Species Limits and Hybridization in Andean Leaf-Eared Mice ().

Leaf-eared mice (genus ) are among the most widespread and abundant small mammals in the Andean Altiplano, but species boundaries and distributional limits are often poorly delineated due to sparse survey data from remote mountains and high-elevation deserts. Here, we report a combined analysis of mitochondrial DNA variation and whole-genome sequence (WGS) variation in mice to delimit species boundaries, to assess the timescale of diversification of the group, and to examine evidence for interspecific hybridization. Estimates of divergence based on data suggest that most diversification of occurred during the past 3 million years.

Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements.

Pangenome methods have the potential to uncover hitherto undiscovered sequences missing from established reference genomes, making them useful to study evolutionary and speciation processes in diverse organisms. The cichlid fishes of the East African Rift Lakes represent one of nature's most phenotypically diverse vertebrate radiations, but single-nucleotide polymorphism (SNP)-based studies have revealed little sequence difference, with 0.1%-0.

Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes.

Background: East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. We set out to bridge this gap and to understand the interactions between TEs and their cichlid hosts.

Species limits and hybridization in Andean leaf-eared mice ().

Leaf-eared mice (genus ) are among the most widespread and abundant small mammals in the Andean Altiplano, but species boundaries and distributional limits are often poorly delineated due to sparse survey data from remote mountains and high-elevation deserts. Here we report a combined analysis of mitochondrial DNA variation and whole-genome sequence (WGS) variation in mice to delimit species boundaries, to assess the timescale of diversification of the group, and to examine evidence for interspecific hybridization. Estimates of divergence dates suggest that most diversification of occurred during the past 3 million years.

Rotate: A command-line program to rotate circular DNA sequences to start at a given position or string.

Sequences derived from circular DNA molecules (i.e. most bacterial, viral and plastid genomes) are expected to be linearised and rotated to a common start position for most downstream analyses including alignment.

Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes.

East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development.

Gene losses in the common vampire bat illuminate molecular adaptations to blood feeding.

Vampire bats are the only mammals that feed exclusively on blood. To uncover genomic changes associated with this dietary adaptation, we generated a haplotype-resolved genome of the common vampire bat and screened 27 bat species for genes that were specifically lost in the vampire bat lineage. We found previously unknown gene losses that relate to reduced insulin secretion ( and ), limited glycogen stores (), and a unique gastric physiology ().

Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation.

Background: Baleen whales (Mysticeti) are the largest animals on earth and their evolutionary history has been studied in detail, but some relationships still remain contentious. In particular, reconstructing the phylogenetic position of the gray whales (Eschrichtiidae) has been complicated by evolutionary processes such as gene flow and incomplete lineage sorting (ILS). Here, whole-genome sequencing data of the extant baleen whale radiation allowed us to identify transposable element (TE) insertions in order to perform phylogenomic analyses and measure germline insertion rates of TEs.