Atlas of clinically distinct cell states and ecosystems across human solid tumors.

Determining how cells vary with their local signaling environment and organize into distinct cellular communities is critical for understanding processes as diverse as development, aging, and cancer. Here we introduce EcoTyper, a machine learning framework for large-scale identification and validation of cell states and multicellular communities from bulk, single-cell, and spatially resolved gene expression data. When applied to 12 major cell lineages across 16 types of human carcinoma, EcoTyper identified 69 transcriptionally defined cell states. Most states were specific to neoplastic tissue, ubiquitous across tumor types, and significantly prognostic. By analyzing cell-state co-occurrence patterns, we discovered ten clinically distinct multicellular communities with unexpectedly strong conservation, including three with myeloid and stromal elements linked to adverse survival, one enriched in normal tissue, and two associated with early cancer development. This study elucidates fundamental units of cellular organization in human carcinoma and provides a framework for large-scale profiling of cellular ecosystems in any tissue.

Diverse pathways to speciation revealed by marine snails.

Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems.

Divergence and gene flow history at two large chromosomal inversions underlying ecotype differentiation in the long-snouted seahorse.

Chromosomal inversions can play an important role in divergence and reproductive isolation by building and maintaining distinct allelic combinations between evolutionary lineages. Alternatively, they can take the form of balanced polymorphisms that segregate within populations until one arrangement becomes fixed. Many questions remain about how inversion polymorphisms arise, how they are maintained over the long term, and ultimately, whether and how they contribute to speciation. The long-snouted seahorse (Hippocampus guttulatus) is genetically subdivided into geographic lineages and marine-lagoon ecotypes, with shared structural variation underlying lineage and ecotype divergence. Here, we aim to characterize structural variants and to reconstruct their history and suspected role in ecotype formation. We generated a near chromosome-level genome assembly and described genome-wide patterns of diversity and divergence through the analysis of 112 whole-genome sequences from Atlantic, Mediterranean, and Black Sea populations. By also analysing linked-read sequencing data, we found evidence for two chromosomal inversions that were several megabases in length and showed contrasting allele frequency patterns between lineages and ecotypes across the species range. We reveal that these inversions represent ancient intraspecific polymorphisms, one likely being maintained by divergent selection and the other by pseudo-overdominance. A possible selective coupling between the two inversions was further supported by the absence of specific haplotype combinations and a putative functional interaction between the two inversions in reproduction. Lastly, we detected gene flux eroding divergence between inverted alleles at varying levels for the two inversions, with a likely impact on their dynamics and contribution to divergence and speciation.

Metabolomic profiling of wild rooibos (Aspalathus linearis) ecotypes and their antioxidant-derived phytopharmaceutical potential.

INTRODUCTION: Aspalathus linearis (commonly known as rooibos) is endemic to the Cape Floristic Region of South Africa and is a popular herbal drink and skin phytotherapeutic ingredient, with health benefits derived primarily from its unique phenolic content. Several, seemingly habitat-specific ecotypes from the Cederberg (Western Cape) and Northern Cape have morphological, ecological, genetic and biochemical differences. OBJECTIVES AND METHODS: Despite the commercial popularity of the cultivated variety, the uncultivated ecotypes are largely understudied. To address gaps in knowledge about the biochemical constituency, ultra-performance liquid chromatography-mass spectrometry analysis of fifteen populations was performed, enabling high-throughput metabolomic fingerprinting of 50% (v/v) methanolic extracts. Antioxidant screening of selected populations was performed via three assays and antimicrobial activity on two microbial species was assessed. The metabolomic results were corroborated with total phenolic and flavonoid screening of the extracts. RESULTS AND DISCUSSION: Site-specific chemical lineages of rooibos ecotypes were confirmed via multivariate data analyses. Important features identified via PLS-DA disclosed higher relative abundances of certain tentative metabolites (e.g., rutin, aspalathin and apiin) present in the Dobbelaarskop, Blomfontein, Welbedacht and Eselbank sites, in comparison to other locations. Several unknown novel metabolites (e.g., m/z 155.0369, 231.0513, 443.1197, 695.2883) are responsible for metabolomic separation of the populations, four of which showed higher amounts of key metabolites and were thus selected for bioactivity analysis. The Welbedacht and Eselbank site 2 populations consistently displayed higher antioxidant activities, with 2,2-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) radical scavenging activities of 679.894 ± 3.427 µmol Trolox/g dry matter and 635.066 ± 5.140 µmol Trolox/g dry matter, respectively, in correlation with a high number of phenolic and flavonoid compounds. The contribution of the individual metabolites to the pharmacological effectiveness of rooibos remains unknown and as such, further structural elucidation and phytopharmacological testing is thus urgently needed.

