► Polyploids have lower speciation and higher extinction rates than diploids. ► Rapid polyploid speciation expected by reciprocal gene loss models is questioned. ► Gene duplication rates probably ...exceed single nucleotide mutation rates owing to paleopolyploidy. ► Dosage-balance may not explain paralog retention patterns for all plant genomes.
Polyploidy, or whole genome duplication, is recognized as an important feature of eukaryotic genome evolution. Among eukaryotes, polyploidy has probably had the largest evolutionary impact on vascular plants where many contemporary species are of recent polyploid origin. Genomic analyses have uncovered evidence of at least one round of polyploidy in the ancestry of most plants, fueling speculation that genome duplications lead to increases in net diversity. In spite of the frequency of ancient polyploidy, recent analyses have found that recently formed polyploid species have higher extinction rates than their diploid relatives. These results suggest that despite leaving a substantial legacy in plant genomes, only rare polyploids survive over the long term and most are evolutionary dead-ends.
Premise of the Study
Polyploidy or whole‐genome duplication (WGD) pervades the evolutionary history of angiosperms. Despite extensive progress in our understanding of WGD, the role of these events in ...promoting diversification is still not well understood. We seek to clarify the possible association between WGD and diversification rates in flowering plants.
Methods
Using a previously published phylogeny spanning all land plants (31,749 tips) and WGD events inferred from analyses of the 1000 Plants (1KP) transcriptome data, we analyzed the association of WGDs and diversification rates following numerous WGD events across the angiosperms. We used a stepwise AIC approach (MEDUSA), a Bayesian mixture model approach (BAMM), and state‐dependent diversification analyses (MuSSE) to investigate patterns of diversification. Sister‐clade comparisons were used to investigate species richness after WGDs.
Key Results
Based on the density of 1KP taxon sampling, 106 WGDs were unambiguously placed on the angiosperm phylogeny. We identified 334–530 shifts in diversification rates. We found that 61 WGD events were tightly linked to changes in diversification rates, and state‐dependent diversification analyses indicated higher speciation rates for subsequent rounds of WGD. Additionally, 70 of 99 WGD events showed an increase in species richness compared to the sister clade.
Conclusions
Forty‐six of the 106 WGDs analyzed appear to be closely associated with upshifts in the rate of diversification in angiosperms. Shifts in diversification do not appear more likely than random within a four‐node lag phase following a WGD; however, younger WGD events are more likely to be followed by an upshift in diversification than older WGD events.
Polyploidy or whole genome duplication (WGD) is a major contributor to genome evolution and diversity. Although polyploidy is recognized as an important component of plant evolution, it is generally ...considered to play a relatively minor role in animal evolution. Ancient polyploidy is found in the ancestry of some animals, especially fishes, but there is little evidence for ancient WGDs in other metazoan lineages. Here we use recently published transcriptomes and genomes from more than 150 species across the insect phylogeny to investigate whether ancient WGDs occurred during the evolution of Hexapoda, the most diverse clade of animals. Using gene age distributions and phylogenomics, we found evidence for 18 ancient WGDs and six other large-scale bursts of gene duplication during insect evolution. These bursts of gene duplication occurred in the history of lineages such as the Lepidoptera, Trichoptera, and Odonata. To further corroborate the nature of these duplications, we evaluated the pattern of gene retention from putative WGDs observed in the gene age distributions. We found a relatively strong signal of convergent gene retention across many of the putative insect WGDs. Considering the phylogenetic breadth and depth of the insect phylogeny, this observation is consistent with polyploidy as we expect dosage balance to drive the parallel retention of genes. Together with recent research on plant evolution, our hexapod results suggest that genome duplications contributed to the evolution of two of the most diverse lineages of eukaryotes on Earth.
The present study investigates the relationship between night-time screen-based media devices (SBMD) use, which refers to use within 1 h before sleep, in both lit and dark rooms, and sleep outcomes ...and health-related quality of life (HRQoL) among 11 to 12-year-olds.
