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36 results for “lineage selection”
Data from: Environmentally independent selection for hybrids between divergent freshwater stickleback lineages in semi-natural ponds
<p>Hybridization following secondary contact of genetically divergent populations can influence the range expansion of invasive species, though specific outcomes depend on the environmental dependence of hybrid fitness. Here, using two genetically and ecologically divergent threespine stickleback lineages that differ in their history of freshwater colonization, we estimate fitness variation of parental lineages and hybrids in semi-natural freshwater ponds with contrasting histories of nutrient loading. In our experiment, we found that fish from the older freshwater lineage (Lake Geneva) and hybrids outperformed fish from the younger freshwater lineage (Lake Constance) in terms of both growth and survival, regardless of the environmental context of our ponds. Across all ponds, hybrids exhibited the highest survival. Although wild- caught adult populations differed in their functional and defence morphology, it is unclear which of these traits underlie the fitness differences observed among juveniles in our experiment. Overall, our work suggests that when hybrid fitness is insensitive to environmental conditions, as observed here, introgression may promote population-expansion into unoccupied habitats and accelerate invasion success.</p>
Data from: Biogeography of shell morphology in over-exploited shellfish reveals adaptive tradeoffs on human-inhabited islands and incipient selectively driven lineage bifurcation
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Data from: Environmentally independent selection for hybrids between divergent freshwater stickleback lineages in semi-natural ponds
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Data from: Transgenerational selection driven by divergent ecological impacts of hybridizing lineages
Dynamic interactions between ecological conditions and the phenotypic composition of populations likely play an important role in evolution, but the direction and strength of these feedbacks remain difficult to characterize. We investigated these dynamics across two generations of threespine sticklebacks from two evolutionary lineages undergoing secondary contact and hybridization. Independently manipulating the density and lineage of adults in experimental mesocosms led to contrasting ecosystem conditions with strong effects on total survival in a subsequent generation of juveniles. Ecosystem modifications by adults also varied the strength of selection on competing hybrid and non-hybrid juveniles. This variation in selection indicated (1) a negative eco-evolutionary feedback driven by lineage-specific resource depletion and dependence and (2) a large performance advantage of hybrid juveniles in depleted environments. This work illustrates the importance of interactions between phenotype, population density and the environment in shaping selection and evolutionary trajectories, especially in the context of range expansion with secondary contact and hybridization.
Data from: Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation
A species' genetic diversity bears the marks of evolutionary processes that have occurred throughout its history. However, robust detection of selection in wild populations is difficult and often impeded by lack of replicate tests. Here, we investigate selection in pink salmon (Oncorhynchus gorbuscha) using genome scans coupled with inference from a haploid-assisted linkage map. Pink salmon have a strict 2-year semelparous life history which has resulted in temporally isolated (allochronic) lineages that remain sympatric through sharing of spawning habitats in alternate years. The lineages differ in a range of adaptive traits, suggesting different genetic backgrounds. We used genotyping by sequencing of haploids to generate a high-density linkage map with 7035 loci and screened an existing panel of 8036 loci for signatures of selection. The linkage map enabled identification of novel genomic regions displaying signatures of parallel selection shared between lineages. Furthermore, 24 loci demonstrated divergent selection and differences in genetic diversity between lineages, suggesting that adaptation in the 2 lineages has arisen from different pools of standing genetic variation. Findings have implications for understanding asynchronous population abundances as well as predicting future ecosystem impacts from lineage-specific responses to climate change.
Data from: Strong selection against hybrids maintains a narrow contact zone between morphologically cryptic lineages in a rainforest lizard
Phenotypically cryptic lineages comprise an important yet understudied part of biodiversity; in particular, we have much to learn about how these lineages are formed and maintained. To better understand the evolutionary significance of such lineages, we studied a hybrid zone between two morphologically-cryptic phylogeographic lineages in the rainforest lizard, Lampropholis coggeri. Analyzing a multilocus genetic dataset through cline inference, individual-based methods and population measures of disequilibrium and using simulations to explore our genetic results in context of theoretical expectations, we inferred the processes maintaining this hybrid zone. We find that these lineages meet in a hybrid zone that is narrow (~400 m) relative to inferred dispersal rate. Further, the hybrid zone exhibits substantial genetic disequilibrium and sharply coincident and largely concordant clines. Based on our knowledge about the region's biogeography, the species' natural history, and our simulation results, we suggest that strong selection against hybrids structures this system. As all clines show a relatively narrow range of introgression, we posit that this hybrid zone might not yet be in equilibrium. Nonetheless, our results clearly show that phylogeographic lineages can evolve substantial reproductive isolation without concomitant morphological diversification, suggesting that such lineages can constitute a significant component of evolutionary diversity.
