Biology subjects

Asar, Y.

Publications and source records attributed to Asar, Y..

6 recordsLinked to original sources

bioRxiv2026

Rates of molecular and morphological evolution are uncoupled across the eukaryote Tree of Life

A vast degree of phenotypic variation can be seen across lineages of eukaryotes. Although at least part of this diversity has a genomic basis, it is unclear whether there are broad-scale links that can be detected between rates of genomic and phenotypic evolution. The presence of a correlation would imply the action of shared drivers, such as mutational or adaptive processes that occur on a genome- and organism-wide scale. We investigated this question by using a phylogenetic approach to test for correlations between molecular and morphological evolutionary rates. We analysed 60 data sets of combined nucleotide sequences and discrete morphological characters, representing a diverse range of eukaryotes that include alveolates, plants, invertebrates, fishes, and tetrapods. Using a maximum-likelihood phylogenetic approach based on sister-pair contrasts, we found very little evidence of any link between rates of molecular and morphological evolution, a striking result given the scale and taxonomic breadth of our analyses. Our results point to contrasting evolutionary dynamics underlying genomes and phenotypic traits, most likely involving differing extents of selection. These processes have also led to greater variation in morphological evolutionary rates across lineages, whereas molecular evolution is more clocklike. Our results have implications for how evolutionary change should be modelled in phylogenetic analyses of combined data sets. Overall, our study reveals the discrepancies in evolutionary drivers that act at the genomic and phenotypic levels across the eukaryotic Tree of Life.

evolutionary biology↗

bioRxiv2026

Developmental stage-dependent decoupling of molecular and phenotypic responses to heat in wheat grain

Heatwaves during flowering and grain development threaten global wheat production, yet the extent to which developmental stage shapes molecular and phenotypic responses remains unclear. Here, we investigated whether heat stress (36/29{degrees}C for 48 h) imposed at closely spaced developmental stages surrounding anthesis generates stage-specific molecular responses that are associated with subsequent effects on grain properties. Heat exposure increased floret abortion most strongly when it was imposed at the trinucleate stage (TN; [~]48%) compared with the binucleate (BN) and early post-anthesis stages. Methylation levels were largely unaffected by prior heat treatments; however, heat induced stage- and locus-specific methylation changes, particularly at BN. Spatial RNA-seq revealed tissue-specific heat responses that were distinctively different in BN and TN. Integrated metabolomic analyses revealed stage-dependent metabolic reprogramming, including shifts towards stress-associated pathways. Despite heat stress at BN generating broader molecular reprogramming in developing grain, exposure at TN produced stronger effects on grain set and composition, revealing a decoupling between the magnitude of responses and phenotypic outcomes. Together, these findings demonstrate that subtle differences in developmental stage influence the complex molecular responses to heat and subsequent grain properties.

plant biology↗

bioRxiv2025

Unveiling the tempo of molecular and morphological evolution across the Tree of Life

The evolution of Earths vast genetic and morphological diversity has been explained by an array of macroevolutionary models. At opposite ends of the spectrum lie two contrasting evolutionary models: phyletic gradualism and punctuated equilibria. Under a phyletic gradualism framework, evolutionary change accumulates along lineages and species are steadily transformed into new forms over time. In contrast, under punctuated equilibria, evolutionary change tends to occur in bursts at speciation events. Previous studies of molecular and morphological data have found varying levels of support for the two evolutionary models. We examined these models using comprehensive molecular and morphological data sets from 40 clades across the Tree of Life. Testing for associations between species richness and the amount of evolutionary change in sister clades, we find little evidence to support the punctuated equilibria model. However, we found high levels of among-lineage rate variation in molecular evolution and particularly morphological evolution. Our comparison of coding and non-coding genomic regions revealed contrasting patterns of among-lineage rate variation, without clear trends across taxa. Our study confirms that heterotachy is a dominant feature in macroevolution and that molecular and morphological evolution cannot simply be described by either a gradual or punctuated model.

