Single nucleotide polymorphism (SNP) discovery and genotyping are essential to genetic mapping. There remains a need for simple, inexpensive platform that allows high-density SNP in large populations. Here we describe the sequencing of restriction-site associated DNA (RAD) tags, which identified more than 13,000 SNPs, mapped three traits two model organisms, using less half capacity one Illumina run. We demonstrated different marker densities can be attained by choice restriction enzyme....

Most adaptation is thought to occur through the fixation of numerous alleles at many different loci. Consequently, independent evolution similar phenotypes predicted genetic mechanisms. The basis still largely unknown, however, and it unclear whether new environments utilizes ubiquitous small-effect polygenic variation or large-effect a small number To address this question, we examined bony armor loss in three freshwater populations Alaskan threespine stickleback, Gasterosteus aculeatus ,...

Population genomic studies are beginning to provide a more comprehensive view of dynamic genome-scale processes in evolution. Patterns architecture, such as islands increased divergence, may be important for adaptive population differentiation and speciation. We used next-generation sequencing data examine the patterns local long-distance linkage disequilibrium (LD) across oceanic freshwater populations threespine stickleback, useful model evolution looked associations between LD signatures...

Understanding how genetic variation is partitioned across genomes within and among populations a fundamental problem in ecological evolutionary genetics. To address this problem, we studied the threespine stickleback fish, which has repeatedly undergone parallel phenotypic differentiation when oceanic fish have invaded freshwater habitats. While significant research been performed using from geographic regions that deglaciated last 20 000 years, less focused on predate glacial maximum. We...

How do developmental mechanisms evolve to control changing skeletal morphology, the shapes and sizes of individual bones? We address this question with studies opercle (OP), a large facial bone that has undergone marked morphological evolution in ray-finned fish. Attributes for analysis motivated us examine how OP shape size develop threespine sticklebacks, model system understanding vertebrate evolution. find when Alaskan anadromous fish take up permanent residence lakes, they smaller...

The role of environment as a selective agent is well‐established. Environment might also influence evolution by altering the expression genetic variation associated with phenotypes under selection. Far less known about this phenomenon, particularly its contribution to in novel environments. We investigated how affected evolvability body size threespine stickleback (Gasterosteus aculeatus). Gasterosteus aculeatus well suited addressing question due rapid smaller numerous freshwater...

Animal hosts must co-exist with beneficial microbes while simultaneously being able to mount rapid, non-specific, innate immune responses pathogenic microbes. How this balance is achieved not fully understood, and disruption of relationship can lead disease. Excessive inflammatory resident are characteristic certain gastrointestinal pathologies such as bowel disease (IBD). The dysregulation IBD has complex genetic underpinnings that cannot be recapitulated single-gene-knockout models. A...

Much of animal-associated microbiome research has been conducted in species for which little is known their natural ecology and evolution. Microbiome studies that combine population genetic, environment, geographic data for wild organisms can be very informative, especially in situations where host genetic variation the environment both influence variation. The few have related population genetic and populations have constrained by observation-based...

Latinx individuals have been disproportionately affected during the COVID-19 pandemic caused by spread of SARS-CoV-2. It is imperative to evaluate newly developed preventive interventions assess their effect on health disparities.To examine effectiveness a culturally tailored outreach intervention designed increase SARS-CoV-2 testing rates among populations.In this cluster randomized trial performed from February 1 August 31, 2021, in community settings 9 Oregon counties, 38 sites were...

Evolution of similar phenotypes in independent populations is often taken as evidence adaptation to the same fitness optimum. However, genetic architecture traits might cause evolution proceed more toward particular phenotypes, and less others, independently adaptive value traits. Freshwater Alaskan threespine stickleback have repeatedly evolved distinctive opercle shape after divergence from an oceanic ancestor. Here we demonstrate that this pattern parallel widespread, distinguishing...

Oceanic threespine sticklebacks have repeatedly and independently evolved new morphologies upon invasions of freshwater habitats. A consistent derived feature the form across populations geography is a shape change opercle, large early developing facial bone. We show that principal multivariate axis describing opercle development from young larva to full adult stage oceanic fish matches evolutionary associated with relocation habitat. The phenotype adults closely resembles bone in juveniles....