Salt tolerance in a neotropical orchid in the absence of local adaptation to salt spray.

PREMISE: Salt tolerance has rarely been investigated regionally in the neotropics and even more rarely in Orchidaceae, one of the largest families. Therefore, investigating local adaptation to salt spray and its physiological basis in Epidendrum fulgens, a neotropical orchid species, brings important new insights. METHODS: We assessed the degree of salt tolerance in E. fulgens by testing whether coastal populations are more tolerant to salt, which could point to local adaptation. To understand the physiological basis of such salt tolerance, we exposed wild-collected individuals to salt spray for 60 days, then measured leaf expansion, osmotic potential, sodium leaf concentration, chlorophyll leaf index, chlorophyll fluorescence, relative growth rate, and pressure-volume curves. RESULTS: There is no local adaptation to salt spray since both inland and coastal plants have a high tolerance to salt stress. This tolerance is explained by the ability to tolerate high concentrations of salt in leaf tissues, which is related to the high succulence displayed by this species. CONCLUSIONS: We showed an unprecedented salt tolerance level for an orchid species, highlighting our limited knowledge of that trait beyond the traditional studied groups. Another interesting finding is that salt tolerance in E. fulgens is linked to succulence, is widespread, and is not the result of local adaptation. We suggest that E. fulgens and its allied species could be an interesting group to explore the evolution of important traits related to tolerance to salt stress, like succulence.

Differential capacity of phragmites ecotypes in remediation of inorganic contaminants in coastal ecosystems: Implications for climate change.

Remediating inorganic pollutants is an important part of protecting coastal ecosystems, which are especially at risk from the effects of climate change. Different Phragmites karka (Retz) Trin. ex Steud ecotypes were gathered from a variety of environments, and their abilities to remove inorganic contaminants from coastal wetlands were assessed. The goal is to learn how these ecotypes process innovation might help reduce the negative impacts of climate change on coastal environments. The Phragmites karka ecotype E1, found in a coastal environment in Ichkera that was impacted by residential wastewater, has higher biomass production and photosynthetic pigment content than the Phragmites karka ecotypes E2 (Kalsh) and E3 (Gatwala). Osmoprotectant accumulation was similar across ecotypes, suggesting that all were able to successfully adapt to polluted marine environments. The levels of both total soluble sugars and proteins were highest in E2. The amount of glycine betaine (GB) rose across the board, with the highest levels being found in the E3 ecotype. The study also demonstrated that differing coastal habitats significantly influenced the antioxidant activity of all ecotypes, with E1 displaying the lowest superoxide dismutase (SOD) activity, while E2 exhibited the lowest peroxidase (POD) and catalase (CAT) activities. Significant morphological changes were evident in E3, such as an expansion of the phloem, vascular bundle, and metaxylem cell areas. When compared to the E3 ecotype, the E1 and E2 ecotypes showed striking improvements across the board in leaf anatomy. Mechanistic links between architectural and physio-biochemical alterations are crucial to the ecological survival of different ecotypes of Phragmites karka in coastal environments affected by climate change. Their robustness and capacity to reduce pollution can help coastal ecosystems endure in the face of persistent climate change.

Conservation genomics of wolves: The global impact of RK Wayne's research.

