High total water loss driven by low-fat diet in desert-adapted mice.

Availability of food resources is an important driver of survival. Populations must either relocate or adapt to persist in environments where food availability is changing. An optimal diet balances energy gain, water regulation, and nutrition.

Impacts of dietary fat on multi tissue gene expression in the desert-adapted cactus mouse.

Understanding the relationship between dietary fat and physiological responses is crucial in species adapted to arid environments where water scarcity is common. In this study, we present a comprehensive exploration of gene expression across five tissues (kidney, liver, lung, gastrointestinal tract and hypothalamus) and 17 phenotypic measurements, investigating the effects of dietary fat in the desert-adapted cactus mouse (Peromyscus eremicus). We show impacts on immune function, circadian gene regulation and mitochondrial function for mice fed a lower-fat diet compared with mice fed a higher-fat diet.

The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system.

A common goal in evolutionary biology is to discern the mechanisms that produce the astounding diversity of morphologies seen across the tree of life. Aposematic species, those with a conspicuous phenotype coupled with some form of defence, are excellent models to understand the link between vivid colour pattern variations, the natural selection shaping it, and the underlying genetic mechanisms underpinning this variation. Mimicry systems in which species share a conspicuous phenotype can provide an even better model for understanding the mechanisms of colour production in aposematic species, especially if comimics have divergent evolutionary histories.

Impacts of dietary fat on multi tissue gene expression in the desert-adapted cactus mouse.

Understanding the relationship between dietary fat and physiological responses is crucial in species adapted to arid environments where water scarcity is common. In this study, we present a comprehensive exploration of gene expression across five tissues (kidney, liver, lung, gastrointestinal tract, and hypothalamus) and 19 phenotypic measurements, investigating the effects of dietary fat in the desert-adapted cactus mouse ( ). We show impacts on immune function, circadian gene regulation, and mitochondrial function for mice fed a lower-fat diet compared to mice fed a higher-fat diet.

When the tap runs dry: The multi-tissue gene expression and physiological responses of water deprived .

The harsh and dry conditions of desert environments have resulted in genomic adaptations, allowing for desert organisms to withstand prolonged drought, extreme temperatures, and limited food resources. Here, we present a comprehensive exploration of gene expression across five tissues (kidney, liver, lung, gastrointestinal tract, and hypothalamus) and 19 phenotypic measurements to explore the whole-organism physiological and genomic response to water deprivation in the desert-adapted cactus mouse (). The findings encompass the identification of differentially expressed genes and correlative analysis between phenotypes and gene expression patterns across multiple tissues.

When the tap runs dry: the physiological effects of acute experimental dehydration in Peromyscus eremicus.

Desert organisms have evolved physiological, biochemical and genomic mechanisms to survive the extreme aridity of desert environments. Studying desert-adapted species provides a unique opportunity to investigate the survival strategies employed by organisms in some of the harshest habitats on Earth. Two of the primary challenges faced in desert environments are maintaining water balance and thermoregulation.

White-nose syndrome restructures bat skin microbiomes.

Inherent complexities in the composition of microbiomes can often preclude investigations of microbe-associated diseases. Instead of single organisms being associated with disease, community characteristics may be more relevant. Longitudinal microbiome studies of the same individual bats as pathogens arrive and infect a population are the ideal experiment but remain logistically challenging; therefore, investigations like our approach that are able to correlate invasive pathogens to alterations within a microbiome may be the next best alternative.

When the tap runs dry: The physiological effects of acute experimental dehydration in .

Desert organisms have evolved physiological, biochemical, and genomic mechanisms to survive the extreme aridity of desert environments. Studying desert-adapted species provides a unique opportunity to investigate the survival strategies employed by organisms in some of the harshest habitats on Earth. Two of the primary challenges faced in desert environments are maintaining water balance and thermoregulation.

Chromosome size affects sequence divergence between species through the interplay of recombination and selection.

The structure of the genome shapes the distribution of genetic diversity and sequence divergence. To investigate how the relationship between chromosome size and recombination rate affects sequence divergence between species, we combined empirical analyses and evolutionary simulations. We estimated pairwise sequence divergence among 15 species from three different mammalian clades-Peromyscus rodents, Mus mice, and great apes-from chromosome-level genome assemblies.

Prolactin and prolactin receptor expression in the HPG axis and crop during parental care in both sexes of a biparental bird (Columba livia).

During breeding, multiple circulating hormones, including prolactin, facilitate reproductive transitions in species that exhibit parental care. Prolactin underlies parental behaviors and related physiological changes across many vertebrates, including birds and mammals. While circulating prolactin levels often fluctuate across breeding, less is known about how relevant target tissues vary in their prolactin responsiveness via prolactin receptor (PRLR) expression.

Disentangling environmental drivers of circadian metabolism in desert-adapted mice.

Metabolism is a complex phenotype shaped by natural environmental rhythms, as well as behavioral, morphological and physiological adaptations. Metabolism has been historically studied under constant environmental conditions, but new methods of continuous metabolic phenotyping now offer a window into organismal responses to dynamic environments, and enable identification of abiotic controls and the timing of physiological responses relative to environmental change. We used indirect calorimetry to characterize metabolic phenotypes of the desert-adapted cactus mouse (Peromyscus eremicus) in response to variable environmental conditions that mimic their native environment versus those recorded under constant warm and constant cool conditions, with a constant photoperiod and full access to resources.

The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system.

