Biology subjects

Weng, Y.-M.

Publications and source records attributed to Weng, Y.-M..

5 recordsLinked to original sources

bioRxiv2023

Shared features underlying compact genomes and extreme habitat use in chironomid midges

Non-biting midges (family Chironomidae) are found throughout the world in a diverse array of aquatic and terrestrial habitats, can often tolerate harsh conditions such as hypoxia or desiccation, and have consistently compact genomes. Yet we know little about the shared molecular basis for these attributes and how they have evolved across the family. Here, we address these questions by first creating high-quality, annotated reference assemblies for Tanytarsus gracilentus (subfamily Chironominae, tribe Tanytarsini) and Parochlus steinenii (subfamily Podonominae). Using these and other publicly available assemblies, we created a time-calibrated phylogenomic tree for family Chironomidae with outgroups from order Diptera. We used this phylogeny to test for features associated with compact genomes, as well as examining patterns of gene family evolution and positive selection that may underlie chironomid habitat tolerances. Our results suggest that compact genomes evolved in the most recent common ancestor of Chironomidae and Ceratopogonidae, and that this occurred mainly through reductions in non-coding regions (introns, intergenic sequences, and repeat elements). Gene families that significantly expanded in Chironomidae included biological processes that may relate to tolerance of stressful environments, such as temperature homeostasis, inflammatory response, melanization defense response, and trehalose transport. We identified a number of genes with evidence for positive selection in Chironomidae, notably sulfonylurea receptor, peroxiredoxin-1, and protein kinase D. Our results help to understand the genomic basis for the small genomes and extreme habitat use in this widely distributed group. Significance StatementChironomid midges are known for having small genomes and being able to tolerate many forms of environmental stress, yet little is known of the shared features of their genomes that may underlie these traits. We found that reductions in non-coding regions coincide with small chironomid genomes, and we identified duplicated and/or selected genes that may equip chironomids to tolerate harsh conditions. These results describe the key genomic changes in chironomid midges that may explain their ability to inhabit a range of extreme habitats across the world.

genomics↗

bioRxiv2023

A high-quality genome assembly of the ghost moth Druceiella hillmani provides new evidence of genome size augmentation in Hepialidae

Ghost moths are an unusual family of primitive moths (Lepidoptera: Hepialidae) known for their large body size and crepuscular adult activity. These moths represent an ancient lineage, frequently have soil dwelling larvae, and are adapted to high elevations, deserts, and other extreme environments. Despite being rather speciose with more than 700 species, there is a dearth of genomic resources for the family. Here, we present the first high quality, publicly available hepialid genome, generated from an Andean species of ghost moth, Druceiella hillmani. Our genome assembly has a length of 2,586 Mbp with contig N50 of 28.1 Mb and N50 of 29, and BUSCO completeness of 97.1%, making it one of the largest genomes in the order Lepidoptera. Our assembly is a vital resource for future research on ghost moth genomics.

evolutionary biology↗

bioRxiv2023

New genome reveals molecular signatures of adaptation to nocturnality in moth-like butterflies (Hedylidae)

Nearly all animals have a preferred period of daily activity (diel-niche), which is strongly influenced by the light environment. Sensory systems, particularly vision, are adapted to light, and evolutionary transitions to novel light environments, especially light limited ones, can impose strong constraints on eye evolution, color, and motion vision. The adaptive changes in sensory abilities of animals during these transitions, both at the genetic and neural levels, are largely unexplored. Butterflies and moths, with their diverse diel-niche shifts, are an ideal group for investigating the gene evolution linked to these transitions. While most butterflies are day-flying, hedylid butterflies are unique in being primarily nocturnal, and they represent an important evolutionary shift from diurnality to nocturnality in this clade. Here, we sequence the first high-quality Hedylidae genome and functionally annotate genes to understand genomic changes associated with shifts in diel niche. Comparing Hedylidae visual genes against day- and night-flying Lepidoptera species revealed that visual genes are highly conserved, with no major losses. However, hedylid butterfly opsins were more similar to nocturnal moths than their diurnal congeners. Tests on the evolutionary rates (dN/dS) confirmed that color vision opsins were under strong selection, similar to nocturnal moths. We propose that a convergent event of sequence evolution took place when these butterflies became nocturnal, approximately 98 million years ago.

evolutionary biology↗

bioRxiv2023

The genomic landscape of metallic color variation in ground beetles

The metallic color variation of beetles is a spectacular feature that has inspired diverse human cultures. However, little is known about the genetic basis of this trait or its ecological importance. In this study, we characterize the geographical distribution, optical mechanism, genetic basis, and ecological and evolutionary importance of metallic color variation in the Nebria ingens complex, an alpine ground beetle in the Sierra Nevada, California. We find that elytral color varies continuously across two allopatric species (from black N. ingens to green N. riversi), with hybrid populations showing intermediate coloration, and we demonstrate that the metallic color is generated from multilayer reflectors in the epicuticle of the elytra. By applying association mapping in natural populations (wild-GWAS) using high-density genotype variants, we identify five promising candidate genes covarying with metallic variation, with known roles in cuticle formation and pigmentation pathways. This finding, together with a significant correlation between color variation and water availability, suggests that metallic variation evolves as a local adaptation to environmental variation in the N. ingens complex.

evolutionary biology↗

bioRxiv2023

Evidence for admixture and rapid evolution during glacial climate change in an alpine specialist

The pace of current climate change is expected to be problematic for alpine flora and fauna, as their adaptive capacity may be limited by small population size. Yet despite substantial genetic drift following post-glacial recolonization of alpine habitats, alpine species are notable for their success in surviving highly heterogeneous environments. Population genomic analyses demonstrating how alpine species have adapted to novel environments with limited genetic diversity remain rare, yet are important in understanding the potential for species to respond to contemporary climate change. In this study, we explored the evolutionary history of alpine ground beetles in the Nebria ingens complex, including the demographic and adaptive changes that followed the last glacier retreat. Using whole genome data from hundreds of beetles, to test alternative models of evolutionary divergence in the species complex, we found evidence that the Nebria ingens complex has been formed by past admixture of lineages responding to glacial cycles. Recolonization of alpine sites involved a distributional range shift to higher elevation, which was accompanied by a reduction in suitable habitat and the emergence of complex spatial genetic structure. We also used genome-wide association and genotype-environment association methods to look for genetic pathways involved in adaptation to heterogeneous new environments during this range shift. The identified genes were enriched for functions broadly associated with abiotic stress responses, with strong evidence for adaptation to hypoxia-related pathways. The results demonstrate that despite rapid environmental changes, alpine beetles in the N. ingens complex have shown rapid physiological evolution.

evolutionary biology↗