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116 results for “Bottlenecks”
Data from: Phylogeny of Leavenworthia S-alleles suggests unidirectional mating system evoution and enhanced positive selection following an ancient population bottleneck
The adoption of self-fertilization from an ancestral outcrossing state is one of the most common evolutionary transitions in the flowering plants. In the mustard family, outcrossing is typically enforced by sporophytic self-incompatibility (SI), but there are also many self-compatible species. The genus Leavenworthia contains taxa that either possess or lack SI. Here we present data showing that SI is associated with strict outcrossing and that there is widespread trans-specific sequence polymorphism at the locus involved in the recognition of self-pollen (the S-locus). This ancestral polymorphism is consistent with the presence of an outcrossing mating system in the common ancestor of Leavenworthia species, and suggests that there have been several independent losses of SI in the group. When compared with other mustard species, the bulk of Leavenworthia S-allele sequences are highly diverged from those found in other Brassicaceae and show relatively low levels of nucleotide diversity, a pattern that suggests the common ancestor of the genus likely underwent a strong population bottleneck. The hypothesis of post-bottleneck S-locus rediversification is supported by tests showing stronger positive selection acting on S-alleles from Leavenworthia than those found in other Brassicaceae.
Data from: Regular bottlenecks and restrictions to somatic fusion prevent the accumulation of mitochondrial defects in Neurospora
The replication and segregation of the multi-copy mitochondrial DNA (mtDNA) are not under strict control of the nuclear DNA. Within-cell selection may thus favour variants with an intracellular selective advantage but a detrimental effect on cell fitness. High relatedness among the mtDNA variants of an individual is predicted to disfavour such deleterious selfish genetic elements, but experimental evidence for this hypothesis is scarce. We studied the effect of mtDNA relatedness on the opportunities for suppressive mtDNA variants in the fungus Neurospora carrying the mitochondrial mutator plasmid pKALILO (pKAL). During growth, this plasmid integrates into the mitochondrial genome, generating suppressive mtDNA variants. These mtDNA variants gradually replace the wild-type mtDNA, ultimately culminating in growth arrest and death. We show that regular sequestration of mtDNA variation is required for effective selection against suppressive mtDNA variants. First, bottlenecks in the number of mtDNA copies from which a 'Kalilo' culture started significantly increased the maximum lifespan and variation in life span among cultures. Second, restrictions to somatic fusion among fungal individuals, either by using anastomosis-deficient mutants or by generating allotype diversity, prevented the accumulation of suppressive mtDNA variants. We discuss the implications of these results for the somatic accumulation of mitochondrial defects during ageing.
Lymph node metastases develop through a wider evolutionary bottleneck than distant metastases
<div class="WordSection1"> <p>Genetic diversity among metastases is poorly understood but contains important information about disease evolution at secondary sites. Here we investigate inter- and intra-lesion heterogeneity for two types of metastases that associate with different clinical outcomes: lymph node and distant organ metastases in human colorectal cancer. We develop a rigorous mathematical framework for quantifying metastatic phylogenetic diversity. Distant metastases are typically monophyletic and genetically similar to each other. Lymph node metastases, in contrast, display high levels of inter-lesion diversity. We validate these findings by analyzing 317 multi-region biopsies from an independent cohort of 20 patients. We further demonstrate higher levels of intra-lesion heterogeneity in lymph node than in distant metastases. Our results show that fewer primary tumor lineages seed distant metastases than lymph node metastases, indicating that the two sites are subject to different levels of selection. Thus, lymph node and distant metastases develop through fundamentally different evolutionary mechanisms.</p> </div>
Data from: Host population bottlenecks drive parasite extinction during antagonistic coevolution
Host-parasite interactions are often characterized by large fluctuations in host population size, and we investigated how such host bottlenecks affected coevolution between a bacterium and a virus. Previous theory suggests that host bottlenecks should provide parasites with an evolutionary advantage, but instead we found that phages were rapidly driven to extinction when coevolving with hosts exposed to large genetic bottlenecks. This was caused by the stochastic loss of sensitive bacteria, which are required for phage persistence and infectivity evolution. Our findings emphasize the importance of feedbacks between ecological and coevolutionary dynamics, and how this feedback can qualitatively alter coevolutionary dynamics.