A common goal in evolutionary biology is to discern the mechanisms that produce the astounding diversity of morphologies seen across the tree of life. Aposematic species, those with a conspicuous phenotype coupled with some form of defence, are excellent models to understand the link between vivid colour pattern variations, the natural selection shaping it, and the underlying genetic mechanisms underpinning this variation. Mimicry systems in which multiple species share the same conspicuous phenotype can provide an even better model for understanding the mechanisms of colour production in aposematic species, especially if comimics have divergent evolutionary histories.

Feather Gene Expression Elucidates the Developmental Basis of Plumage Iridescence in African Starlings.

Iridescence is widespread in the living world, occurring in organisms as diverse as bacteria, plants, and animals. Yet, compared to pigment-based forms of coloration, we know surprisingly little about the developmental and molecular bases of the structural colors that give rise to iridescence. Birds display a rich diversity of iridescent structural colors that are produced in feathers by the arrangement of melanin-containing organelles called melanosomes into nanoscale configurations, but how these often unusually shaped melanosomes form, or how they are arranged into highly organized nanostructures, remains largely unknown.

Signal, bias, and the role of transcriptome assembly quality in phylogenomic inference.

Background: Phylogenomic approaches have great power to reconstruct evolutionary histories, however they rely on multi-step processes in which each stage has the potential to affect the accuracy of the final result. Many studies have empirically tested and established methodology for resolving robust phylogenies, including selecting appropriate evolutionary models, identifying orthologs, or isolating partitions with strong phylogenetic signal. However, few have investigated errors that may be initiated at earlier stages of the analysis.

Limited Evidence for Parallel Evolution Among Desert-Adapted Peromyscus Deer Mice.

Warming climate and increasing desertification urge the identification of genes involved in heat and dehydration tolerance to better inform and target biodiversity conservation efforts. Comparisons among extant desert-adapted species can highlight parallel or convergent patterns of genome evolution through the identification of shared signatures of selection. We generate a chromosome-level genome assembly for the canyon mouse (Peromyscus crinitus) and test for a signature of parallel evolution by comparing signatures of selective sweeps across population-level genomic resequencing data from another congeneric desert specialist (Peromyscus eremicus) and a widely distributed habitat generalist (Peromyscus maniculatus), that may be locally adapted to arid conditions.

A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses.

Metabarcoding studies provide a powerful approach to estimate the diversity and abundance of organisms in mixed communities in nature. While strategies exist for optimizing sample and sequence library preparation, best practices for bioinformatic processing of amplicon sequence data are lacking in animal diet studies. Here we evaluate how decisions made in core bioinformatic processes, including sequence filtering, database design, and classification, can influence animal metabarcoding results.

The Genome of the Softshell Clam Mya arenaria and the Evolution of Apoptosis.

Apoptosis is a fundamental feature of multicellular animals and is best understood in mammals, flies, and nematodes, with the invertebrate models being thought to represent a condition of ancestral simplicity. However, the existence of a leukemia-like cancer in the softshell clam Mya arenaria provides an opportunity to re-evaluate the evolution of the genetic machinery of apoptosis. Here, we report the whole-genome sequence for M.

Stress-mediated convergence of splicing landscapes in male and female rock doves.

Background: The process of alternative splicing provides a unique mechanism by which eukaryotes are able to produce numerous protein products from the same gene. Heightened variability in the proteome has been thought to potentiate increased behavioral complexity and response flexibility to environmental stimuli, thus contributing to more refined traits on which natural and sexual selection can act. While it has been long known that various forms of environmental stress can negatively affect sexual behavior and reproduction, we know little of how stress can affect the alternative splicing associated with these events, and less still about how splicing may differ between sexes.

A linked-read approach to museomics: Higher quality de novo genome assemblies from degraded tissues.

High-throughput sequencing technologies are a proposed solution for accessing the molecular data in historical specimens. However, degraded DNA combined with the computational demands of short-read assemblies has posed significant laboratory and bioinformatics challenges for de novo genome assembly. Linked-read or "synthetic long-read" sequencing technologies, such as 10× Genomics, may provide a cost-effective alternative solution to assemble higher quality de novo genomes from degraded tissue samples.

Comparative and population genomics approaches reveal the basis of adaptation to deserts in a small rodent.

Organisms that live in deserts offer the opportunity to investigate how species adapt to environmental conditions that are lethal to most plants and animals. In the hot deserts of North America, high temperatures and lack of water are conspicuous challenges for organisms living there. The cactus mouse (Peromyscus eremicus) displays several adaptations to these conditions, including low metabolic rate, heat tolerance, and the ability to maintain homeostasis under extreme dehydration.

Divergent selection and drift shape the genomes of two avian sister species spanning a saline-freshwater ecotone.

The role of species divergence due to ecologically based divergent selection-or ecological speciation-in generating and maintaining biodiversity is a central question in evolutionary biology. Comparison of the genomes of phylogenetically related taxa spanning a selective habitat gradient enables discovery of divergent signatures of selection and thereby provides valuable insight into the role of divergent ecological selection in speciation. Tidal marsh ecosystems provide tractable opportunities for studying organisms' adaptations to selective pressures that underlie ecological divergence.

A novel CRISPR/Cas9 associated technology for sequence-specific nucleic acid enrichment.

Massively parallel sequencing technologies have made it possible to generate large quantities of sequence data. However, as research-associated information is transferred into clinical practice, cost and throughput constraints generally require sequence-specific targeted analyses. Therefore, sample enrichment methods have been developed to meet the needs of clinical sequencing applications.