scholarly journals Evolution of flower color genes in petunias and their wild relatives

2021 ◽  
Author(s):  
Lucas Wheeler ◽  
Joseph F. Walker ◽  
Julienne Ng ◽  
Rocio Deanna ◽  
Amy Dunbar-Wallis ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Flower Color ◽  
Strongly Correlated ◽  
Flavonoid Pathway ◽  
Evolutionary Transitions ◽  
Coding Regions ◽  
Trace Back ◽  
Molecular Evolutionary Rates ◽  
Myb Genes ◽  
Rates Of Molecular Evolution

Evolutionary transitions in flower color often trace back to changes in the flavonoid biosynthetic pathway and its regulators. In angiosperms, this pathway produces a range of red, purple, and blue anthocyanin pigments. Transcription factor (TF) complexes involving members of the MYB, bHLH, and WD40 protein families control the expression of pathway enzymes. Here, we investigate flavonoid pathway evolution in the Petunieae clade of the tomato family (Solanaceae). Using transcriptomic data from 69 species of Petunieae, we estimated a new phylogeny for the clade. For the 65 species with floral transcriptomes, we retrieved transcripts encoding homologs of 18 enzymes and transcription factors to investigate patterns of evolution across genes and lineages. We found that TFs exhibit faster rates of molecular evolution than their targets, with the highly specialized MYB genes evolving fastest. Using the largest comparative dataset to date, we recovered little support for the hypothesis that upstream enzymes evolve slower than those occupying more downstream positions. However, expression levels inversely correlated with molecular evolutionary rates, while shifts in floral pigmentation were weakly related to changes affecting coding regions. Nevertheless, shifts in floral pigmentation and presence/absence patterns of MYB transcripts are strongly correlated. Intensely pigmented and patterned species express homologs of all three main MYB anthocyanin activators in petals, while pale or white species express few or none. Our findings reinforce the notion that regulators of the flavonoid pathway have a dynamic history, involving higher rates of molecular evolution than structural components, along with frequent changes in expression during color transitions.

scholarly journals Molecular Evolution of Duplicated Amylase Gene Regions in Drosophila melanogaster: Evidence of Positive Selection in the Coding Regions and Selective Constraints in the cis-Regulatory Regions

Genetics ◽  
2001 ◽  
Vol 157 (2) ◽  
pp. 667-677
Author(s):  
Hitoshi Araki ◽  
Nobuyuki Inomata ◽  
Tsuneyuki Yamazaki
Keyword(s):  
Drosophila Melanogaster ◽  
Molecular Evolution ◽  
Positive Selection ◽  
Natural Populations ◽  
Sliding Window ◽  
Selective Constraint ◽  
Proximal Region ◽  
Coding Regions ◽  
Asian Populations ◽  
Flanking Region

Abstract In this study, we randomly sampled Drosophila melanogaster from Japanese and Kenyan natural populations. We sequenced duplicated (proximal and distal) Amy gene regions to test whether the patterns of polymorphism were consistent with neutral molecular evolution. Fst between the two geographically distant populations, estimated from Amy gene regions, was 0.084, smaller than reported values for other loci, comparing African and Asian populations. Furthermore, little genetic differentiation was found at a microsatellite locus (DROYANETSB) in these samples (Gst′=−0.018). The results of several tests (Tajima's, Fu and Li's, and Wall's tests) were not significantly different from neutrality. However, a significantly higher level of fixed replacement substitutions was detected by a modified McDonald and Kreitman test for both populations. This indicates that positive selection occurred during or immediately after the speciation of D. melanogaster. Sliding-window analysis showed that the proximal region 1, a part of the proximal 5′ flanking region, was conserved between D. melanogaster and its sibling species, D. simulans. An HKA test was significant when the proximal region 1 was compared with the 5′ flanking region of Alcohol dehydrogenase (Adh), indicating a severe selective constraint on the Amy proximal region 1. These results suggest that natural selection has played an important role in the molecular evolution of Amy gene regions in D. melanogaster.

scholarly journals Understanding the Overdispersed Molecular Clock

Genetics ◽  
2000 ◽  
Vol 154 (3) ◽  
pp. 1403-1417 ◽  
Author(s):  
David J Cutler
Keyword(s):  
Molecular Evolution ◽  
Molecular Clock ◽  
Time Scale ◽  
Population Parameter ◽  
Deleterious Mutations ◽  
Slow Time ◽  
Slow Time Scale ◽  
Key Population ◽  
Protein Encoding ◽  
Rates Of Molecular Evolution

