Adaptive evolution in response to varying environments, leading to population divergence, is among the most intriguing processes of speciation. However, the extent to which these adaptive processes effectively drive population divergence amidst ongoing gene flow remains controversial. Our study addresses this by analyzing population genetic structure, gene flow, and genomic divergence between lineages of a tapeworm parasite (Ligula intestinalis) isolated from sympatric fish hosts. This parasite, which must overcome host immunological defenses for successful infection, significantly impacts host health. Utilizing genome-wide Single Nucleotide Polymorphisms (SNPs) and transcriptome data, we investigated whether host species impose distinct selection pressures on parasite populations. Genetic clustering analyses revealed clear divergence, with parasites from bream (Abramis brama) forming a distinct genetic cluster separate from those infecting roach (Rutilus rutilus), rudd (Scardinius erythrophthalmus), and bleak (Alburnus alburnus). Demographic modeling indicated isolation with continuous gene flow as the most plausible scenario for this divergence. Selection analyses identified 896 SNPs under selection, displaying low to moderate nucleotide diversity and genetic divergence compared with neutral loci. Transcriptome profiling supported these findings, revealing distinct gene expression profiles between parasite populations. Examination of selected SNPs and differentially expressed genes identified candidate genes linked to immune evasion mechanisms, potentially driving ecological speciation. This research highlights the interplay of host specificity, population demography, and disruptive selection in ecological speciation. By dissecting genomic factors, our study improves the understanding of mechanisms facilitating population divergence despite ongoing gene flow.

• Klíčová slova
• differential gene expression, ecological speciation, gene flow, host-associated genetic differentiation, sympatric evolution,
• MeSH
• Cestoda * genetika   MeSH
• genetická variace MeSH
• interakce hostitele a parazita genetika   MeSH
• jednonukleotidový polymorfismus MeSH
• nemoci ryb parazitologie   genetika   MeSH
• populační genetika MeSH
• ryby * parazitologie   genetika   MeSH
• selekce (genetika) MeSH
• tok genů * MeSH
• transkriptom MeSH
• vznik druhů (genetika) * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

In the arid landscapes of the Arabian Peninsula, high levels of cryptic diversity among reptiles, and especially in geckos, have recently been revealed. Mountain ranges within the peninsula were shown to contain the highest richness of reptile endemicity, serving as refugia to species less adapted to the hyper-arid conditions of the lowlands. With up to 19 endemic reptile species, the Hajar Mountains of southeastern Arabia are a clear example of this pattern. Owing to its old geological history, complex topography and geographic isolation from the rest of the peninsula, this mountain range rises as a hotspot of reptile biodiversity and endemicity in Arabia, and provides the perfect scenario to study the processes of evolution and diversification of reptiles in arid mountain ranges. In the present study we investigate the systematics of the Pristurus rupestris species complex, a group of geckos exhibiting cryptic morphological traits along with a remarkably deep evolutionary history. Initially considered a single species distributed throughout coastal Arabia, and with some scattered populations at the Horn of Africa, several recent studies have shown that Pristurus rupestris actually comprises a species complex restricted to the Hajar Mountains of southeastern Arabia. Here, we utilize an integrative approach assembling several morphological, genetic, genomic, and ecological datasets to resolve this long-standing systematic challenge. Results support the existence of four new cryptic Pristurus species in the Hajar Mountains with three new Oman endemics. While no unique diagnostic morphological characters were identified, some slight morphological differences occur between species, especially among high-elevation species relative to the rest. Despite the lack of clear morphological differentiation, extreme levels of genetic variation were found between species with genetic distances of up to 24% in the 12S mitochondrial marker, resulting from deep divergence times of up to 10 mya. Moreover, all species have been found in sympatry with at least another representative of the species complex and without any signs of apparent and ongoing gene flow among them. These findings yield profound implications for conservation efforts, as one of these newly described species presents an extremely restricted distribution (only known from a single locality and three individuals), requiring immediate attention for protection. Overall, this study sheds light on the hidden diversity within the P. rupestris species complex, emphasizing the importance of preserving biodiversity in the face of ongoing environmental changes, while highlighting, once again, the Hajar Mountains of southeastern Arabia as a cradle of reptile biodiversity.

• MeSH
• biodiverzita MeSH
• fylogeneze MeSH
• genomika MeSH
• ještěři * genetika   klasifikace   anatomie a histologie   MeSH
• vznik druhů (genetika) * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Arábie MeSH

Speciation is a continuous process driven by genetic, geographic, and ecological barriers to gene flow. It is widely investigated in multicellular eukaryotes, yet we are only beginning to comprehend the relative importance of mechanisms driving the emergence of barriers to gene flow in microbial populations. Here, we explored the diversification of the nearly ubiquitous soil cyanobacterium Microcoleus. Our dataset consisted of 291 genomes, of which 202 strains and eight herbarium specimens were sequenced for this study. We found that Microcoleus represents a global speciation continuum of at least 12 lineages, which radiated during Eocene/Oligocene aridification and exhibit varying degrees of divergence and gene flow. The lineage divergence has been driven by selection, geographical distance, and the environment. Evidence of genetic divergence and selection was widespread across the genome, but we identified regions of exceptional differentiation containing candidate genes associated with stress response and biosynthesis of secondary metabolites.

