Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear understanding of their fitness consequences. Here, we study whether WGDs result in greater diversity of genomic structural variants (SVs) and how they influence evolutionary dynamics in a plant genus, Cochlearia (Brassicaceae). By using long-read sequencing and a graph-based pangenome, we find both negative and positive interactions between WGDs and SVs. Masking of recessive mutations due to WGDs leads to a progressive accumulation of deleterious SVs across four ploidal levels (from diploids to octoploids), likely reducing the adaptive potential of polyploid populations. However, we also discover putative benefits arising from SV accumulation, as more ploidy-specific SVs harbor signals of local adaptation in polyploids than in diploids. Together, our results suggest that SVs play diverse and contrasting roles in the evolutionary trajectories of young polyploids.
The remarkable fish biodiversity encompasses also great sex chromosome variability. Harttia catfish belong to Neotropical models for karyotype and sex chromosome research. Some species possess one of the three male-heterogametic sex chromosome systems, XY, X1X2Y or XY1Y2, while other members of the genus have yet uncharacterized modes of sex determination. Particularly the XY1Y2 multiple sex chromosome system shows a relatively low incidence among vertebrates, and it has not been yet thoroughly investigated. Previous research suggested two independent X-autosome fusions in Harttia which led to the emergence of XY1Y2 sex chromosome system in three of its species. In this study, we investigated evolutionary trajectories of synteny blocks involved in this XY1Y2 system by probing six Harttia species with whole chromosome painting (WCP) probes derived from the X (HCA-X) and the chromosome 9 (HCA-9) of H. carvalhoi. We found that both painting probes hybridize to two distinct chromosome pairs in Amazonian species, whereas the HCA-9 probe paints three chromosome pairs in H. guianensis, endemic to Guyanese drainages. These findings demonstrate distinct evolutionary fates of mapped synteny blocks and thereby elevated karyotype dynamics in Harttia among the three evolutionary clades.
- Publication type
- Journal Article MeSH
Recent years have improved our understanding of the plasticity of cell types behind inducing, building, and maintaining different types of teeth. The latest efforts were aided by progress in single-cell transcriptomics, which helped to define not only cell states with mathematical precision but also transitions between them. This includes new aspects of dental epithelial and mesenchymal stem cell niches and beyond. These recent efforts revealed continuous and fluid trajectories connecting cell states during dental development and exposed the natural plasticity of tooth-building progenitors. Such "developmental" plasticity seems to be employed for organizing stem cell niches in adult continuously growing teeth. Furthermore, transitions between mature cell types elicited by trauma might represent a replay of embryonic continuous cell states. Alternatively, they could constitute transitions that evolved de novo, not known from the developmental paradigm. In this review, we discuss and exemplify how dental cell types exhibit plasticity during dynamic processes such as development, self-renewal, repair, and dental replacement. Hypothetically, minor plasticity of cell phenotypes and greater plasticity of transitions between cell subtypes might provide a better response to lifetime challenges, such as damage or dental loss. This plasticity might be additionally harnessed by the evolutionary process during the elaboration of dental cell subtypes in different animal lineages. In turn, the diversification of cell subtypes building teeth brings a diversity of their shape, structural properties, and functions.
- MeSH
- Regeneration physiology MeSH
- Tooth * MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
BACKGROUND: Animals form complex symbiotic associations with their gut microbes, whose evolution is determined by an intricate network of host and environmental factors. In many insects, such as Drosophila melanogaster, the microbiome is flexible, environmentally determined, and less diverse than in mammals. In contrast, mammals maintain complex multispecies consortia that are able to colonize and persist in the gastrointestinal tract. Understanding the evolutionary and ecological dynamics of gut microbes in different hosts is challenging. This requires disentangling the ecological factors of selection, determining the timescales over which evolution occurs, and elucidating the architecture of such evolutionary patterns. RESULTS: We employ experimental evolution to track the pace of the evolution of a common gut commensal, Lactiplantibacillus plantarum, within invertebrate (Drosophila melanogaster) and vertebrate (Mus musculus) hosts and their respective diets. We show that in Drosophila, the nutritional environment dictates microbial evolution, while the host benefits L. plantarum growth only over short ecological timescales. By contrast, in a mammalian animal model, L. plantarum evolution results to be divergent between the host intestine and its diet, both phenotypically (i.e., host-evolved populations show higher adaptation to the host intestinal environment) and genomically. Here, both the emergence of hypermutators and the high persistence of mutated genes within the host's environment strongly differed from the low variation observed in the host's nutritional environment alone. CONCLUSIONS: Our results demonstrate that L. plantarum evolution diverges between insects and mammals. While the symbiosis between Drosophila and L. plantarum is mainly determined by the host diet, in mammals, the host and its intrinsic factors play a critical role in selection and influence both the phenotypic and genomic evolution of its gut microbes, as well as the outcome of their symbiosis.
