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388 results for “gene loss”
Fig. 5 in Loss and Gain of Group I Introns in the Mitochondrial Gene of the Scleractinia (Cnidaria; Anthozoa).
Fig. 5. Bayesian estimates of divergence times in scleractinians. The basal axis is a geologic time scale in units of million years ago (mya). Different time intervals are labeled with abbreviations (Cam, Cambrian; Ord, Ordovician; Sil, Silurian; Dev, Devonian; Car, Carboniferous; Per, Permian; Tri, Triassic; Jur, Jurassic; Cre, Cretaceous; Pal, Paleogene; Neo, Neogene). The chart below the phylogenetic tree gives the extinction rate (solid line) and origination rate (dashed line) in different geological periods, which were modified from Kiessling (2004) with major extinction events labeled with abbreviations (Rhae, Rhaetian; Plie, Pliensbachian; Kimm, Kimmeridgian; Ceno, Cenomanian; Maa, Maastrichtian, KT-extinction). Species with different types of intron are labeled with symbols: ●, Intron-729 (I729); ▲, Intron-893 (I893); ■, Intron-876 (I876).
Fig. 4 in Loss and Gain of Group I Introns in the Mitochondrial Gene of the Scleractinia (Cnidaria; Anthozoa).
Fig. 4. Comparison of phylogenetic trees between the cox1 exon (left side) and intron (right side) in complex corals and corallimorpharians (A) and in sponges and robust corals (B). Tree topologies presenting the phylogenetic relationships of exons and introns were consensus trees between the maximum-likelihood analysis and Bayesian algorism. Numbers on branches are Shimedaira- Hasegawa-like/posterior probabilities. Dashed lines are potential changes in phylogenetic positions between the exon and intron trees.
Fig. 3 in Loss and Gain of Group I Introns in the Mitochondrial Gene of the Scleractinia (Cnidaria; Anthozoa).
Fig. 3. Phylogeny and characteristics of cox1 intron traits in hexacorals. The tree topology was constructed with Mrbayes. Numbers labeled on branches are Shimodaira-Hasegawa-like support/posterior probabilities. Species with different types of introns are labeled with symbols: ●, Intron-729 (I729); ▲, Intron-893 (I893); ■, Intron-876 (I876).
Fig. 1 in Loss and Gain of Group I Introns in the Mitochondrial Gene of the Scleractinia (Cnidaria; Anthozoa).
Fig. 1. Secondary structures of representative cox1 introns in anthozoans. A: Corallimorpharian (Rhodactis howesii); B: basal and complex corals (Gardeneris hawaiinesis); C: robust corals (Diploastrea heliopora); D: actiniarian (Metridinium senile); E: poriferian (Plakortis angulospiculatus); F: zoantharian (Savalia savaglia). Features of the secondary structure indicate the characteristics of group I introns: 10 helical elements P1~P10; consensus primary structures P, Q, R, and S in hollow letters; internal guide sequence, IGS. Initial and terminal sites of the predicted open reading frame are labeled "ORF start" and "ORF stop", respectively.
Supplementary data for: Selection on visual opsin genes in diurnal Neotropical frogs and loss of the SWS2 opsin in poison frogs
<p><span></span></p> <p><span></span></p> <p>Amphibians are ideal for studying visual system evolution because their biphasic (aquatic and terrestrial) life history and ecological diversity expose them to a broad range of visual conditions. Here we evaluate signatures of selection on visual opsin genes across Neotropical anurans and focus on three diurnal clades that are well-known for the concurrence of conspicuous colors and chemical defense (i.e., aposematism): poison frogs (Dendrobatidae), Harlequin toads (Bufonidae: <em>Atelopus</em>), and pumpkin toadlets (Brachycephalidae: <em>Brachycephalus</em>). We found evidence of positive selection on 44 amino acid sites in LWS, SWS1, SWS2, and RH1 opsin genes, of which one in LWS and two in RH1 have been previously identified as spectral tuning sites in other vertebrates. Given that anurans have mostly nocturnal habits, the patterns of selection revealed new sites that might be important in spectral tuning for frogs, potentially for adaptation to diurnal habits and for color-based intraspecific communication. Furthermore, we provide evidence that SWS2, normally expressed in rod cells in frogs and some salamanders, has likely been lost in the ancestor of Dendrobatidae, suggesting that under low-light levels, dendrobatids have inferior wavelength discrimination compared to other frogs. This loss might follow the origin of diurnal activity in dendrobatids and could have implications for their chemical ecology, biodiversity, and behavior. Our analyses show that assessments of opsin diversification in understudied groups could expand our understanding of the role of sensory system evolution in ecological adaptation.</p>
Data from: Same trait, different genes: pelvic spine loss in three brook stickleback populations in Alberta
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Supplementary data for: Selection on visual opsin genes in diurnal Neotropical frogs and loss of the SWS2 opsin in poison frogs
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Data from: Species tree estimation and the impact of gene loss following whole-genome duplication
<p>Whole-genome duplication (WGD) has been demonstrated to occur broadly and repeatedly in the evolutionary history of eukaryotes, and is recognized as a prominent evolutionary force, especially in plants. Immediately following WGD, most genes are present in two copies as paralogs. Due to this redundancy, one copy of a paralog pair commonly undergoes pseudogenization and is eventually lost. When speciation occurs shortly after WGD, however, differential loss of paralogs may lead to spurious phylogenetic inference resulting from the inclusion of pseudoorthologs – paralogous genes mistakenly identify as orthologs because they are present in single copes within each sampled species. The influence and impact of including pseudoorthologs versus true orthologs as result of gene extinction (or incomplete laboratory sampling) in a phylogenetic context is only recently starting to gain empirical attention. Moreover, few of these studies have yet to investigate this phenomenon in an explicit coalescent framework. Here, using mathematical models, numerous simulated data sets, and two newly assembled empirical data sets, we assess the effect of pseudoorthologs on species tree estimation under varying levels of incomplete lineage sorting (ILS) and different patterns of gene loss following WGD. When gene loss occurs in the terminal branches of the species tree, the alignment-based (BPP) and gene-tree-based (ASTRAL, MP-EST, and STAR) coalescent methods are adversely affected as the level of ILS increases. This can be greatly improved by sampling a sufficiently large number of genes. Under the same circumstances, however, concatenation methods consistently estimate incorrect species trees as the number of sampled genes increases. Furthermore, pseudoorthologs can mislead species tree inference if gene loss occurs in the internal branches of the species tree, where both coalescent and concatenation methods are prone to produce inconsistent results. However, pseudoorthologs are problematic when filtering only for single-copy genes in phylogenomic data sets. Pruning orthologs or even randomly selecting a copy from multi-copy genes can avoid most of those pseudoorthologs. These results underscore the importance of understanding the influence of pseudoorthologs in the phylogenomics era.</p>