The Gulf pipefish Syngnathus scovelli has emerged as an important species for studying sexual selection, development, and physiology. Comparative evolutionary genomics research involving fishes from Syngnathidae depends on having a high-quality genome assembly annotation. However, the first S. assembled using short-read sequences smaller RNA-sequence dataset limited contiguity relatively poor Here, PacBio long-read high-fidelity proximity ligation library, we generate improved to obtain 22...

Seadragons are a remarkable lineage of teleost fishes in the family Syngnathidae, renowned for having evolved male pregnancy. Comprising three known species, seadragons widely recognized and admired their fantastical body forms coloration, specific habitat requirements have made them flagship representatives marine conservation natural history interests. Until recently, gap has been lack significant genomic resources seadragons. We produced gene-annotated, chromosome-scale genome models...

Summary How does development evolve to produce a skeletal element with new shape? We extend our previous study of morphological evolution and the opercle, large facial bone favorable attributes for both comparative analyses. The opercle becomes prominently reshaped when Alaskan anadromous stickleback fish into resident freshwater lacustrine forms. use geometric morphometrics examine shape change which includes prominent dilation along one axis, coupled diminution orthogonal axis. During...

The common pattern of replicated evolution a consistent shape—environment relationship might reflect selection acting in similar ways within each environment, but divergently among environments. However, phenotypic depends on the availability additive genetic variation as well direction selection, implicating bias distribution variance potential contributor to evolution. Allometry, between shape and size, is source that poorly understood. threespine stickleback, Gasterosteus aculeatus,...

Multicellular organisms interact with resident microbes in important ways, and a better understanding of host-microbe interactions is aided by tools such as high-throughput 16S sequencing. However, rigorous evaluation the veracity these different context from which they were developed has often lagged behind. Our goal was to perform one critical test examining how variation tissue preparation DNA isolation could affect inferences about gut microbiome between two genetically divergent lines...

A major focus of host-microbe research is to understand how genetic differences, various magnitudes, among hosts translate differences in their microbiomes. This has been challenging for animal hosts, including humans, because it difficult control environmental variables tightly enough isolate direct effects on the microbiome. Our work stickleback fish a significant contribution our experimental approach allowed strict over factors, standardization microbiome from earliest stage development...

Comparing ontogenetic patterns within a well‐described evolutionary context aids in inferring mechanisms of change, including heterochronies or deletion developmental pathways. Because selection acts on phenotypes throughout ontogeny, any within‐taxon variation has implications for evolvability. We compare order and timing locomotion defensive traits three populations threespine stickleback that have evolutionarily divergent adult forms. This analysis adds to the growing understanding...

Species such as threespine stickleback (Gasterosteus aculeatus) that inhabit divergent selective environments and have diversified on different time scales can be of value for understanding evolutionary processes. Here we synthesize high-resolution genotypic phenotypic data to explore a largely unstudied distribution populations living in oceanic freshwater habitats along coastal inland regions Oregon. Many aquatic Oregon remained unglaciated during the last ice age, meaning some extant lake...

Abstract Selection, via host immunity, is often required to foster beneficial microbial symbionts and suppress deleterious pathogens. In animals, the immune system at center of this relationship. Failed system-microbial interactions can result in a persistent inflammatory response which indiscriminately attacks resident microbes, times cells themselves, leading diseases such as Ulcerative Colitis, Crohn’s Disease, Psoriasis. Host genetic variation has been linked both microbiome diversity...

Gynogenetic embryos - those inheriting only maternal DNA can be experimentally created by fertilizing eggs with radiation-treated sperm containing inactivated paternal chromosomes. Diploidy in the zygotes maintained through prevention of second meiosis or restored preventing first mitosis after chromosome complement has been replicated. These gynogenetic organisms are useful many fields including aquaculture, evolutionary biology and genomics. Although have numerous species, completeness...

Abstract The Gulf pipefish Syngnathus scovelli has emerged as an important species in the study of sexual selection, development, and physiology, among other topics. fish family Syngnathidae, which includes pipefishes, seahorses, seadragons, become increasingly attractive target for comparative research ecological evolutionary genomics. These endeavors depend on having a high-quality genome assembly annotation. However, first version S. was generated by short-read sequencing annotated using...

Abstract Multicellular organisms interact with resident microbes in important ways, and a better understanding of host-microbe interactions is aided by tools such as high-throughput 16S sequencing. However, rigorous evaluation the veracity these different context from which they were developed has often lagged behind. Our goal was to perform one critical test examining how variation tissue preparation DNA isolation could affect inferences about gut microbiome between two genetically...