- MeSH
- Drosophila melanogaster genetics MeSH
- Drosophila MeSH
- Microbiota * MeSH
- Mice MeSH
- Mammals MeSH
- Gastrointestinal Microbiome * MeSH
- Symbiosis MeSH
- Animals MeSH
- Check Tag
- Mice MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
Myxozoa is a group of endoparasitic cnidarians covering almost 2600 species but merely 53 species, mostly from the genus Chloromyxum, have been reported from sharks, rays, and skates (Elasmobranchii). Elasmobranchs play a key role in the study of evolutionary trajectories of myxozoans as they represent ancestral vertebrate hosts. Our study provides new data on Chloromyxum spp. from 57 elasmobranchs, covering 20 species from geographical regions and host groups not previously investigated, such as Lamniformes and Hexanchiformes, the most basal phylogenetic shark lineage. In total, 28% of elasmobranchs were infected with Chloromyxum spp., indicating high diversity. Of the seven distinguished species, six are formally described based on morphological, morphometric, and genetic (18S rDNA) data. Comprehensive co-phylogenetic analyses and ancestral state reconstruction revealed that parasite and host phylogenies are clearly correlated, resulting in a distinct phylogenetic separation of chloromyxids from selachid (shark) vs. batoid (ray and skate) hosts. Species infecting the most ancient elasmobranchs formed a sublineage, branching off in the middle of the Chloromyxum sensu stricto clade. Our findings indicate that chloromyxids likely invaded an ancestral elasmobranch prior the time of divergence of shark and batoid lineages. Our analyses did not show a clear phylogeographic pattern of Chloromyxum parasites, probably due to the cosmopolitan distribution and migratory behaviour of many elasmobranch hosts, but geographical sampling must be extended to confirm or refute this observation. This study provides a complex view on species diversity, phylogeny, evolution, host-parasite co-phylogeny, and the phylogeographic origin of Chloromyxum species from elasmobranchs. Our results highlight the importance of adding missing data from previously un- or undersampled geographical regions and host species which results in a more accurate estimate of myxozoan biodiversity and a better understanding of the evolution of this parasite group in their hosts and in the different oceans of our planet.
- MeSH
- Elasmobranchii * genetics parasitology MeSH
- Phylogeny MeSH
- Myxozoa * genetics MeSH
- Parasites * MeSH
- Fishes parasitology MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
BACKGROUND: Lineage-specific gene expansions represent one of the driving forces in the evolutionary dynamics of unique phylum traits. Myxozoa, a cnidarian subphylum of obligate parasites, are evolutionarily altered and highly reduced organisms with a simple body plan including cnidarian-specific organelles and polar capsules (a type of nematocyst). Minicollagens, a group of structural proteins, are prominent constituents of nematocysts linking Myxozoa and Cnidaria. Despite recent advances in the identification of minicollagens in Myxozoa, the evolutionary history and diversity of minicollagens in Myxozoa and Cnidaria remain elusive. RESULTS: We generated new transcriptomes of two myxozoan species using a novel pipeline for filtering of closely related contaminant species in RNA-seq data. Mining of our transcriptomes and published omics data confirmed the existence of myxozoan Ncol-4, reported only once previously, and revealed a novel noncanonical minicollagen, Ncol-5, which is exclusive to Myxozoa. Phylogenetic analyses support a close relationship between myxozoan Ncol-1-3 with minicollagens of Polypodium hydriforme, but suggest independent evolution in the case of the myxozoan minicollagens Ncol-4 and Ncol-5. Additional genome- and transcriptome-wide searches of cnidarian minicollagens expanded the dataset to better clarify the evolutionary trajectories of minicollagen. CONCLUSIONS: The development of a new approach for the handling of next-generation data contaminated by closely related species represents a useful tool for future applications beyond the field of myxozoan research. This data processing pipeline allowed us to expand the dataset and study the evolution and diversity of minicollagen genes in Myxozoa and Cnidaria. We identified a novel type of minicollagen in Myxozoa (Ncol-5). We suggest that the large number of minicollagen paralogs in some cnidarians is a result of several recent large gene multiplication events. We revealed close juxtaposition of minicollagens Ncol-1 and Ncol-4 in myxozoan genomes, suggesting their common evolutionary history. The unique gene structure of myxozoan Ncol-5 suggests a specific function in the myxozoan polar capsule or tubule. Despite the fact that myxozoans possess only one type of nematocyst, their gene repertoire is similar to those of other cnidarians.
Despite the benefits of phototrophy, many algae have lost photosynthesis and have converted back to heterotrophy. Parasitism is a heterotrophic strategy, with apicomplexans being among the most devastating parasites for humans. The presence of a nonphotosynthetic plastid in apicomplexan parasites suggests their phototrophic ancestry. The discovery of related phototrophic chromerids has unlocked the possibility to study the transition between phototrophy and parasitism in the Apicomplexa. The chromerid Chromera velia can live as an intracellular parasite in coral larvae as well as a free-living phototroph, combining phototrophy and parasitism in what I call photoparasitism. Since early-branching apicomplexans live extracellularly, their evolution from an intracellular symbiont is unlikely. In this opinion article I discuss possible evolutionary trajectories from an extracellular photoparasite to an obligatory apicomplexan parasite.