evolutionary biology↗

bioRxiv2024

Evolutionary rates of nuclear and organellar genomes are linked in land plants

O_LIPlants carry genetic material in three compartments, the nuclear, mitochondrial, and chloroplast genomes. These genomes interact with each other to various degrees and are subject to shared evolutionary drivers exerted by their host organisms. However, it is not clear whether the three plant genomes display covarying evolutionary signals. C_LIO_LIWe tested for correlated evolutionary rates between nuclear and organellar genomes using extensive data sets from the major clades of land plants (Embryophyta), including mosses, ferns, gymnosperms, and angiosperms. To examine the evolutionary dynamics in parasitic angiosperms, which are under distinctive selective pressures, we analysed data sets from mistletoes, broomrapes, sandalwoods, and rafflesias. C_LIO_LIEvolutionary rates of nuclear and organellar genomes were positively linked in land plants, except in the parasitic angiosperms. We also found similar positive correlations for rates of nonsynonymous and synonymous change between nuclear and organellar genomes. Our results also reveal extensive evolutionary rate variation across land plant taxa. C_LIO_LIOverall, we find that nuclear, mitochondrial, and chloroplast genomes in land plants share similar drivers of mutaNon rates, despite considerable variaNon in life history, morphology, and genome sizes among clades. Our findings lay the foundaNon for further exploraNon of the impact of co-evoluNonary interacNons on shared evoluNonary rates between genomes. C_LI

evolutionary biology↗

bioRxiv2022

Evaluating the accuracy of methods for detecting correlated rates of molecular and morphological evolution

Determining the link between genomic and phenotypic evolution is a fundamental goal in evolutionary biology. Insights into this link can be gained by using a phylogenetic approach to test for correlations between rates of molecular and morphological evolution. However, there has been persistent uncertainty about the relationship between these rates, partly because conflicting results have been obtained using various methods that have not been examined in detail. We carried out a simulation study to evaluate the performance of five statistical methods for detecting correlated rates of evolution. Our simulations explored the evolution of molecular sequences and morphological characters under a range of conditions. Of the methods tested, Bayesian relaxed-clock estimation of branch rates was able to detect correlated rates of evolution correctly in the largest number of cases. This was followed by correlations of root-to-tip distances, Bayesian model selection, independent sister-pairs contrasts, and likelihood-based model selection. As expected, the power to detect correlated rates increased with the amount of data, both in terms of tree size and number of morphological characters. Likewise, the performance of all five methods improved when there was greater rate variation among lineages. We then applied these methods to a data set from flowering plants and did not find evidence of a correlation in evolutionary rates between genomic data and morphological characters. The results of our study have practical implications for phylogenetic analyses of combined molecular and morphological data sets, and highlight the conditions under which the links between genomic and phenotypic rates of evolution can be evaluated quantitatively.

evolutionary biology↗

bioRxiv2021

Patterns of gene expression in pollen of cotton (Gossypium hirsutum) indicate down-regulation as a feature of thermotolerance

Reproductive performance in plants is impaired as maximum temperatures consistently approach 40{degrees}C. However, the timing of heatwaves critically affects their impact. We studied the molecular responses of cotton male reproductive stages, to investigate the vulnerability of maturing pollen to high temperature. Tetrads, uninucleate and binucleate microspores, and mature pollen were subjected to SWATH-MS and RNA-seq analyses after exposure to 38/28{degrees}C (day/night) for 5 days. The results indicated that molecular signatures were down-regulated over developmental stages in response to heat. This was more evident in leaves where three-quarters of differentially changed proteins were decreased in abundance. Functional analysis showed that translation of genes increased in tetrads after exposure to heat; however, the reverse pattern was observed in mature pollen and leaves. Proteins involved in transport were highly abundant in tetrads, whereas in later stages of development and leaves, heat suppressed cell-to-cell communication. Moreover, a large number of heat shock proteins (HSPs) were identified in heat-affected tetrads, but these proteins were less abundant in mature pollen and leaves. We speculate that the sensitivity of tetrad cells to heat is related to increased activity of translation involved in non-essential pathways. Molecular signatures during pollen development after heatwaves provide markers for future genetic improvement.

plant biology↗