuro et al. (in J Evol Biol 26:1866–1874, 2013). However, the latter investigation employed a somewhat coarse sampling of forewing and hindwing outlines and reported results that were at odds in some ways with expectations given the mapping of landscape and water-body preference over the Trithemis cladogram produced by Damm et al. (in Mol Phylogenet Evol 54:870–882, 2010). To further explore the link between species-specific wing shape variation and habitat we studied a new sample of 27 Trithemis species employing a more robust statistical test for phylogenetic covariation, more comprehensive representations of Trithemis wing morphology and a wider range of morphometric data-analysis procedures.

Results

Contrary to the Outomuro et al. (in J Evol Biol 26:1866–1874, 2013) report, our results indicate that no statistically significant pattern of phylogenetic covariation exists in our Trithemis forewing and hindwing data and that both male and female wing datasets exhibit substantial shape differences between species that inhabit open and forested landscapes and species that hunt over temporary/standing or running water bodies. Among the morphometric analyses performed, landmark data and geometric morphometric data-analysis methods yielded the worst performance in identifying ecomorphometric shape distinctions between Trithemis habitat guilds. Direct analysis of wing images using an embedded convolution (deep learning) neural network delivered the best performance. Bootstrap and jackknife tests of group separations and discriminant-function stability confirm that our results are not artifacts of overtrained discriminant systems or the “curse of dimensionality” despite the modest size of our sample.

Conclusion

Our results suggest that Trithemis wing morphology reflects the environment’s “push” to a much greater extent than phylogeny’s “pull”. In addition, they indicate that close attention should be paid to the manner in which morphologies are sampled for morphometric analysis and, if no prior information is available to guide sampling strategy, the sample that most comprehensively represents the morphologies of interest should be obtained. In many cases this will be digital images (2D) or scans (3D) of the entire morphology or morphological feature rather than sparse sets of landmark/semilandmark point locations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-01978-y.

Large-scale analysis of MicroRNA expression in motor neuron-like cells derived from human umbilical cord blood mesenchymal stem cells

Motor neuron diseases such as spinal cord injuries and amyotrophic lateral sclerosis are known as the most common disorders worldwide. Using stem cells (e.g., human umbilical cord blood mesenchymal stem cells) is currently a potent medical approach for modulating the impact of neural damages and regeneration of spinal cord injuries. MicroRNAs (miRNA) are taken into account as principal regulators during differentiation. The miRNAs play a significant role in stem cell self-renewal and fate determination. There are few studies on how miRNAs regulate neural differentiation in stem cells. The purpose of this study is to explore miRNA profiles of CB-MSCs during differentiation into motor neuron-like cells. Human CB-MSCs were isolated and characterized using flow cytometry. Cell differentiation has been induced by combining retinoic acid (RA) and sonic hedgehog (Shh) in a two-step protocol for 14 days. Then, cell differentiation was confirmed by immunocytochemistry and flow cytometry. The miRNA was analyzed using Illumina/Solexa sequencing platform. In this regard, three libraries were prepared to investigate the effect of these two biological morphogens on the miRNA profile of the differentiating cells. These libraries were Control (non-treated CB-MSCs), Test 1 (RA + /Shh +), and Test 2 (RA-/Shh-). Quantitative RT-PCR was employed to verify miRNA expression. CB-MSCs were spindle-shaped in morphology, and they did not express hematopoietic markers. After differentiation, the cells expressed motor neuron markers (i.e., Islet-1, SMI-32, and ChAT) at the protein level after 14 days. The analysis of miRNA sequencing demonstrated a significant up-regulation of miR-9-5p and miR-324-5p in Test 1 (RA + /Shh +). Also, there is a considerable down-regulation of mir-137 and let-7b in Test 2 (RA-/Shh-). These results have been obtained by comparing them with the Control library. Indeed, they were responsible for neuron and motor neuron differentiation and suppression of proliferation in neural progenitor cells. Furthermore, significant up-regulation was detected in some novel microRNAs involved in cholinergic, JAK-STAT, and Hedgehog and MAPK signaling pathways. CB-MSCs are potent to express motor neuron markers. This procedure has been performed by developing a two-week protocol and employing Shh and RA. The miRNA profile analysis showed a significant up-regulation in the expression of some miRs involved in neuron differentiation and motor neuron maturation. MiR-9-5p and miR-324-5p were up-regulated at the early stage of differentiation. Also, miR-137 and miR-let-7b were downregulated in the absence of RA and Shh. Furthermore, several novel miRNAs involved in cholinergic, Hedgehog, MAPK, and JAK-STAT signaling pathways have been detected. However, further studies are still necessary to validate their functions during motor neuron generation and maturation.

