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opencc-by-4.0Feb 2014View details →

Figure 1 in The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review

Figure 1. Relationships between molluscan classes as recovered by Smith et al. (2011).

opencc-by-4.0Feb 2014View details →

Figure 3 in The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review

Figure 3. Summary tree of phylogenetic relationships between higher taxa.

opencc-zeroDec 2016View details →

Data from: Convergently evolved toxic secondary metabolites in plants drive the parallel molecular evolution of insect resistance

Natural selection imposed by natural toxins has led to striking levels of convergent evolution at the molecular level. Cardiac glycosides represent a group of plant toxins that block the Na,K-ATPase, a vital membrane protein in animals. Several herbivorous insects have convergently evolved resistant Na,K-ATPases, and in some species, convergent gene duplications have also arisen, likely to cope with pleiotropic costs of resistance. To understand the genetic basis and predictability of these adaptations, we studied five independent lineages of leaf-mining flies (Diptera: Agromyzidae). These flies have colonized host plants in four botanical families that convergently evolved cardiac glycosides of two structural types: cardenolides and bufadienolides. We compared each of six fly species feeding on such plants to a phylogenetically related but nonadapted species. Irrespective of the type of cardiac glycoside in the host plant, five out of six exposed species displayed substitutions in the cardiac glycoside–binding site of the Na,K-ATPase that were previously described in other insect orders; in only one species was the gene duplicated. In vitro assays of nervous tissue extractions confirmed that the substitutions lead to increased resistance of the Na,K-ATPase. Our results demonstrate that target site insensitivity of Na,K-ATPase is a common response to dietary cardiac glycosides leading to highly predictable amino acid changes; nonetheless, convergent evolution of gene duplication for this multifunctional enzyme appears more constrained.

opencc-zeroDec 2012View details →

Data from: Taller plants have lower rates of molecular evolution

Rates of molecular evolution have a central role in our understanding of many aspects of species' biology. However, the causes of variation in rates of molecular evolution remain poorly understood, particularly in plants. Here we show that height accounts for about one-fifth of the among-lineage rate variation in the chloroplast and nuclear genomes of plants. This relationship holds across 138 families of flowering plants, and when accounting for variation in species richness, temperature, ultraviolet radiation, latitude and growth form. Our observations can be explained by a link between height and rates of genome copying in plants, and we propose a mechanistic hypothesis to account for this—the 'rate of mitosis' hypothesis. This hypothesis has the potential to explain many disparate observations about rates of molecular evolution across the tree of life. Our results have implications for understanding the evolutionary history and future of plant lineages in a changing world.

opencc-zeroDec 2013View details →

Data from: Molecular evolution accompanying functional divergence of duplicated genes along the plant starch biosynthesis pathway

Background: Starch is the main source of carbon storage in the Archaeplastida. The Starch Biosynthesis Pathway (SBP) emerged from cytosolic glycogen metabolism shortly after plastid endosymbiosis and was redirected to the plastid stroma during the green lineage divergence. The SBP is a complex network of genes, most of which are members of large multigene families. While some gene duplications occurred in the Archaeplastida ancestor, most were generated during the SBP redirection process, and the remaining few paralogs were generated through compartmentalization or tissue specialization during the evolution of the land plants. In the present study, we tested models of duplicated gene evolution in order to understand the evolutionary forces that have led to the development of SBP in angiosperms. We combined phylogenetic analyses and tests on the rates of evolution along branches emerging from major duplication events in six gene families encoding SBP enzymes. Results: We found evidence of positive selection along branches following cytosolic or plastidial specialization in two starch phosphorylases and identified numerous residues that exhibited changes in volume, polarity or charge. Starch synthases, branching and debranching enzymes functional specializations were also accompanied by accelerated evolution. However, none of the sites targeted by selection corresponded to known functional domains, catalytic or regulatory. Interestingly, among the 13 duplications tested, 7 exhibited evidence of positive selection in both branches emerging from the duplication, 2 in only one branch, and 4 in none of the branches. Conclusions: The majority of duplications were followed by accelerated evolution targeting specific residues along both branches. This pattern was consistent with the optimization of the two sub-functions originally fulfilled by the ancestral gene before duplication. Our results thereby provide strong support to the so-called "Escape from Adaptive Conflict" (EAC) model. Because none of the residues targeted by selection occurred in characterized functional domains, we propose that enzyme specialization has occurred through subtle changes in affinity, activity or interaction with other enzymes in complex formation, while the basic function defined by the catalytic domain has been maintained.