• MeSH
• fylogeneze MeSH
• genetický drift * MeSH
• genom MeSH
• tok genů MeSH
• vznik druhů (genetika) * MeSH
• Publikační typ
• časopisecké články MeSH

The sympatric occurrence of closely related lineages displaying conserved morphological and ecological traits is often characteristic of free-living microbes. Gene flow, recombination, selection, and mutations govern the genetic variability between these cryptic lineages and drive their differentiation. However, sequencing conservative molecular markers (e.g., 16S rRNA) coupled with insufficient population-level sampling hindered the study of intra-species genetic diversity and speciation in cyanobacteria. We used phylogenomics and a population genomic approach to investigate the extent of local genomic diversity and the mechanisms underlying sympatric speciation of Laspinema thermale. We found two cryptic lineages of Laspinema. The lineages were highly genetically diverse, with recombination occurring more frequently within than between them. That suggests the existence of a barrier to gene flow, which further maintains divergence. Genomic regions of high population differentiation harbored genes associated with possible adaptations to high/low light conditions and stress stimuli, although with a weak diversifying selection. Overall, the diversification of Laspinema species might have been affected by both genomic and ecological processes.

• Klíčová slova
• cryptic species, cyanobacteria, gene flow, phylogenomics, recombination, sympatric speciation,
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Tartary buckwheat (Fagopyrum tataricum) is a nutritionally balanced and flavonoid-rich crop plant that has been in cultivation for 4000 years and is now grown globally. Despite its nutraceutical and agricultural value, the characterization of its genetics and its domestication history is limited. RESULTS: Here, we report a comprehensive database of Tartary buckwheat genomic variation based on whole-genome resequencing of 510 germplasms. Our analysis suggests that two independent domestication events occurred in southwestern and northern China, resulting in diverse characteristics of modern Tartary buckwheat varieties. Genome-wide association studies for important agricultural traits identify several candidate genes, including FtUFGT3 and FtAP2YT1 that significantly correlate with flavonoid accumulation and grain weight, respectively. CONCLUSIONS: We describe the domestication history of Tartary buckwheat and provide a detailed resource of genomic variation to allow for genomic-assisted breeding in the improvement of elite cultivars.

• Klíčová slova
• Buckwheat, Domestication, GWAS, Genomic variation,
• MeSH
• celogenomová asociační studie * MeSH
• domestikace * MeSH
• Fagopyrum genetika   metabolismus   MeSH
• flavonoidy metabolismus   MeSH
• genetická variace MeSH
• genetické techniky MeSH
• jednonukleotidový polymorfismus MeSH
• regulace genové exprese u rostlin MeSH
• šlechtění rostlin MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Čína MeSH
• Názvy látek
• flavonoidy MeSH

BACKGROUND: Microsporidia are spore-forming obligate intracellular parasites that include both emerging pathogens and economically important disease agents. However, little is known about the genetic diversity of microsporidia. Here, we investigated patterns of geographic population structure, intraspecific genetic variation, and recombination in two microsporidian taxa that commonly infect cladocerans of the Daphnia longispina complex in central Europe. Taken together, this information helps elucidate the reproductive mode and life-cycles of these parasite species. METHODS: Microsporidia-infected Daphnia were sampled from seven drinking water reservoirs in the Czech Republic. Two microsporidia species (Berwaldia schaefernai and microsporidium lineage MIC1) were sequenced at the internal transcribed spacer (ITS) region, using the 454 pyrosequencing platform. Geographical structure analyses were performed applying Fisher's exact tests, analyses of molecular variance, and permutational MANOVA. To evaluate the genetic diversity of the ITS region, the number of polymorphic sites and Tajima's and Watterson's estimators of theta were calculated. Tajima's D was also used to determine if the ITS in these taxa evolved neutrally. Finally, neighbour similarity score and pairwise homology index tests were performed to detect recombination events. RESULTS: While there was little variation among Berwaldia parasite strains infecting different host populations, the among-population genetic variation of MIC1 was significant. Likewise, ITS genetic diversity was lower in Berwaldia than in MIC1. Recombination signals were detected only in Berwaldia. CONCLUSION: Genetic tests showed that parasite populations could have expanded recently after a bottleneck or that the ITS could be under negative selection in both microsporidia species. Recombination analyses might indicate cryptic sex in Berwaldia and pure asexuality in MIC1. The differences observed between the two microsporidian species present an exciting opportunity to study the genetic basis of microsporidia-Daphnia coevolution in natural populations, and to better understand reproduction in these parasites.

• Klíčová slova
• Cryptic sex, Genetic diversity, Internal transcribed spacer, Microsporidia, Recombination,
• MeSH
• Daphnia mikrobiologie   MeSH
• fylogeografie MeSH
• genetická variace * MeSH
• haplotypy MeSH
• intergenová DNA * MeSH
• metagenomika MeSH
• Microsporidia genetika   MeSH
• rekombinace genetická MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH
• Názvy látek
• intergenová DNA * MeSH