Variant Call File (VCF) for Genome-wide polymorphism and genic selection in feral and domesticated lineages of Cannabis sativa
<p>A comprehensive understanding of the degree to which genomic variation is maintained by selection versus drift and gene flow is lacking in many important species such as <em>Cannabis</em> <em>sativa </em>(<em>C. sativa</em>), one of the oldest known crops to be cultivated by humans worldwide. We generated whole genome resequencing data across diverse samples of feralized (escaped domesticated lineages) and domesticated lineages of <em>C. sativa</em>. We performed analyses to examine population structure, and genome wide scans for FST, balancing selection, and positive selection. Our analyses identified evidence for sub-population structure and further support the Asian origin hypothesis of this species. Feral plants sourced from the U.S. exhibited broad regions on chromosomes 4 and 10 with high <span>𝐹̅</span>ST which may indicate chromosomal inversions maintained at high frequency in this sub-population. Both our balancing and positive selection analyses identified loci that may reflect differential selection for traits favored by natural selection and artificial selection in feral versus domesticated sub-populations. In the U.S. feral sub-population, we found six loci related to stress response under balancing selection and one gene involved in disease resistance under positive selection, suggesting local adaptation to new climates and biotic interactions. In the marijuana sub-population, we identified the gene <em>SMALLER TRICHOMES</em> <em>WITH VARIABLE BRANCHES 2 </em>to be under positive selection which suggests artificial selection for increased tetrahydrocannabinol yield. Overall the data generated, and results obtained from our study help to form a better understanding of the evolutionary history in <em>C. sativa</em>.</p>
Data from: Parallel signatures of selection in temporally-isolated lineages of pink salmon
Studying the effect of similar environments on diverse genetic backgrounds has long been a goal of evolutionary biologists with studies typically relying on experimental approaches. Pink salmon, a highly-abundant and widely-ranging salmonid, provide a naturally-occurring opportunity to study the effects of similar environments on divergent genetic backgrounds due to a strict two-year semelparous life-history. The species is composed of two reproductively-isolated lineages with overlapping ranges that share the same spawning and rearing environments in alternate years. We used restriction site-associated DNA (RAD) sequencing to discover and genotype approximately 8,000 SNP loci in three population pairs of even- and odd-year pink salmon along a latitudinal gradient in North America. We found greater differentiation within the odd-year than the even-year lineage and greater differentiation in the southern pair from Puget Sound than in the northern Alaskan population pairs. We identified 15 SNPs reflecting signatures of parallel selection using both a differentiation-based method (BAYESCAN) and an environmental correlation method (BAYENV). These SNPs represent genomic regions that may be particularly informative in understanding adaptive evolution in pink salmon and exploring how differing genetic backgrounds within a species respond to selection from the same natural environment.
Data from: Strong selection against hybrids maintains a narrow contact zone between morphologically cryptic lineages in a rainforest lizard
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Data from: Transgenerational selection driven by divergent ecological impacts of hybridizing lineages
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Data from: Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation
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Data from: Parallel signatures of selection in temporally-isolated lineages of pink salmon
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Variant Call File (VCF) for Genome-wide polymorphism and genic selection in feral and domesticated lineages of Cannabis sativa
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Data from: Lineages evolved under stronger sexual selection show superior ability to invade conspecific competitor populations
Despite limitations on offspring production, almost all multicellular species use sex to reproduce. Sex gives rise to sexual selection, a widespread force operating through competition and choice within reproduction, however, it remains unclear whether sexual selection is beneficial for total lineage fitness, or if it acts as a constraint. Sexual selection could be a positive force because of selection on improved individual condition and purging of mutation load, summing into lineages with superior fitness. On the other hand, sexual selection could negate potential net fitness through the actions of sexual conflict, or because of tensions between investment in sexually selected and naturally selected traits. Here, we explore these ideas using a multigenerational invasion challenge to measure consequences of sexual selection for the overall net fitness of a lineage. After applying experimental evolution under strong versus weak regimes of sexual selection for 77 generations with the flour beetle Tribolium castaneum, we measured the overall ability of introductions from either regime to invade into conspecific competitor populations across eight generations. Results showed that populations from stronger sexual selection backgrounds had superior net fitness, invading more rapidly and completely than counterparts from weak sexual selection backgrounds. Despite comprising only 10% of each population at the start of the invasion experiment, colonizations from strong sexual selection histories eventually achieved near total introgression, almost completely eliminating the original competitor genotype. Population genetic simulations using the design and parameters of our experiment indicate that this invasion superiority could be explained if strong sexual selection had improved both juvenile and adult fitness, in both sexes. Using a combination of empirical and modeling approaches, our findings therefore reveal positive and wide-reaching impacts of sexual selection for net population fitness when facing the broad challenge of invading competitor populations across multiple generations.
Genome-wide patterns of selection-drift variation strongly associate with organismal traits across the green plant lineage
<p>Gene alignments and trees</p>
Data from: Lineages evolved under stronger sexual selection show superior ability to invade conspecific competitor populations
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Lineage tracing of acute myeloid leukemia reveals the impact of hypomethylating agents on chemoresistance selection
GEO Series GSE134506. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Subfamily-Selective PCR primers for the Human LINE1 L1PA Lineage
GEO Series GSE301759. Homo sapiens. 6 samples. Type: Other.
A double negative thymocyte specific enhancer augments Notch1 signaling to direct early T cell progenitor expansion, lineage restriction and b-selection.
GEO Series GSE211079. Mus musculus. 34 samples. Type: Expression profiling by high throughput sequencing.
Lineage-specific super-enhancer activates genes in a promoter-selective manner
GEO Series GSE121438. Mus musculus. 14 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.