RK Wayne has arguably been the most influential geneticist of canids, famously promoting the conservation of wolves in his homeland, the United States. His influence has been felt in other countries and regions outside the contiguous United States, where he inspired others, also including former graduate students and research fellows of his, to use modern molecular techniques to examine the evolutionary biology of canids to inform the conservation and management of wolves. In this review, we focus on the implications of Wayne's work on wolves outside the United States. He envisioned a clear future for wolf conservation research, involving the study of wolves' ecological and genetic diversity, and the description of ecotypes requiring conservation. He also documented widespread hybridization among canids and introgression of DNA from domestic dogs to wolves, a process that started dozens of thousands of years ago. His work therefore calls for innovative studies, such as examining the potential fitness benefits of introgression. Inspired by his results, for example, on the purging of deleterious alleles in small populations, wolf researchers should use novel molecular tools to challenge other conservation genetics paradigms. Overall, RK Wayne's work constitutes a call for answers, which as scientists or citizens concerned with conservation matters, we are obliged to address, as we contribute to monitoring and maintaining biodiversity during our period of dramatic transformations of the biosphere.

Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient.

Microbial community responses to environmental change are largely associated with ecological processes; however, the potential for microbes to rapidly evolve and adapt remains relatively unexplored in natural environments. To assess how ecological and evolutionary processes simultaneously alter the genetic diversity of a microbiome, we conducted two concurrent experiments in the leaf litter layer of soil over 18 mo across a climate gradient in Southern California. In the first experiment, we reciprocally transplanted microbial communities from five sites to test whether ecological shifts in ecotypes of the abundant bacterium, Curtobacterium, corresponded to past adaptive differentiation. In the transplanted communities, ecotypes converged toward that of the native communities growing on a common litter substrate. Moreover, these shifts were correlated with community-weighted mean trait values of the Curtobacterium ecotypes, indicating that some of the trait variation among ecotypes could be explained by local adaptation to climate conditions. In the second experiment, we transplanted an isogenic Curtobacterium strain and tracked genomic mutations associated with the sites across the same climate gradient. Using a combination of genomic and metagenomic approaches, we identified a variety of nonrandom, parallel mutations associated with transplantation, including mutations in genes related to nutrient acquisition, stress response, and exopolysaccharide production. Together, the field experiments demonstrate how both demographic shifts of previously adapted ecotypes and contemporary evolution can alter the diversity of a soil microbiome on the same timescale.

Comparison of metabolomic reconfiguration between Columbia and Landsberg ecotypes subjected to the combination of high salinity and increased irradiance.

BACKGROUND: Plants growing in the field are subjected to combinations of abiotic stresses. These conditions pose a devastating threat to crops, decreasing their yield and causing a negative economic impact on agricultural production. Metabolic responses play a key role in plant acclimation to stress and natural variation for these metabolic changes could be key for plant adaptation to fluctuating environmental conditions. RESULTS: Here we studied the metabolomic response of two Arabidopsis ecotypes (Columbia-0 [Col] and Landsberg erecta-0 [Ler]), widely used as genetic background for Arabidopsis mutant collections, subjected to the combination of high salinity and increased irradiance. Our findings demonstrate that this stress combination results in a specific metabolic response, different than that of the individual stresses. Although both ecotypes displayed reduced growth and quantum yield of photosystem II, as well as increased foliar damage and malondialdehyde accumulation, different mechanisms to tolerate the stress combination were observed. These included a relocation of amino acids and sugars to act as potential osmoprotectants, and the accumulation of different stress-protective compounds such as polyamines or secondary metabolites. CONCLUSIONS: Our findings reflect an initial identification of metabolic pathways that differentially change under stress combination that could be considered in studies of stress combination of Arabidopsis mutants that include Col or Ler as genetic backgrounds.

Polygenic routes lead to parallel altitudinal adaptation in Heliosperma pusillum (Caryophyllaceae).