We analysed baseline data from a large cohort of 6616 adolescents from 39 schools in and around London, United Kingdom, participating in the Study of Cognition Adolescents and Mobile Phone (SCAMP). Adolescents self-reported their use of any SBMD (mobile phone, tablet, laptop, television etc.). Sleep variables were derived from self-reported weekday and/or weekend bedtime, sleep onset latency (SOL) and wake time. Sleep quality was assessed using four standardised dimensions from the Swiss Health Survey. HRQoL was estimated using the KIDSCREEN-10 questionnaire.
Over two-thirds (71.5%) of adolescents reported using at least one SBMD at night-time, and about a third (32.2%) reported using mobile phones at night-time in darkness. Night-time mobile phone and television use was associated with higher odds of insufficient sleep duration on weekdays (Odds Ratio, OR = 1.82, 95% Confidence Interval, CI 1.59, 2.07 and OR = 1.40, 95% CI 1.23, 1.60, respectively). Adolescents who used mobile phones in a room with light were more likely to have insufficient sleep (OR = 1.32, 95% CI 1.10, 1.60) and later sleep midpoint (OR = 1.64, 95% CI 1.37, 1.95) on weekends compared to non-users. The magnitude of these associations was even stronger for those who used mobile phones in darkness for insufficient sleep duration on weekdays (OR = 2.13, 95% CI 1.79, 2.54) and for later sleep midpoint on weekdays (OR = 3.88, 95% CI 3.25, 4.62) compared to non-users. Night-time use of mobile phones was associated with lower HRQoL and use in a dark room was associated with even lower KIDSCREEN-10 score (β = –1.18, 95% CI –1.85, –0.52) compared to no use.
We found consistent associations between night-time SBMD use and poor sleep outcomes and worse HRQoL in adolescents. The magnitude of these associations was stronger when SBMD use occurred in a dark room versus a lit room.
•Globally, adolescents are sleeping shorter than the recommended duration.•The prevalence of SBMD use particularly mobile phones is increasing.•Our study is the first to investigate SBMD use in light/darkness and adolescents' sleep and HRQoL•Night-time SBMD use was associated with a high risk of poor HRQoL and sleep outcomes.•The magnitude of these associations was stronger when SBMD use occurred in darkness.
Polyploid speciation entails substantial and rapid postzygotic reproductive isolation of nascent species that are initially sympatric with one or both parents. Despite strong postzygotic isolation, ...ecological niche differentiation has long been thought to be important for polyploid success. Using biogeographic data from across vascular plants, we tested whether the climatic niches of polyploid species are more differentiated than their diploid relatives and if the climatic niches of polyploid species differentiated faster than those of related diploids. We found that polyploids are often more climatically differentiated from their diploid parents than the diploids are from each other. Consistent with this pattern, we estimated that polyploid species generally have higher rates of multivariate niche differentiation than their diploid relatives. In contrast to recent analyses, our results confirm that ecological niche differentiation is an important component of polyploid speciation and that niche differentiation is often significantly faster in polyploids.
Polyploid speciation entails substantial and rapid postzygotic reproductive isolation of nascent species that are initially sympatric with one or both parents. Despite strong postzygotic isolation, ecological niche differentiation has long been thought to be important for polyploid success. Using biogeographic data from across vascular plants, we tested whether the climatic niches of polyploid species are more differentiated than their diploid relatives and if the climatic niches of polyploid species differentiated faster than those of related diploids.
frequency of polyploid speciation in vascular plants Wood, Troy E; Takebayashi, Naoki; Barker, Michael S ...