A functional central limit theorem on non-stationary random fields with nested spatial structure

In this paper, we establish a functional central limit theorem on high dimensional random fields in the context of model-based survey analysis. For strongly-mixing non-stationary random fields, we provide an upper bound for the fourth moment of the finite population total. This inequality is the generalization of a key tool for proving functional central limit theorems in Rio (Asymptotic theory of weakly dependent random processes, Springer, Berlin, 2017). Under the nested sampling strategy, we introduce assumptions on strongly-mixing coefficients and quantile functions to show that a functional stochastic process asymptotically approaches to a Gaussian process.

Adaptation and ecological speciation in seasonally varying environments at high latitudes: Drosophila virilis group

Living in high latitudes and altitudes sets specific requirements on species’ ability to forecast seasonal changes and to respond to them in an appropriate way. Adaptation into diverse environmental conditions can also lead to ecological speciation through habitat isolation or by inducing changes in traits that influence assortative mating. In this review, we explain how the unique time-measuring systems of Drosophila virilis group species have enabled the species to occupy high latitudes and how the traits involved in species reproduction and survival exhibit strong linkage with latitudinally varying photoperiodic and climatic conditions. We also describe variation in reproductive barriers between the populations of two species with overlapping distributions and show how local adaptation and the reinforcement of prezygotic barriers have created partial reproductive isolation between conspecific populations. Finally, we consider the role of species-specific chromosomal inversions and the X chromosome in the development of reproductive barriers between diverging lineages.

High frequency of social polygyny reveals little costs for females in a songbird

Mating system theory predicts that social polygyny—when one male forms pair bonds with two females—may evolve by female choice in species with biparental care. Females will accept a polygynous male if the benefit of mating with a male providing high-quality genes or rearing resources outweighs the cost of sharing mate assistance in parental care. Based on this rationale, we hypothesise that the population frequency of social polygyny (FSP) varies due to changes in mate sharing costs caused by changing environmental conditions. We predicted that: (1) polygamous females (i.e. mated with a polygynous male) pay a survival cost compared to monogamous females; (2) FSP would be higher in years with better rearing conditions and (3) the difference in survival rates between monogamous and polygamous females would be small following years with higher FSP. We tested these predictions using regression and multistate analyses of capture-recapture data of pied flycatchers, Ficedula hypoleuca, in central Spain collected over 26 years (1990–2016). Monogamous females had a higher mean survival rate than polygamous females (prediction 1), but there was no difference in survival between polygynous and monogamous males. In addition, FSP was positively associated with annual reproductive success (a proxy of the quality of rearing conditions—prediction 2). Finally, following years with high FSP, the survival of polygamous females was similar to that of monogamous females (prediction 3), while the chance of breeding in a polygamous state for 2 years in a row increased for both males and females. Our findings suggest that fluctuating environmental conditions may be a necessary but neglected aspect of understanding social polygyny mechanisms.

Shedding light on toxicity of SARS-CoV-2 peptides in aquatic biota: A study involving neotropical mosquito larvae (Diptera: Culicidae)

Knowledge about how the COVID-19 pandemic can affect aquatic wildlife is still extremely limited, and no effect of SARS-CoV-2 or its structural constituents on invertebrate models has been reported so far. Thus, we investigated the presence of the 2019-new coronavirus in different urban wastewater samples and, later, evaluated the behavioral and biochemical effects of the exposure of Culex quinquefasciatus larvae to two SARS-CoV-2 spike protein peptides (PSPD-2002 and PSPD-2003) synthesized in our laboratory. Initially, our results show the contamination of wastewater by the new coronavirus, via RT-qPCR on the viral N1 gene. On the other hand, our study shows that short-term exposure (48 h) to a low concentration (40 μg/L) of the synthesized peptides induced changes in the locomotor and the olfactory-driven behavior of the C. quinquefascitus larvae, which were associated with increased production of ROS and AChE activity (cholinesterase effect). To our knowledge, this is the first study that reports the indirect effects of the COVID-19 pandemic on the larval phase of a freshwater invertebrate species. The results raise concerns at the ecological level where the observed biological effects may lead to drastic consequences.