Data from: Transcriptional remodeling upon light removal in a model cnidarian: losses and gains in gene expression
Organismal responses to light:dark cycles can result from two general processes: (i) direct response to light or (ii) a free-running rhythm (i.e., a circadian clock). Previous research in cnidarians has shown that candidate circadian clock genes have rhythmic expression in the presence of diel lighting, but these oscillations appear to be lost quickly after removal of the light cue. Here, we measure whole-organism gene expression changes in 136 transcriptomes of the sea anemone Nematostella vectensis, entrained to a light:dark environment and immediately following light cue removal to distinguish two broadly defined responses in cnidarians: light entrainment and circadian regulation. Direct light exposure resulted in significant differences in expression for hundreds of genes, including more than 200 genes with rhythmic, 24-hour periodicity. Removal of the lighting cue resulted in the loss of significant expression for 80% of these genes after one day, including most of the hypothesized cnidarian circadian genes. Further, 70% of these candidate genes were phase shifted. Most surprisingly, thousands of genes, some of which are involved in oxidative stress, DNA damage response, and chromatin modification, had significant differences in expression in the 24 hours following light removal, suggesting that loss of the entraining cue may induce a cellular stress response. Together, our findings suggest that a majority of genes with significant differences in expression for anemones cultured under diel lighting are largely driven by the primary photoresponse rather than a circadian clock when measured at the whole animal level. These results provide context for the evolution of cnidarian circadian biology and help to disassociate two commonly confounded factors driving oscillating phenotypes.
Rapid reduction of Paraoxonase expression followed by inactivation across semiaquatic mammals suggests adaptive benefit of gene loss
<p>Convergent adaptation to the same environment by multiple lineages frequently involves rapid evolutionary change at the same genes, implicating these genes as important for environmental adaptation. Such adaptive molecular changes may yield either change or loss of function; loss of protein function can eliminate newly deleterious proteins or reduce energy necessary for protein production. We previously found a striking case of recurrent pseudogenization of the Paraoxonase 1 (Pon1) gene among aquatic mammal lineages – Pon1 became a pseudogene at least six times independently in aquatic and semiaquatic mammals with clear genetic lesions, such as stop codons and frameshifts. Here, we assess the landscape and pace of pseudogenization by studying Pon1 sequences, expression levels, and blood plasma activity across four major aquatic and semiaquatic mammal lineages: pinnipeds, cetaceans, otters, and beavers. We also observed in beavers and pinnipeds an unexpected reduction in expression of Pon3, a paralog with similar expression patterns but different substrate preferences. Ultimately, in all lineages with aquatic/semiaquatic members, we find that preceding any coding level pseudogenization events in Pon1, there is a drastic decrease in expression, followed by relaxed selection, thus allowing for accumulation of disrupting mutations. The recurrent and rapid loss of Pon1 even suggests that it is adaptive in aquatic mammals. Accordingly, we examined diving and dietary traits across pinniped species as potential driving forces of Pon1 loss. We found that loss is best correlated with diving activity and is likely the result of selective pressures associated with hypoxia and hypoxia-induced inflammation.</p>
A Study of Alirocumab in Participants With Autosomal Dominant Hypercholesterolemia (ADH) and Gain-of-Function Mutations (GOFm) of the Proprotein Convertase Subtilisin Kexin 9 (PCSK9) Gene or Loss-of-F
ClinicalTrials.gov study NCT01604824. IPD Sharing: Not stated. Countries: 2. Publications: 2.
A Study of DB-OTO, an Adeno-Associated Virus (AAV) Based Gene Therapy, in Children/Infants With Hearing Loss Due to Otoferlin Mutations
ClinicalTrials.gov study NCT05788536. IPD Sharing: YES. Countries: 4. Publications: 1.
DupLoss-2: Improved phylogenomic species tree inference under gene duplication and loss
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Data from: Repeated loss of function at HD mating-type genes and of recombination suppression without mating-type locus linkage in anther-smut fungi
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Illuminating the mystery of thylacine extinction: A role for relaxed selection and gene loss
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Rapid reduction of Paraoxonase expression followed by inactivation across semiaquatic mammals suggests adaptive benefit of gene loss
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Data from: Short-term sleep loss alters cytokine gene expression in brain and peripheral tissues and increases plasma corticosterone of zebra finch (Taeniopygia guttata)
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A novel loss-of-function KCNB1 gene variant in a twin with global developmental delay and seizures
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Data from: Loss-of-function mutations in the fruit softening gene POLYGALACTURONASE1 doubled fruit firmness in strawberry
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Data from: Transcriptional remodeling upon light removal in a model cnidarian: losses and gains in gene expression
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