Understanding how organisms adapt to the environment is a major goal of modern biology. Parallel evolution-the independent evolution of similar phenotypes in different populations-provides a powerful framework to investigate the evolutionary potential of populations, the constraints of evolution, its repeatability and therefore its predictability. Here, we quantified the degree of gene expression and functional parallelism across replicated ecotype formation in Heliosperma pusillum (Caryophyllaceae), and gained insights into the architecture of adaptive traits. Population structure analyses and demographic modelling support a previously formulated hypothesis of parallel polytopic divergence of montane and alpine ecotypes. We detect a large proportion of differentially expressed genes (DEGs) underlying divergence within each replicate ecotype pair, with a strikingly low number of shared DEGs across pairs. Functional enrichment of DEGs reveals that the traits affected by significant expression divergence are largely consistent across ecotype pairs, in strong contrast to the nonshared genetic basis. The remarkable redundancy of differential gene expression indicates a polygenic architecture for the diverged adaptive traits. We conclude that polygenic traits appear key to opening multiple routes for adaptation, widening the adaptive potential of organisms.

Integrating top-down and bottom-up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone.

Understanding the phenotypic and genetic architecture of reproductive isolation is a long-standing goal of speciation research. In several systems, large-effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine "top-down" and "bottom-up" approaches with demographic modelling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to gene flow between two divergent red- and yellow-flowered ecotypes of Mimulus aurantiacus. Several candidate isolating traits and anonymous single nucleotide polymorphism loci under divergent selection have been identified, but their genomic positions remain unknown. Here, we report findings from demographic analyses that indicate this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted by widespread barrier loci across the genome. Using a novel, geographic cline-based genome scan, we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few "islands of speciation." Quantitative trait locus (QTL) mapping reveals that most floral traits are highly polygenic, with little evidence that QTL colocalize, indicating that most traits are genetically independent. Finally, we find little evidence that QTL and candidate barrier loci overlap, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow other than pollinator isolation may play an important role in this system.

Plant size directly correlates with water use efficiency in Arabidopsis.

Plant transpiration is a fundamental process that determines plant water use efficiency (WUE), thermoregulation, nutrition, and growth. How transpiration impacts on such essential physiological aspects and how the environment modulates these effects are fundamental questions about which little is known. We investigated the genetic and environmental factors underlying natural variation in plant transpiration and water use efficiency in a population of natural Arabidopsis thaliana accessions grown under homogeneous conditions. As expected, we observed large variation of total transpiration capacity, transpiration per surface unit, and WUE among A. thaliana accessions. Despite the variation of stomatal density and ABA content in the population, WUE did not correlate with any of these parameters. On the contrary, a surprising direct correlation was found between WUE and projected leaf area, with bigger plants displaying a more efficient use of water. Importantly, genome-wide association studies further supported our observations through the identification of several loci involved in WUE variation, mutations in which caused a simultaneous reduction in plant size and a decrease in WUE. Altogether, our results strongly suggest that, although WUE depends on many parameters, plant size is an adaptive trait with respect to water use in A. thaliana.

Local adaptation to hummingbirds and bees in Salvia stachydifolia: insights into pollinator shifts in a Southern Andean sage.

BACKGROUND AND AIMS: Differences among populations in pollinator assemblages can lead to local adaptation mosaics in which plants evolve different floral morphologies and attractive traits. Mountain habitats may promote local adaptation because of differences in environmental conditions with altitude, causing changes in pollinators, and because mountaintops can act as isolated habitats. We studied if the differences in floral shape, size and nectar traits in Salvia stachydifolia can be attributed to variations in the relative contribution of hummingbirds and insects. METHODS: We studied eight populations of S. stachydifolia in natural and under common garden conditions, to assess whether population differences have a genetic component. We recorded pollinators, their behaviour and visitation rates, and characterized pollinator assemblages. In addition, we measured nectar volume and concentration, and collected flowers to describe floral shape and size variation using geometric morphometric methods. We then applied an unsupervised learning algorithm to identify ecotypes based on morphometric traits. Finally, we explored whether populations with different pollinator assemblages had different climatic and/or elevation preferences. KEY RESULTS: We found that variation in the identity of the main pollinators was associated with differences among populations in all traits, as expected under a local adaptation scenario. These differences persisted in the common garden, suggesting that they were not due to phenotypic plasticity. We found S. stachydifolia populations were pollinated either by bees, by hummingbirds or had mixed pollination. We identified two ecotypes that correspond to the identity of the main pollinator guilds, irrespective of climate or altitude. CONCLUSIONS: Variation in S. stachydifolia floral traits did not follow any evident association with bioclimatic factors, suggesting that populations may have diverged as the product of historical isolation on mountaintops. We suggest that differences among populations point to incipient speciation and an ongoing pollinator shift.