Molecular mechanisms underlying responses of the Antarctic coral Malacobelemnon daytoni to ocean acidification

Benthic organisms of the Southern Ocean are particularly vulnerable to ocean acidification (OA), as they inhabit cold waters where calcite-aragonite saturation states are naturally low. OA most strongly affects animals with calcium carbonate skeletons or shells, such as corals and mollusks. We exposed the abundant cold-water coral Malacobelemnon daytoni from an Antarctic fjord to low pH seawater (LpH) (7.68 ± 0.17) to test its physiological responses to OA, at the level of gene expression (RT-PCR) and enzyme activity. Corals were exposed in short- (3 days) and long-term (54 days) experiments to two pCO₂ conditions (ambient and elevated pCO₂ equaling RCP 8.5, IPCC 2019, approximately 372.53 and 956.78 μatm, respectively). Of the eleven genes studied through RT-PCR, six were significantly upregulated compared with control in the short-term in the LpH condition, including the antioxidant enzyme superoxide dismutase (SOD), Heat Shock Protein 70 (HSP70), Toll-like receptor (TLR), galaxin and ferritin. After long-term exposure to low pH conditions, RT-PCR analysis showed seven genes were upregulated. These include the mannose-binding C-Lectin and HSP90. Also, the expression of TLR and galaxin, among others, continued to be upregulated after long-term exposure to LpH. Expression of carbonic anhydrase (CA), a key enzyme involved in calcification, was also significantly upregulated after long-term exposure. Our results indicated that, after two months, M. daytoni is not acclimatized to this experimental LpH condition. Gene expression profiles revealed molecular impacts that were not evident at the enzyme activity level. Consequently, understanding the molecular mechanisms behind the physiological processes in the response of a coral to LpH is critical to understanding the ability of polar species to cope with future environmental changes. Approaches integrating molecular tools into Antarctic ecological and/or conservation research make an essential contribution given the current ongoing OA processes.

Evolution of the Avian Eggshell Biomineralization Protein Toolkit - New Insights From Multi-Omics

The avian eggshell is a remarkable biomineral, which is essential for avian reproduction; its properties permit embryonic development in the desiccating terrestrial environment, and moreover, are critically important to preserve unfertilized egg quality for human consumption. This calcium carbonate (CaCO₃) bioceramic is made of 95% calcite and 3.5% organic matrix; it protects the egg contents against microbial penetration and mechanical damage, allows gaseous exchange, and provides calcium for development of the embryonic skeleton. In vertebrates, eggshell occurs in the Sauropsida and in a lesser extent in Mammalia taxa; avian eggshell calcification is one of the fastest known CaCO₃ biomineralization processes, and results in a material with excellent mechanical properties. Thus, its study has triggered a strong interest from the researcher community. The investigation of eggshell biomineralization in birds over the past decades has led to detailed characterization of its protein and mineral constituents. Recently, our understanding of this process has been significantly improved using high-throughput technologies (i.e., proteomics, transcriptomics, genomics, and bioinformatics). Presently, more or less complete eggshell proteomes are available for nine birds, and therefore, key proteins that comprise the eggshell biomineralization toolkit are beginning to be identified. In this article, we review current knowledge on organic matrix components from calcified eggshell. We use these data to analyze the evolution of selected matrix proteins and underline their role in the biological toolkit required for eggshell calcification in avian species. Amongst the panel of eggshell-associated proteins, key functional domains are present such as calcium-binding, vesicle-binding and protein-binding. These technical advances, combined with progress in mineral ultrastructure analyses, have opened the way for new hypotheses of mineral nucleation and crystal growth in formation of the avian eggshell, including transfer of amorphous CaCO₃ in vesicles from uterine cells to the eggshell mineralization site. The enrichment of multi-omics datasets for bird species is critical to understand the evolutionary context for development of CaCO₃ biomineralization in metazoans, leading to the acquisition of the robust eggshell in birds (and formerly dinosaurs).