- MeSH
- Apicomplexa classification metabolism physiology MeSH
- Biological Evolution * MeSH
- Phototrophic Processes * MeSH
- Humans MeSH
- Parasites classification metabolism physiology MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
The quasi-natural meandering type of alluvial rivers is quite unusual in Central European watersheds. The lack of extensive regulation allows such rivers to shift along their floodplain and cause erosion of natural and agricultural lands. Description of channel morphometric parameters over decadal timescales allows a better understanding of such river systems like Sajó River (Slovakia-Hungary) where no preliminary work is available regarding channel dynamics. In addition, to just describing the geomorphic processes, the environmental management implications of these meandering rivers need to be investigated as well. Thus, this study represents a bend-scale morphological analysis on the 124 km long section of the Sajó River in the Hungarian territory in eight different periods between 1952 and 2011. Archive aerial imagery, orthophotographs and topographical maps were organized into a database, then GIS-based analyses were performed to quantify the rate and extent of channel shifts, bend development and the area of erosion/accretion. On the bend scale, we have calculated several morphometric parameters (bend length, chord, amplitude, the radius of curvature) to quantify the evolutionary trajectory of reaches. Hydrological time series data were evaluated to reveal its possible role in the processes. Based on the available GIS-data of natural elements and anthropogenic intervention, we delineated 12 different reaches showing similar characteristics, from which six reaches were defined as natural. According to the morphometric parameters of the natural reaches, channel widths became narrower and the planform became more concentrated spatially in most of the reaches while the overall sinuosity of almost all natural reaches increased. Although artificial cutoffs mainly reduced the reach complexity, in some cases, they have accelerated the bend development downstream in the following few years. Erosion and accretion activity were higher in the periods when the discharge was higher than the effective discharge but its effect became less apparent in the second half of the investigated time period. By 1980, major artificial cutoffs and bank protection works were carried out that could have an impact in reducing the potential channel shifting. Based on our results, we propose a possible preservation and some modifications along the Hungarian part of the Sajó River reaches to be carried out by the local river management authorities. We conclude that this study provides a detailed demonstration of the Sajó River morphodymanics which can be used for further land planning to avoid harmful consequences of recent bank erosion processes not only along the Sajó River, but other similar rivers in Europe.
All 100+ bedbug species (Cimicidae) are obligate blood-sucking parasites [1, 2]. In general, blood sucking (hematophagy) is thought to have evolved in generalist feeders adventitiously taking blood meals [3, 4], but those cimicid taxa currently considered ancestral are putative host specialists [1, 5]. Bats are believed to be the ancestral hosts of cimicids [1], but a cimicid fossil [6] predates the oldest known bat fossil [7] by >30 million years (Ma). The bedbugs that parasitize humans [1, 8] are host generalists, so their evolution from specialist ancestors is incompatible with the "resource efficiency" hypothesis and only partially consistent with the "oscillation" hypothesis [9-16]. Because quantifying host shift frequencies of hematophagous specialists and generalists may help to predict host associations when vertebrate ranges expand by climate change [17], livestock, and pet trade in general and because of the previously proposed role of human pre-history in parasite speciation [18-20], we constructed a fossil-dated, molecular phylogeny of the Cimicidae. This phylogeny places ancestral Cimicidae to 115 mya as hematophagous specialists with lineages that later frequently populated bat and bird lineages. We also found that the clades, including the two major current urban pests, Cimex lectularius and C. hemipterus, separated 47 mya, rejecting the notion that the evolutionary trajectories of Homo caused their divergence [18-21]. VIDEO ABSTRACT.
Ribosomal DNA (rDNA) loci encoding 5S and 45S (18S-5.8S-28S) rRNAs are important components of eukaryotic chromosomes. Here, we set up the animal rDNA database containing cytogenetic information about these loci in 1343 animal species (264 families) collected from 542 publications. The data are based on in situ hybridisation studies (both radioactive and fluorescent) carried out in major groups of vertebrates (fish, reptiles, amphibians, birds, and mammals) and invertebrates (mostly insects and mollusks). The database is accessible online at www.animalrdnadatabase.com . The median number of 45S and 5S sites was close to two per diploid chromosome set for both rDNAs despite large variation (1-74 for 5S and 1-54 for 45S sites). No significant correlation between the number of 5S and 45S rDNA loci was observed, suggesting that their distribution and amplification across the chromosomes follow independent evolutionary trajectories. Each group, irrespective of taxonomic classification, contained rDNA sites at any chromosome location. However, the distal and pericentromeric positions were the most prevalent (> 75% karyotypes) for 45S loci, while the position of 5S loci was more variable. We also examined potential relationships between molecular attributes of rDNA (homogenisation and expression) and cytogenetic parameters such as rDNA positions, chromosome number, and morphology.