Genomic signatures of ecological divergence between savanna and forest populations of a Neotropical tree.

BACKGROUND AND AIMS: In eastern Neotropical South America, the Cerrado, a large savanna vegetation, and the Atlantic Forest harbour high biodiversity levels, and their habitats are rather different from each other. The biomes have intrinsic evolutionary relationships, with high lineage exchange that can be attributed, in part, to a large contact zone between them. The genomic study of ecotypes, i.e. populations adapted to divergent habitats, can be a model to study the genomic signatures of ecological divergence. Here, we investigated two ecotypes of the tree Plathymenia reticulata, one from the Cerrado and the other from the Atlantic Forest, which have a hybrid zone in the ecotonal zone of Atlantic Forest-Cerrado. METHODS: The ecotypes were sampled in the two biomes and their ecotone. The evolutionary history of the divergence of the species was analysed with double-digest restriction site-associated DNA sequencing. The genetic structure and the genotypic composition of the hybrid zone were determined. Genotype-association analyses were performed, and the loci under putative selection and their functions were investigated. KEY RESULTS: High divergence between the two ecotypes was found, and only early-generation hybrids were found in the hybrid zone, suggesting a partial reproductive barrier. Ancient introgression between the Cerrado and Atlantic Forest was not detected. The soil and climate were associated with genetic divergence in Plathymenia ecotypes and outlier loci were found to be associated with the stress response, with stomatal and root development and with reproduction. CONCLUSIONS: The high genomic, ecological and morphophysiological divergence between ecotypes, coupled with partial reproductive isolation, indicate that the ecotypes represent two species and should be managed as different evolutionary lineages. We advise that the forest species should be re-evaluated and restated as vulnerable. Our results provide insights into the genomic mechanisms underlying the diversification of species across savanna and forest habitats and the evolutionary forces acting in the species diversification in the Neotropics.

Incomplete partitioning of pollinators by Linum suffruticosum and its coflowering congeners.

PREMISE: Linum suffruticosum shows variations in pollinator fit, pollen pickup, and local pollinators that predict pollen deposition rates. The species often coflowers with other Linum species using the same pollinators. We investigated whether L. suffruticosum trait variation could be explained by local patterns of pollinator sharing and associated evolution to reduce interspecific pollen transfer. METHODS: Pollinator observations were made in different localities (single species, coflowering with other congeners). Floral traits were measured to detect differences across populations and from coflowering species. Reproductive costs were quantified using interspecific hand pollinations and measures of pollen-tube formation, combined with observations of pollen arrival on stigmas and pollen-tube formation after natural pollination in allopatric and sympatric localities. RESULTS: The size and identity of the most important pollinator of L. suffruticosum and whether there was pollinator sharing with coflowering species appeared to explain floral trait variation related to pollinator fit. The morphological overlap of the flowers of L. suffruticosum with those of coflowering species varied, depending on coflowering species identity. A post-pollination incompatibility system maintains reproductive isolation, but conspecific pollen-tube formation was lower after heterospecific pollination. Under natural pollination at sites of coflowering with congeners, conspecific pollen-tube formation was lower than at single-species localities. CONCLUSIONS: Trait variation in L. suffruticosum appears to respond to the most important local pollinator. Locally, incomplete pollinator partitioning might cause interspecific pollination, imposing reproductive costs. These reproductive costs may generate selection on floral traits for reduced morphological overlap with coflowering congeners, leading to the evolution of pollination ecotypes.

High Structural Diversity of Aeruginosins in Bloom-Forming Cyanobacteria of the Genus Planktothrix as a Consequence of Multiple Recombination Events.

