Introgression in Nine-spined Sticklebacks
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ABSTRACT:
PROVIDER: PRJEB38005 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Whole-genome sequencing of wild nine-spined sticklebacks
| PRJEB39599 | ENA
Project description:Genome sequencing of the nine-spined stickleback (Pungitius pungitius) provides insights into chromosome evolution
| PRJEB33823 | ENA
Project description:Nine-spined stickleback linkage map (parents)
| PRJEB39736 | ENA
Project description:Nine-spined stickleback linkage map (offspring)
| PRJEB39760 | ENA
Project description:BACKGROUND: Comparative genomics approaches help to shed light on evolutionary processes that shape differentiation between lineages. The nine-spined stickleback (Pungitius pungitius) is a closely related species of the ecological 'supermodel' three-spined stickleback (Gasterosteus aculeatus). It is an emerging model system for evolutionary biology research but has garnered less attention and lacks extensive genomic resources. To expand on these resources and aid the study of sticklebacks in a phylogenetic framework, we characterized nine-spined stickleback transcriptomes from brain and liver using deep sequencing. RESULTS: We obtained nearly eight thousand assembled transcripts, of which 3,091 were assigned as putative one-to-one orthologs to genes found in the three-spined stickleback. These sequences were used for evaluating overall differentiation and substitution rates between nine- and three-spined sticklebacks, and to identify genes that are putatively evolving under positive selection. The synonymous substitution rate was estimated to be 7.1 × 10(-9) per site per year between the two species, and a total of 165 genes showed patterns of adaptive evolution in one or both species. A few nine-spined stickleback contigs lacked an obvious ortholog in three-spined sticklebacks but were found to match genes in other fish species, suggesting several gene losses within 13 million years since the divergence of the two stickleback species. We identified 47 SNPs in 25 different genes that differentiate pond and marine ecotypes. We also identified 468 microsatellites that could be further developed as genetic markers in nine-spined sticklebacks. CONCLUSION: With deep sequencing of nine-spined stickleback cDNA libraries, our study provides a significant increase in the number of gene sequences and microsatellite markers for this species, and identifies a number of genes showing patterns of adaptive evolution between nine- and three-spined sticklebacks. We also report several candidate genes that might be involved in differential adaptation between marine and freshwater nine-spined sticklebacks. This study provides a valuable resource for future studies aiming to identify candidate genes underlying ecological adaptation in this and other stickleback species.
| S-EPMC4046692 | biostudies-literature
Project description:Introgressive hybridization is an important process in evolution but challenging to identify, undermining the efforts to understand its role and significance. On the contrary, many analytical methods assume direct descent from a single common ancestor, and admixture among populations can violate their assumptions and lead to seriously biased results. A detailed analysis of 888 whole-genome sequences of nine-spined sticklebacks (Pungitius pungitius) revealed a complex pattern of population ancestry involving multiple waves of gene flow and introgression across northern Europe. The two recognized lineages were found to have drastically different histories, and their secondary contact zone was wider than anticipated, displaying a smooth gradient of foreign ancestry with some curious deviations from the expected pattern. Interestingly, the freshwater isolates provided peeks into the past and helped to understand the intermediate states of evolutionary processes. Our analyses and findings paint a detailed picture of the complex colonization history of northern Europe and provide backdrop against which introgression and its role in evolution can be investigated. However, they also expose the challenges in analyses of admixed populations and demonstrate how hidden admixture and colonization history misleads the estimation of admixture proportions and population split times.
| S-EPMC9828525 | biostudies-literature
Project description:Sleep is a complex and conserved biological process that affects several body functions and behaviors. Evidence suggests that there is a reciprocal interaction between sleep and immunity. For instance, fragmented sleep can increase the probability of parasitic infections and reduce the ability to fight infections. Moreover, viral and bacterial infections alter the sleep patterns of infected individuals. However, the effects of macro-parasitic infections on sleep remain largely unknown. In this study, we investigated whether macro-parasite infections could alter the sleep of their hosts. We experimentally infected three-spined sticklebacks (Gasterosteus aculeatus) with the tapeworm Schistocephalus solidus and used a hidden Markov model to characterize sleep behavior in sticklebacks. One to four days after parasite exposure, infected fish showed no difference in sleep compared with non-exposed fish, whereas fish that were exposed-but-not-infected slept less during daytime. 29-32 days after exposure, infected fish slept more than uninfected fish, while exposed-but-not-infected fish slept less than non-exposed fish. Using brain transcriptomics, we identified immune- and sleep-associated genes that potentially underlie the observed behavioral changes. These results provide insights into the complex association between macro-parasite infection, immunity, and sleep in fish and may thus contribute to a better understanding of reciprocal interactions between sleep and immunity.
2024-06-13 | GSE269460 | GEO
Project description:The data comes from a study, where three-spined sticklebacks (Gasterosteus aculeatus) were exposed to di-n-butyl phthalate (DBP) and 17α ethinyl-oestradiol (EE2) at nominal concentrations 35 μg/L and 40 ng/L, respectively, for four days. The aim of the study was to obtain insight into the acute transcriptional responses putatively associated with endocrine disruption. RNA samples from the testes of eight individuals fish per treatment (including solvent controls, exposed only to DMSO) were used in the microarray analysis, covering the expression of approximately 21000 genes.
2015-10-10 | E-MTAB-3951 | biostudies-arrayexpress