Accompanying VTune results for "An Analysis of Performance Bottlenecks in MRI Pre-Processing"
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Figure 1 from: Wehrmann J, de Boer F, Benjumea R, Cavaillès S, Engelen D, Jansen J, Verhelst B, Vansteelant WMG (2019) Batumi Raptor Count: autumn raptor migration count data from the Batumi bottleneck, Republic of Georgia. ZooKeys 836: 135-157. https://doi.org/10.3897/zookeys.836.29252
Figure 1 The Batumi bottleneck lies in the western coastal part of the trans-Caucasian migration corridor for soaring birds (main map, based on Abuladze 2013) and holds the strongest passage of migrant raptors at the eastern Black Sea flyway. The two hilltop count stations (red dots) are in the foothills of the Lesser Caucasus close to the city of Batumi in southwestern Georgia (inset).
Figure 4 from: Wehrmann J, de Boer F, Benjumea R, Cavaillès S, Engelen D, Jansen J, Verhelst B, Vansteelant WMG (2019) Batumi Raptor Count: autumn raptor migration count data from the Batumi bottleneck, Republic of Georgia. ZooKeys 836: 135-157. https://doi.org/10.3897/zookeys.836.29252
Figure 4 Screenshot of trektellen.org mobile application with the specific screen mode for raptor count at BRC.
Figure 3 from: Wehrmann J, de Boer F, Benjumea R, Cavaillès S, Engelen D, Jansen J, Verhelst B, Vansteelant WMG (2019) Batumi Raptor Count: autumn raptor migration count data from the Batumi bottleneck, Republic of Georgia. ZooKeys 836: 135-157. https://doi.org/10.3897/zookeys.836.29252
Figure 3 Diagram of data management and processing at BRC showing the data registry development from paper based entries in the beginning to the mobile application supported entries since 2015 with subsequent final data processing and upload to the GBIF database
Figure 2 from: Wehrmann J, de Boer F, Benjumea R, Cavaillès S, Engelen D, Jansen J, Verhelst B, Vansteelant WMG (2019) Batumi Raptor Count: autumn raptor migration count data from the Batumi bottleneck, Republic of Georgia. ZooKeys 836: 135-157. https://doi.org/10.3897/zookeys.836.29252
Figure 2 Schematic overview of distance and overlap zones of the two count stations at BRC showing the distance codes relative to the station from West3 (W3) to overhead (O) and East3 (E3).
Figure 5 from: Wehrmann J, de Boer F, Benjumea R, Cavaillès S, Engelen D, Jansen J, Verhelst B, Vansteelant WMG (2019) Batumi Raptor Count: autumn raptor migration count data from the Batumi bottleneck, Republic of Georgia. ZooKeys 836: 135-157. https://doi.org/10.3897/zookeys.836.29252
Figure 5 Hierarchy of morphological groups used to estimate how many "unidentified birds" belong to each species level shown only for target species at BRC.
Fig. 5 in Selectivity of fish ladders: a bottleneck in Neotropical fish movement
Fig. 5. Species richness (rarefaction curves) in the Lajeado fish ladder under flow velocities of 2.3 and 2.8 m.s-1 in the ladder, during months when the discharge was manipulated.
Data from: Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs
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Data from: The effect of population bottlenecks on mutation rate evolution in asexual populations
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Data from: Phylogeny of Leavenworthia S-alleles suggests unidirectional mating system evoution and enhanced positive selection following an ancient population bottleneck
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Data from: Regular bottlenecks and restrictions to somatic fusion prevent the accumulation of mitochondrial defects in Neurospora
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Data from: Divergent evolution peaks under intermediate population bottlenecks during bacterial experimental evolution
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Lymph node metastases develop through a wider evolutionary bottleneck than distant metastases
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Data from: Host population bottlenecks drive parasite extinction during antagonistic coevolution
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Influence of biological and environmental conditions on winter mortality risk of a northern ungulate: evidence for a late-winter survival bottleneck
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Data from: The number of markers and samples needed for detecting bottlenecks under realistic scenarios, with and without recovery: a simulation-based study
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