Many compounds produced by cyanobacteria act as serine protease inhibitors, such as the tetrapeptides aeruginosins (Aer), which are found widely distributed. The structural diversity of Aer is intriguingly high. However, the genetic basis of this remains elusive. In this study, we explored the genetic basis of Aer synthesis among the filamentous cyanobacteria Planktothrix spp. In total, 124 strains, isolated from diverse freshwater waterbodies, have been compared regarding variability within Aer biosynthesis genes and the consequences for structural diversity. The high structural variability could be explained by various recombination processes affecting Aer synthesis, above all, the acquisition of accessory enzymes involved in post synthesis modification of the Aer peptide (e.g., halogenases, glycosyltransferases, sulfotransferases) as well as a large-range recombination of Aer biosynthesis genes, probably transferred from the bloom-forming cyanobacterium Microcystis. The Aer structural composition differed between evolutionary Planktothrix lineages, adapted to either shallow or deep waterbodies of the temperate climatic zone. Thus, for the first time among bloom-forming cyanobacteria, chemical diversification of a peptide family related to eco-evolutionary diversification has been described. It is concluded that various Aer peptides resulting from the recombination event act in chemical defense, possibly as a replacement for microcystins.

Genotyping and Multivariate Regression Trees Reveal Ecological Diversification within the Microcystis aeruginosa Complex along a Wide Environmental Gradient.

Addressing the ecological and evolutionary processes underlying biodiversity patterns is essential to identify the mechanisms shaping community structure and function. In bacteria, the formation of new ecologically distinct populations (ecotypes) is proposed as one of the main drivers of diversification. New ecotypes arise when mutations in key functional genes or acquisition of new metabolic pathways by horizontal gene transfer allow the population to exploit new resources, permitting their coexistence with the parental population. We previously reported the presence of microcystin-producing organisms of the Microcystis aeruginosa complex (toxic MAC) through an 800-km environmental gradient ranging from freshwater to estuarine-marine waters in South America. We hypothesize that the success of toxic MAC in such a gradient is due to the existence of very closely related populations that are ecologically distinct (ecotypes), each specialized to a specific arrangement of environmental variables. Here, we analyzed toxic MAC genetic diversity through quantitative PCR (qPCR) and high-resolution melting analysis (HRMA) of a functional gene (mcyJ, microcystin synthetase cluster). We explored the variability of the mcyJ gene along the environmental gradient by multivariate classification and regression trees (mCART). Six groups of mcyJ genotypes were distinguished and associated with different combinations of water temperature, conductivity, and turbidity. We propose that each mcyJ variant associated with a defined environmental condition is an ecotype (or species) whose relative abundances vary according to their fitness in the local environment. This mechanism would explain the success of toxic MAC in such a wide array of environmental conditions. IMPORTANCE Organisms of the Microcystis aeruginosa complex form harmful algal blooms (HABs) in nutrient-rich water bodies worldwide. MAC HABs are difficult to manage owing to the production of potent toxins (microcystins) that resist water treatment. In addition, the role of microcystins in the ecology of MAC organisms is still elusive, meaning that the environmental conditions driving the toxicity of the bloom are not clear. Furthermore, the lack of coherence between morphology-based and genomic-based species classification makes it difficult to draw sound conclusions about when and where each member species of the MAC will dominate the bloom. Here, we propose that the diversification process and success of toxic MAC in a wide range of water bodies involves the generation of ecotypes, each specialized in a particular niche, whose relative abundance varies according to its fitness in the local environment. This knowledge can improve the generation of accurate prediction models of MAC growth and toxicity, helping to prevent human and animal intoxication.

The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid.