Figure 5 from: Chew M, Abdul Rahim A, Mohd Yusof NY (2018) A new species of Eisothistos (Isopoda, Cymothoida) and first molecular data on six species of Anthuroidea from the Peninsular Malaysia. Zoosystematics and Evolution 94(1): 73-81. https://doi.org/10.3897/zse.94.23000

Figure 5 Eisothistos tiomanensis sp. n. All scales represent 0.1 mm.

Figure 3 from: Chew M, Abdul Rahim A, Mohd Yusof NY (2018) A new species of Eisothistos (Isopoda, Cymothoida) and first molecular data on six species of Anthuroidea from the Peninsular Malaysia. Zoosystematics and Evolution 94(1): 73-81. https://doi.org/10.3897/zse.94.23000

Figure 3 Eisothistos tiomanensis sp. n. All scales represent 0.1 mm.

Figure 2 from: Chew M, Abdul Rahim A, Mohd Yusof NY (2018) A new species of Eisothistos (Isopoda, Cymothoida) and first molecular data on six species of Anthuroidea from the Peninsular Malaysia. Zoosystematics and Evolution 94(1): 73-81. https://doi.org/10.3897/zse.94.23000

Figure 2 Apanthura stocki. All scales represent 0.1 mm.

Figure 4 from: Chew M, Abdul Rahim A, Mohd Yusof NY (2018) A new species of Eisothistos (Isopoda, Cymothoida) and first molecular data on six species of Anthuroidea from the Peninsular Malaysia. Zoosystematics and Evolution 94(1): 73-81. https://doi.org/10.3897/zse.94.23000

Figure 4 Eisothistos tiomanensis sp. n. All scales represent 0.1 mm.

opencc-by-sa-4.0Apr 2018View details →

Environmental fluctuations accelerate molecular evolution of thermal tolerance in a marine diatom

Data (other than molecular data, which are in the Sequence Read Archive as Bioproject PRJNA397360) for "Environmental fluctuations accelerate molecular evolution of thermal tolerance in a marine diatom" https://doi.org/10.1038/s41467-018-03906-5.  1. "Data Figure01 natcomms Schaum et al.xlsx" contains data to analyse (and produce Figure 1A and B) for the fitness trajectories and thermal tolerance curves of growth. 2. The raw growth rate data for the thermal tolerance curves of growth are provided in  separate files:  Data_thermal_tolerance_growth_t000.csv,Data_thermal_tolerance_growth_t100.csv,Data_thermal_tolerance_growth_t300.csv contain the growth rates across a temperature gradient for the ancestor (t000), the evolved samples after 100 generations (t100) and after 300 generations (t300). In these files, assayT is the assay temperature in degrees C, selected is the selection regime, and bore is the biological replicate. r is the growth rate, K is carrying capacity. quasi r2 (or 2) is a measure of the goodness of the fit that the growth rate was calculated from.  pa is an identification column that gives a unique name to individual bioreplicate/ assay temperature/selection regime combinations.  3. Photosynthesis and respiration data for Figure 2 a-e is contained in the files "tdep_metab_t300_32" for 32 degree C data after 300 generations "tdep_metab_t000" for the ancestor "tdep_metab_all_else" for all other metabolism data, i.e. photosynthesis and respiration data after 100 and 300 generations of evolution in all selection environments.  As this is a large amount of data, they are saved in RDS format. they can be opened in any version of R using the command readRDS(name of file here).  4. File "Data_cell_volume_CNratio_etc" contains pg C per cell, CN ratios, NP ratios, and CN ratios, as well as cell volume and chlorophyll to carbon ratios for all selection regimes in the ancestor and the evolved lineages.  5. File "Data_cell_size_RNAProtein_etc.csv" contains data on size in µm, RNA and protein per cell, as well as silicate per cell.

Molecular Characterization of Patients With Acute Myeloid Leukemia and the Impact of Clonal Evolution in the Response to Therapeutic Treatments

ClinicalTrials.gov study NCT06764459. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.

Molecular Profile of the Evolution of Inclusion Body Myositis

ClinicalTrials.gov study NCT03299335. IPD Sharing: Not stated. Countries: 1. Publications: 0.

Visual Study of Molecular Genotype in Glioma Evolution

ClinicalTrials.gov study NCT03750890. IPD Sharing: Not stated. Countries: 1. Publications: 0.

Analysis of Clinical and Molecular Genetic Data Influencing the Evolution and Response to Therapy of ADPKD Patients (Autosomal Dominant Polycystic Kidney Disease)

ClinicalTrials.gov study NCT02887729. IPD Sharing: Not stated. Countries: 1. Publications: 0.

openGEO-OpenMay 2019View details →

geo24/100

Global DNA methylation reflects spatial heterogeneity and molecular evolution of lung adenocarcinomas

GEO Series GSE114989. Homo sapiens. 40 samples. Type: Methylation profiling by genome tiling array.