adaptation

Pervasive genomic signatures of local adaptation to altitude across highland specialist Andean hummingbird populations

Populations along steep environmental gradients are subject to differentiating selection that can result in local adaptation, despite countervailing gene flow and genetic drift. In montane systems, where species are often restricted to narrow ranges …

Adapt or Live: Adaptation, Convergent Evolution, and Plesiomorphy

A diversity of cranial phenotypes and feeding ecologies characterizes phyllostomid bats. However, many subfamilies share a similar insect-feeding morphotype, apparently stable over millions of generations. Is the diversity of phyllostomid traits …

Six reference-quality genomes reveal evolution of bat adaptations

Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity and unique immunity. High-quality genomes are crucial for understanding the molecular basis and evolution of these traits. Here we incorporated long-read sequencing and state-of-the-art scaffolding protocols1 to generate, to our knowledge, the first reference-quality genomes of six bat species (Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pipistrellus kuhlii and Molossus molossus). We integrated gene projections from our ‘Tool to infer Orthologs from Genome Alignments’ (TOGA) software with de novo and homology gene predictions as well as short- and long-read transcriptomics to generate highly complete gene annotations. To resolve the phylogenetic position of bats within Laurasiatheria, we applied several phylogenetic methods to comprehensive sets of orthologous protein-coding and noncoding regions of the genome, and identified a basal origin for bats within Scrotifera. Our genome-wide screens revealed positive selection on hearing-related genes in the ancestral branch of bats, which is indicative of laryngeal echolocation being an ancestral trait in this clade. We found selection and loss of immunity-related genes (including pro-inflammatory NF-κB regulators) and expansions of anti-viral APOBEC3 genes, which highlights molecular mechanisms that may contribute to the exceptional immunity of bats. Genomic integrations of diverse viruses provide a genomic record of historical tolerance to viral infection in bats. Finally, we found and experimentally validated bat-specific variation in microRNAs, which may regulate bat-specific gene-expression programs. Our reference-quality bat genomes provide the resources required to uncover and validate the genomic basis of adaptations of bats, and stimulate new avenues of research that are directly relevant to human health and disease1.

The allometry of daily energy expenditure in hummingbirds: an energy budget approach

Within‐clade allometric relationships represent standard laws of scaling between energy and size, and their outliers provide new avenues for physiological and ecological research. According to the metabolic level boundaries hypothesis, metabolic …

Tissue Collection of Bats for-Omics Analyses and Primary Cell Culture

As high-throughput sequencing technologies advance, standardized methods for high quality tissue acquisition and preservation allow for the extension of these methods to non-model organisms. A series of protocols to optimize tissue collection from …

Parallel molecular evolution in pathways, genes, and sites in high-elevation hummingbirds revealed by comparative transcriptomics

High-elevation organisms experience shared environmental challenges that include low oxygen availability, cold temperatures, and intense ultraviolet radiation. Consequently, repeated evolution of the same genetic mechanisms may occur across …

Molecular evolution of growth hormone and insulin-like growth factor 1 receptors in long-lived, small-bodied mammals

Mammals typically display a robust positive relationship between lifespan and body size. Two groups that deviate markedly from this pattern are bats and African mole-rats, with members of both groups being extremely long-lived given their body size, …