Recent ecotypic differentiation provides unique opportunities to investigate the genomic basis and architecture of local adaptation, while offering insights into how species form and persist. Sockeye salmon (Oncorhynchus nerka) exhibit migratory and resident ("kokanee") ecotypes, which are further distinguished into shore-spawning and stream-spawning reproductive ecotypes. Here, we analysed 36 sockeye (stream-spawning) and kokanee (stream- and shore-spawning) genomes from a system where they co-occur and have recent common ancestry (Okanagan Lake/River in British Columbia, Canada) to investigate the genomic basis of reproductive and migratory behaviour. Examination of the genomic landscape of differentiation, differences in allele frequencies and genotype-phenotype associations revealed three main blocks of sequence differentiation on chromosomes 7, 12 and 20, associated with migratory behaviour, spawning location and spawning timing. Structural variants identified in these same areas suggest they could contribute to ecotypic differentiation directly as causal variants or via maintenance of their genomic architecture through recombination suppression mechanisms. Genes in these regions were related to spatial memory and swimming endurance (SYNGAP, TPM3), as well as eye and brain development (including SIX6), potentially associated with differences in migratory behaviour and visual habitats across spawning locations, respectively. Additional genes (GREB1L, ROCK1) identified here have been associated with timing of migration in other salmonids and could explain variation in timing of O. nerka spawning. Together, these results based on the joint analysis of sequence and structural variation represent a significant advance in our understanding of the genomic landscape of ecotypic differentiation at different stages in the speciation continuum.

Distinct Composition and Assembly Processes of Bacterial Communities in a River from the Arid Area: Ecotypes or Habitat Types?

The composition, function, and assembly mechanism of the bacterial community are the focus of microbial ecology. Unsupervised machine learning may be a better way to understand the characteristics of bacterial metacommunities compared to the empirical habitat types. In this study, the composition, potential function, and assembly mechanism of the bacterial community in the arid river were analysed. The Dirichlet multinomial mixture method recognised four ecotypes across the three habitats (biofilm, water, and sediment). The bacterial communities in water are more sensitive to human activities. Bacterial diversity and richness in water decreased as the intensity of human activities increased from the region of water II to water I. Significant differences in the composition and potential function profile of bacterial communities between water ecotypes were also observed, such as higher relative abundance in the taxonomic composition of Firmicutes and potential function of plastic degradation in water I than those in water II. Habitat filtering may play a more critical role in the assembly of bacterial communities in the river biofilm, while stochastic processes dominate the assembly process of bacterial communities in water and sediment. In water I, salinity and mean annual precipitation were the main drivers shaping the biogeography of taxonomic structure, while mean annual temperature, total organic carbon, and ammonium nitrogen were the main environmental factors influencing the taxonomic structure in water II. These results would provide conceptual frameworks about choosing habitat types or ecotypes for the research of microbial communities among different niches in the aquatic environment.

Tunisian camel casein gene characterization reveals similarities and differences with Sudanese and Nigerian populations.

Milk is a primary protein source that has always played a role in mammalian health. Despite the intensification of research projects on dromedary and the knowledge of the genetic diversity at the casein loci, the genetic structure of the Tunisian camel population still needs exploration. This study sought to determine the genetic diversity of 3 casein gene variants in 5 Tunisian camel ecotypes: c.150G>T at CSN1S1 (αS1-casein), g.2126A>G at CSN2 (ß-casein), and g.1029T>C at CSN3 (κ-casein). The obtained results were compared with data published on Sudanese and Nigerian camels to establish the level of differentiation within and between populations. A total of 159 blood samples were collected from 5 Tunisian camel ecotypes and the extracted DNA was genotyped by PCR-RFLP. A streamlined genotyping protocol was also developed for CSN3. Results indicated that allele T was quite rare (0.06) at CSN1S1 for all ecotypes. Minor allele frequency was found for G (0.462) in CSN2 except for Ardhaoui Medenine ecotype who deviated from the average CSN2 allele frequency of the total population. Allele C showed minor allele frequency of 0.384 in CSN3. Among the Tunisian population, GAT (0.343) was the most represented haplotype in all ecotypes except for Ardhaoui Medenine, where GGC (0.322) was the most frequent one. Significant differences in heterozygosity and local inbreeding were observed across the Tunisian, Sudanese, and Nigerian populations, although the global fixation index indicated that only 2.2% of the genetic variance is related to ecotype differences. Instead, phylogenetic analysis revealed a closer link between the Tunisian and Sudanese populations through a clade subdivision with 3 main branches among the ecotypes. This study represents the first attempt to understand casein gene variability in Tunisian camels; with further study, milk traits and genetic differentiation among populations can be associated with the history of camel domestication.