Abstract Rates of molecular evolution at some protein-encoding loci are more irregular than expected under a simple neutral model of molecular evolution. This pattern of excessive irregularity in protein substitutions is often called the “overdispersed molecular clock” and is characterized by an index of dispersion, R(T) > 1. Assuming infinite sites, no recombination model of the gene R(T) is given for a general stationary model of molecular evolution. R(T) is shown to be affected by only three things: fluctuations that occur on a very slow time scale, advantageous or deleterious mutations, and interactions between mutations. In the absence of interactions, advantageous mutations are shown to lower R(T); deleterious mutations are shown to raise it. Previously described models for the overdispersed molecular clock are analyzed in terms of this work as are a few very simple new models. A model of deleterious mutations is shown to be sufficient to explain the observed values of R(T). Our current best estimates of R(T) suggest that either most mutations are deleterious or some key population parameter changes on a very slow time scale. No other interpretations seem plausible. Finally, a comment is made on how R(T) might be used to distinguish selective sweeps from background selection.

scholarly journals Negative correlation between rates of molecular evolution and flowering cycles in temperate woody bamboos revealed by plastid phylogenomics

2017 ◽  
Vol 17 (1) ◽  
Author(s):  
Peng-Fei Ma ◽  
Maria S. Vorontsova ◽  
Olinirina Prisca Nanjarisoa ◽  
Jacqueline Razanatsoa ◽  
Zhen-Hua Guo ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Negative Correlation ◽  
Woody Bamboos ◽  
Rates Of Molecular Evolution

scholarly journals Does effective population size affect rates of molecular evolution: mitochondrial data for host/parasite species pairs in bees suggests not

2021 ◽  
Author(s):  
Nahid Shokri Bousjein ◽  
Simon Tierney ◽  
Michael Gardner ◽  
Michael Schwarz
Keyword(s):  
Molecular Evolution ◽  
Population Size ◽  
Effective Population Size ◽  
Parasite Species ◽  
Mitochondrial Protein ◽  
Neutral Theory ◽  
Mitochondrial Genes ◽  
Social Parasite ◽  
Effective Population ◽  
Rates Of Molecular Evolution

Adaptive evolutionary theory argues that organisms with larger effective population size (Ne) should have higher rates of adaptive evolution and therefore greater capacity to win evolutionary arm races. However, in some certain cases species with much smaller Ne may be able to survive beside their opponents for an extensive evolutionary time. Neutral theory predicts that accelerated rates of molecular evolution in organisms with exceedingly small Ne is due to the effects of genetic drift and fixation of slightly deleterious mutations. We test this prediction in two obligate social parasite species and their respective host species from the bee tribe Allodapini. The parasites (genus Inquilina) have been locked into a tight coevolutionary arm races with their exclusive hosts (genus Exoneura) for ~15 million years, even though Inquilina exhibit Ne that are an order of magnitude smaller than their host. In this study, we compared rates of molecular evolution between host and parasite using nonsynonymous to synonymous substitution rate ratios (dN/dS) of eleven mitochondrial protein coding genes sequenced from transcriptomes. Tests of selection on mitochondrial genes indicated no significant differences between host and parasite dN/dS, with evidence for purifying selection acting on all mitochondrial genes of host and parasite species. Several potential factors which could weaken the inverse relationship between Ne and rate of molecular evolution are discussed.

GENETIC REPRESENTATION AND GENETIC NEUTRALITY IN GENE EXPRESSION PROGRAMMING

2002 ◽  
Vol 05 (04) ◽  
pp. 389-408 ◽  
Author(s):  
CÂNDIDA FERREIRA
Keyword(s):  
Gene Expression ◽  
Molecular Evolution ◽  
Gene Expression Programming ◽  
Neutral Theory ◽  
Artificial System ◽  
Evolutionary Systems ◽  
Theory Of Evolution ◽  
Coding Regions ◽  
Neutral Mutations

