A. Suh

Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective

The paper presents a crowd-sourcing approach to manually curate and classify transposable elements (TEs) from tardigrade genomes, resulting in the discovery of hundreds of new TEs.

A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats

This study investigates convergent evolution in open-habitat chats using phylogenomic analyses to assess the roles of ILS, introgression, and novel mutations.

Caecilian genomes reveal molecular basis of adaptation and convergent evolution of limblessness in snakes and caecilians.

The paper analyzes caecilian genomes to identify molecular mechanisms underlying limblessness and convergent evolution with snakes, finding shared genetic targets involved in limb development.

The genomic basis of the plant island syndrome in Darwin's giant daisies

This study characterizes the genomic basis of the plant island syndrome in Darwin's giant daisies by analyzing the genome of Scalesia atractyloides, identifying subgenomes, polyploidization events, and genes under selection.

The hidden structural variability in avian genomes

This study identifies high structural variant density on avian W chromosomes using long-read and linked-read assemblies, revealing greater genetic variability than previously thought.

Horizontal transposon transfer and its implications for the ancestral ecology of hydrophiine snakes

The paper examines horizontal transposon transfer in Hydrophiinae snakes to infer their ancestral ecological route from Asia to Australia.

Genome stability is in the eye of the beholder: recent retrotransposon activity varies significantly across avian diversity

This study examines CR1 retrotransposon activity across avian species, finding significant variation in TE expansion rates among orders and clades, challenging the notion of low TE activity in birds.

Recurrent chromosome reshuffling and the evolution of neo-sex chromosomes in parrots

This study identifies recurrent chromosome fusions and gene losses in parrots, revealing the role of transposable elements and genetic drift in neo-sex chromosome evolution.

The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

The paper identifies the avian W chromosome as a reservoir for active endogenous retroviruses, potentially contributing to female-biased mutational load and genetic incompatibilities.

New environment, new invaders - repeated horizontal transfer of LINEs to sea snakes

The paper identifies repeated horizontal transfer of LINE retrotransposons in marine sea snakes, suggesting marine environments facilitate transposon transfer and genomic novelty.

Linked-read sequencing enables haplotype-resolved resequencing at population scale

This study shows that linked-read sequencing at moderate depth can produce high-quality haplotype-resolved genome data for population-scale resequencing in birds.

Programmed DNA elimination of germline development genes in songbirds

The paper identifies and characterizes the germline-restricted chromosome (GRC) in zebra finches, revealing its dynamic evolution and functional role in germline-soma genome differentiation.

Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds

This study investigates the evolutionary history of sex chromosomes in songbirds, identifying four recombination suppression steps and a burst of retrotransposon activity associated with strata formation.

The hidden elasticity of avian and mammalian genomes

The paper investigates genome size homeostasis in mammals and birds by analyzing transposable element (TE) expansion and DNA loss over 100 million years, revealing large segmental deletions as a key mechanism.

De-novo emergence and template switching of SINE retroposons during the early evolution of passerine birds

This study uses SINE retroposon presence/absence patterns to resolve passerine bird phylogeny, finding SINE activity in their common ancestor and recent activity in suboscines via template switching.