A Codon Model for Associating Phenotypic Traits with Altered Selective Patterns of Sequence Evolution

Halabi, Keren; Karin, Eli Levy; Guéguen, Laurent; Mayrose, Itay

doi:10.1093/sysbio/syaa087

Cited by 8 publications

(7 citation statements)

References 76 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This result highlights the importance of developing phylogenetic genotype-tophenotype (PhyloG2P) approaches tailored for detecting the signals of different mechanisms that can alter phenotype, from variation in coding sequences (e.g. Halabi et al 2021) to shifts in gene content (Kiefer et al 2019), to regulatory changes (Hu et al 2019;Larter et al 2018). Integrating these approaches can lead to a deeper understanding of how pathway structure and function shape phenotypic space and the potential for moving through it.…”

Section: Discussionmentioning

confidence: 99%

Transcription factors evolve faster than their structural gene targets in the flavonoid pigment pathway

Wheeler¹,

Walker²,

Ng³

et al. 2021

Preprint

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionmentioning

confidence: 99%

Transcription factors evolve faster than their structural gene targets in the flavonoid pigment pathway

Wheeler¹,

Walker²,

Ng³

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…Second, they assume that the evolution of the phenotype is known without uncertainty.

approaches that can handle uncertainty in the evolution of the phenotype when reconstructing the evolution of gene sequences have recently been proposed, but remain to be extended to the site level ( Halabi et al 2021 ). Third, they rely on the comparison of two scenarios, one of which assumes homogeneity of the process across the phylogeny.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of Methods to Detect Shifts in Directional Selection at the Genome Scale

Duchemin

Lanore

Veber

et al. 2022

Molecular Biology and Evolution

View full text Add to dashboard Cite

Identifying the footprints of selection in coding sequences can inform about the importance and function of individual sites. Analyses of the ratio of non-synonymous to synonymous substitutions (dN/dS) have been widely used to pinpoint changes in the intensity of selection, but cannot distinguish them from changes in the direction of selection, i.e., changes in the fitness of specific amino acids at a given position. A few methods that rely on amino acid profiles to detect changes in directional selection have been designed, but their performance have not been well characterized. In this paper, we investigate the performance of 6 of these methods.We evaluate them on simulations along empirical phylogenies in which transition events have been annotated, and compare their ability to detect sites that have undergone changes in the direction or intensity of selection to that of a widely used dN/dS approach, codeml’s branch-site model A. We show that all methods have reduced performance in the presence of biased gene conversion but not CpG hypermutability. The best profile method, Pelican, a new implementation of (Tamuri et al., 2009), performs as well as codeml in a range of conditions except for detecting relaxations of selection, and performs better when tree length increases, or in the presence of persistent positive selection. It is fast, enabling genome-scale searches for site-wise changes in the direction of selection associated with phenotypic changes.

show abstract

“…Secondly, they assume that the evolution of the phenotype is known without uncertainty. d N /d S approaches that can handle uncertainty in the evolution of the phenotype when reconstructing the evolution of gene sequences have recently been proposed, but remain to be extended to the site level [Halabi et al, 2021]. Thirdly, they rely on the comparison of two scenarios, one of which assumes homogeneity of the process across the phylogeny.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of methods to detect shifts in directional selection at the genome scale

Duchemin

Veber

Boussau

2022

Preprint

View full text Add to dashboard Cite

Identifying the footprints of selection in coding sequences can inform about the importance and function of individual sites. Analyses of the ratio of non-synonymous to synonymous substitutions (dN/dS) have been widely used to pinpoint changes in the intensity of selection, but cannot distinguish them from changes in the direction of selection, i.e., changes in the fitness of specific amino acids at a given position. A few methods that rely on amino acid profiles to detect changes in directional selection have been designed, but their performance have not been well characterized. In this paper, we investigate the performance of 6 of these methods. We evaluate them on simulations along empirical phylogenies in which transition events have been annotated, and compare their ability to detect sites that have undergone changes in the direction or intensity of selection to that of a widely used dN/dS approach, codeml's branch-site model A. We show that all methods have reduced performance in the presence of biased gene conversion but not CpG hypermutability. The best profile method, Pelican, a new implementation of [Tamuri et al., 2009], performs as well as codeml in a range of conditions except for detecting relaxations of selection, and performs better when tree length increases, or in the presence of persistent positive selection. It is fast, enabling genome-scale searches for site-wise changes in the direction of selection associated with phenotypic changes.

show abstract

A Codon Model for Associating Phenotypic Traits with Altered Selective Patterns of Sequence Evolution

Cited by 8 publications

References 76 publications

Transcription factors evolve faster than their structural gene targets in the flavonoid pigment pathway

Transcription factors evolve faster than their structural gene targets in the flavonoid pigment pathway

Evaluation of Methods to Detect Shifts in Directional Selection at the Genome Scale

Evaluation of methods to detect shifts in directional selection at the genome scale

Contact Info

Product

Resources

About