The neutral theory of molecular evolution states that the accumulation of neutral mutations in the genome is fundamental for evolution to occur. The genetic representation of gene expression programming, an artificial genotype/phenotype system, not only allows the existence of non-coding regions in the genome where neutral mutations can accumulate but also allows the controlled manipulation of both the number and the extent of these non-coding regions. Therefore, gene expression programming is an ideal artificial system where the neutral theory of evolution can be tested in order to gain some insights into the workings of artificial evolutionary systems. The results presented in this work show beyond any doubt that the existence of neutral regions in the genome is fundamental for evolution to occur efficiently.

scholarly journals Are rates of molecular evolution in mammals substantially accelerated in warmer environments? Reply

2011 ◽  
Vol 278 (1710) ◽  
pp. 1294-1297 ◽  
Author(s):  
Len N. Gillman ◽  
Paul McBride ◽  
D. Jeanette Keeling ◽  
Howard A. Ross ◽  
Shane D. Wright
Keyword(s):  
Molecular Evolution ◽  
Rates Of Molecular Evolution

scholarly journals Rates and patterns of molecular evolution in marine animals following the Isthmian emergence

1992 ◽  
Vol 6 ◽  
pp. 68-68
Author(s):  
Timothy Collins
Keyword(s):  
Molecular Evolution ◽  
Time Scale ◽  
Published Data ◽  
Rate Variation ◽  
Marine Animals ◽  
Sequence Comparisons ◽  
Western Atlantic ◽  
Taxonomic Groups ◽  
A Site ◽  
Rates Of Molecular Evolution

The marine vicariant event resulting from the Pliocene emergence of the Central American Isthmus presents a unique opportunity for calibrating rates of molecular evolution. The synchronous fragmentation of the ranges of previously widespread taxa into Western Atlantic and Eastern Pacific components (geminates) enables one to make comparisons of rates among higher taxa on the same time scale and to evaluate the regularity of rates of molecular evolution among all species sampled. Other advantages of this approach are that the time scale (approximately 3 Ma) is one of particular interest for evolutionary biologists concerned with speciation and one that minimizes the ambiguities associated with augmentation of divergence values to account for multiple hits at a site. The divergence values derived for geminate pairs are independent, allowing statistical evaluation of variance in rates.The current popularity of the relative rates test as the final arbiter of questions regarding rates and rate variation is primarily a matter of convenience and not a reflection of methodological superiority. A review of the commonly used techniques for calibrating rates of molecular evolution shows that each approach has limitations. Temporally based calibrations of rates are necessary complements to time-independent comparisons.Interpretation of transisthmian molecular comparisons in the literature have in many cases been unduly influenced and confused by molecular clock assumptions and the restriction of studies to single higher-level taxa. Analysis of the apparently contradictory published data as well as new results from sequence comparisons of fishes, urchins and snails suggests a synthesis: taxon specific rates of molecular evolution, with reduced variance within taxonomic groups and great variance among all groups sampled.

Paleontological data and molecular phylogenetic analysis

Paleobiology ◽  
1994 ◽  
Vol 20 (3) ◽  
pp. 259-273 ◽  
Author(s):  
Andrew B. Smith ◽  
D. T. J. Littlewood
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Evolution ◽  
Sequence Data ◽  
Molecular Data ◽  
Total Evidence ◽  
Molecular Phylogenetic Analysis ◽  
Molecular Sequence Data ◽  
Geological Past ◽  
Molecular Phylogenetic ◽  
Rates Of Molecular Evolution

Molecular data are becoming an indispensable tool for the reconstruction of phylogenies. Fossil molecular data remain scarce, but have the potential to resolve patterns of deep branching and provide empirical tests of tree reconstruction techniques. A total evidence approach, combining and comparing complementary morphological, molecular and stratigraphical data from both recent and fossil taxa, is advocated as the most promising way forward because there are several well-established problems that can afflict the analysis of molecular sequence data sometimes resulting in spurious tree topologies. The integration of evidence allows us to: (1) choose suitable taxa for molecular phylogenetic analysis for the question at hand; (2) discriminate between conflicting hypotheses of taxonomic relationship and phylogeny; (3) evaluate procedures and assumptions underlying methods of building trees; and (4) estimate rates of molecular evolution in the geological past. Paleontology offers a set of independent data for comparison and corroboration of analyses and provides the only direct means of calibrating molecular trees, thus giving insight into rates of molecular evolution in the geological past.

Sign in / Sign up

Export Citation Format

Share Document