Proceedings of the National Academy of Sciences - PNAS,
08/2009, Letnik:
106, Številka:
33
Journal Article
Recenzirano
Odprti dostop
Since its discovery in 1907, polyploidy has been recognized as an important phenomenon in vascular plants, and several lines of evidence indicate that most, if not all, plant species ultimately have ...a polyploid ancestry. However, previous estimates of the frequency of polyploid speciation suggest that the formation and establishment of neopolyploid species is rare. By combining information from the botanical community's vast cytogenetic and phylogenetic databases, we establish that 15% of angiosperm and 31% of fern speciation events are accompanied by ploidy increase. These frequency estimates are higher by a factor of four than earlier estimates and lead to a standing incidence of polyploid species within genera of 35% (n = 1,506). Despite this high incidence, we find no direct evidence that polyploid lines, once established, enjoy greater net species diversification. Thus, the widespread occurrence of polyploid taxa appears to result from the substantial contribution of polyploidy to cladogenesis, but not from subsequent increases in diversification rates of polyploid lines.
Polyploidy, the doubling of genomic content, is a widespread feature, especially among plants, yet its macroevolutionary impacts are contentious. Traditionally, polyploidy has been considered an ...evolutionary dead end, whereas recent genomic studies suggest that polyploidy has been a key driver of macroevolutionary success. We examined the consequences of polyploidy on the time scale of genera across a diverse set of vascular plants, encompassing hundreds of inferred polyploidization events. Likelihood-based analyses indicate that polyploids generally exhibit lower speciation rates and higher extinction rates than diploids, providing the first quantitative corroboration of the dead-end hypothesis. The increased speciation rates of diploids can, in part, be ascribed to their capacity to speciate via polyploidy. Only particularly fit lineages of polyploids may persist to enjoy longer-term evolutionary success.
Abstract Premise The history of angiosperms is marked by repeated rounds of ancient whole‐genome duplications (WGDs). Here we used state‐of‐the‐art methods to provide an up‐to‐date view of the ...distribution of WGDs in the history of angiosperms that considers both uncertainty introduced by different WGD inference methods and different underlying species‐tree hypotheses. Methods We used the distribution synonymous divergences ( K s ) of paralogs and orthologs from transcriptomic and genomic data to infer and place WGDs across two hypothesized angiosperm phylogenies. We further tested these WGD hypotheses with syntenic inferences and Bayesian models of duplicate gene gain and loss. Results The predicted number of WGDs in the history of angiosperms (~170) based on the current taxon sampling is largely similar across different inference methods, but varies in the precise placement of WGDs on the phylogeny. K s ‐based methods often yield alternative hypothesized WGD placements due to variation in substitution rates among lineages. Phylogenetic models of duplicate gene gain and loss are more robust to topological variation. However, errors in species‐tree inference can still produce spurious WGD hypotheses, regardless of method used. Conclusions Here we showed that different WGD inference methods largely agree on an average of 3.5 WGD in the history of individual angiosperm species. However, the precise placement of WGDs on the phylogeny is subject to the WGD inference method and tree topology. As researchers continue to test hypotheses regarding the impacts ancient WGDs have on angiosperm evolution, it is important to consider the uncertainty of the phylogeny as well as WGD inference methods.
Brain metastases are associated with a dismal prognosis. Whether brain metastases harbor distinct genetic alterations beyond those observed in primary tumors is unknown. We performed whole-exome ...sequencing of 86 matched brain metastases, primary tumors, and normal tissue. In all clonally related cancer samples, we observed branched evolution, where all metastatic and primary sites shared a common ancestor yet continued to evolve independently. In 53% of cases, we found potentially clinically informative alterations in the brain metastases not detected in the matched primary-tumor sample. In contrast, spatially and temporally separated brain metastasis sites were genetically homogenous. Distal extracranial and regional lymph node metastases were highly divergent from brain metastases. We detected alterations associated with sensitivity to PI3K/AKT/mTOR, CDK, and HER2/EGFR inhibitors in the brain metastases. Genomic analysis of brain metastases provides an opportunity to identify potentially clinically informative alterations not detected in clinically sampled primary tumors, regional lymph nodes, or extracranial metastases.
Decisions for individualized therapies in patients with brain metastasis are often made from primary-tumor biopsies. We demonstrate that clinically actionable alterations present in brain metastases are frequently not detected in primary biopsies, suggesting that sequencing of primary biopsies alone may miss a substantial number of opportunities for targeted therapy.
PDF
