A5030458261- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Environmental DNA in Biodiversity Studies
- Genetic Mapping and Diversity in Plants and Animals
- Avian ecology and behavior
- Physiological and biochemical adaptations
- Molecular Biology Techniques and Applications
- Bat Biology and Ecology Studies
- Genetic and phenotypic traits in livestock
- Evolution and Genetic Dynamics
- Fish Ecology and Management Studies
- Animal Behavior and Reproduction
- Marine Bivalve and Aquaculture Studies
- Genomic variations and chromosomal abnormalities
- Bird parasitology and diseases
- Species Distribution and Climate Change
- Aquatic Invertebrate Ecology and Behavior
- Animal Ecology and Behavior Studies
- Gene Regulatory Network Analysis
- Microbial Community Ecology and Physiology
- Genomics and Rare Diseases
- Protist diversity and phylogeny
- Marine animal studies overview
- Isotope Analysis in Ecology
Okanagan University College
2021-2024
University of British Columbia
2021-2024
Cornell University
2020-2024
Fisheries and Oceans Canada
2024
Louisiana Department of Natural Resources
2020-2024
University of New Hampshire
2018-2022
Queen's University
2015-2021
University of New Hampshire at Manchester
2019
Canadian Food Inspection Agency
2015
The widespread application of high-throughput sequencing in studying evolutionary processes and patterns diversification has led to many important discoveries. However, the barriers utilizing these technologies interpreting resulting data can be daunting for first-time users. We provide an overview a brief primer relevant methods (e.g., whole-genome sequencing, reduced-representation sequence-capture methods, RNA sequencing), as well steps analysis pipelines loci clustering, variant calling,...
Abstract Organisms that live in deserts offer the opportunity to investigate how species adapt environmental conditions are lethal most plants and animals. In hot of North America, high temperatures lack water conspicuous challenges for organisms living there. The cactus mouse ( Peromyscus eremicus ) displays several adaptations these conditions, including low metabolic rate, heat tolerance, ability maintain homeostasis under extreme dehydration. To genomic basis desert adaptation mice, we...
The structure of the genome shapes distribution genetic diversity and sequence divergence. To investigate how relationship between chromosome size recombination rate affects divergence species, we combined empirical analyses evolutionary simulations. We estimated pairwise among 15 species from three different mammalian clades—Peromyscus rodents, Mus mice, great apes—from chromosome-level assemblies. found a strong significant negative correlation in all comparisons within Peromyscus apes...
Abstract The role of recombination in genome evolution has long been studied theory, but until recently empirical investigations had limited to a small number model species. Here, we compare the landscape and collinearity between two populations Atlantic silverside ( Menidia menidia ), fish distributed across steep latitudinal climate gradient North American coast. We constructed separate linkage maps for locally adapted from New York Georgia their interpopulation laboratory cross. First,...
The levels and distribution of standing genetic variation in a genome can provide wealth insights about the adaptive potential, demographic history, structure population or species. As structural variants are increasingly associated with traits important for adaptation speciation, investigating both sequence is essential wholly tapping this potential. Using combination shotgun sequencing, 10x Genomics linked reads proximity-ligation data (Chicago Hi-C), we produced annotated chromosome-level...
Abstract Understanding the adaptive potential of populations and species is pivotal for minimizing loss biodiversity in this era rapid climate change. Adaptive has been estimated various ways, including based on levels standing genetic variation, presence potentially beneficial alleles, and/or severity environmental Kokanee salmon, non‐migratory ecotype sockeye salmon ( Oncorhynchus nerka ), culturally economically important already impacted by effects To assess its vulnerability moving...
Abstract Investigating the extent (or existence) of local adaptation is crucial to understanding how populations adapt. When experiments or fitness measurements are difficult impossible perform in natural populations, genomic techniques allow us investigate through comparison allele frequencies and outlier loci along environmental clines. The thick‐billed murre ( Uria lomvia ) a highly philopatric colonial arctic seabird that occupies significant gradient, shows marked phenotypic differences...
Abstract Warming climate and increasing desertification urge the identification of genes involved in heat dehydration tolerance to better inform target biodiversity conservation efforts. Comparisons among extant desert-adapted species can highlight parallel or convergent patterns genome evolution through shared signatures selection. We generate a chromosome-level assembly for canyon mouse (Peromyscus crinitus) test signature by comparing selective sweeps across population-level genomic...
Abstract Gene regulatory divergence is thought to play an important role in adaptation, yet its extent and underlying mechanisms remain largely elusive for local adaptation with gene flow. Local widespread marine species despite generally high connectivity often associated tightly linked genomic architectures, such as chromosomal inversions. To investigate evolution under flow the of inversions a steep thermal gradient, we generated RNA-seq data from Atlantic silversides (Menidia menidia)...
Quaternary glaciations affected the distribution of many species. Here, we investigate whether Arctic represented a glacial refugium during Last Glacial Maximum or an area secondary contact following ice retreat, by analyzing genetic population structure thick-billed murre (Uria lomvia), seabird that breeds throughout North Atlantic, Pacific and Oceans. The is species socio-economic importance faces numerous threats including hunting, oil pollution, gill netting, climate change. We compared...
SUMMARY Colour morphs associated with different physiological adaptations offer unique opportunities to study the genomic basis of otherwise elusive adaptive traits. These complex balanced polymorphisms are often controlled by groups tightly linked genes, and understanding how these ‘supergenes’ evolve maintained is an active area research in evolutionary biology (Schwander et al . 2014, Thompson Jiggins 2014). Within Atlantic, common murre ( Uria aalge , a colonial seabird) displays plumage...
Abstract Recent ecotypic differentiation provides unique opportunities to investigate the genomic basis and architecture of local adaptation, while offering insights into how species form persist. Sockeye salmon ( Oncorhynchus nerka ) exhibit migratory resident (“kokanee”) ecotypes, which are further distinguished shore‐spawning stream‐spawning reproductive ecotypes. Here, we analysed 36 sockeye (stream‐spawning) kokanee (stream‐ shore‐spawning) genomes from a system where they co‐occur have...
High-throughput sequencing technologies are a proposed solution for accessing the molecular data in historical specimens. However, degraded DNA combined with computational demands of short-read assemblies has posed significant laboratory and bioinformatics challenges de novo genome assembly. Linked-read or "synthetic long-read" technologies, such as 10× Genomics, may provide cost-effective alternative to assemble higher quality genomes from tissue samples. Here, we compare assembly (e.g.,...
Background selection (BGS), the effect that purifying exerts on sites linked to deleterious alleles, is expected be ubiquitous across eukaryotic genomes. The effects of BGS reflect interplay rates and fitness mutations with recombination. A fundamental assumption models recombination are invariant over time. However, in some lineages, evolve rapidly, violating this central assumption. Here, we investigate how rate evolution affects genetic variation under BGS. We show modifies a manner...
Abstract Thanks to a dramatic reduction in sequencing costs followed by rapid development of bioinformatics tools, genome assembly and annotation have become accessible many researchers recent years. Among tetrapods, birds genomes that display features facilitate their annotation, such as small size, low number repeats highly conserved genomic structure. However, we found high heterozygosity could great impact on the quality thick‐billed murre ( Uria lomvia ), an arctic colonial seabird. In...
A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03473-8.
Abstract The structure of the genome shapes distribution genetic diversity and sequence divergence. To investigate how relationship between chromosome size recombination rate affects divergence species, we combined empirical analyses evolutionary simulations. We estimated pairwise among 15 species from three different Mammalian clades - Peromyscus rodents, Mus mice, great apes chromosome-level assemblies. found a strong significant negative correlation in all comparisons within clades, but...
Abstract The levels and distribution of standing genetic variation in a genome can provide wealth insights about the adaptive potential, demographic history, structure population or species. As structural variants are increasingly associated with traits important for adaptation speciation, investigating both sequence is essential wholly tapping this potential. Using combination shotgun sequencing, 10X Genomics linked reads proximity-ligation data (Chicago Hi-C), we produced annotated...
Avian migration is a widespread, complex behavior that has long fascinated both scientists and the general public. Nonetheless, we have not identified genetic environmental controls of migration. Comparisons migratory strategies within among species suggest these differences are associated with personality variation. Recently, studies possible candidate genes for in several avian taxa. Partially species—those which only some individuals migrate, while others remain resident year...
Abstract The impact of genome structure on adaptation is a growing focus in evolutionary biology, revealing an important role for structural variation and recombination landscapes shaping genetic diversity across genomes among populations. This particularly relevant when local occurs despite gene flow, where clustering differentiated loci can maintain locally adapted variants by reducing between them. However, the limited genomic resources non-model species, including reference maps, has...