A5080739414- Genetic diversity and population structure
- Genetic Mapping and Diversity in Plants and Animals
- Genetic and phenotypic traits in livestock
- Bioenergy crop production and management
- Species Distribution and Climate Change
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Plant Reproductive Biology
- Rabbits: Nutrition, Reproduction, Health
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Environmental DNA in Biodiversity Studies
- Microbial Community Ecology and Physiology
- Polar Research and Ecology
- Identification and Quantification in Food
- Ecology and Vegetation Dynamics Studies
- Plant and animal studies
- Animal Ecology and Behavior Studies
- Wildlife Ecology and Conservation
- Fish Ecology and Management Studies
- Plant Ecology and Taxonomy Studies
- Plant Taxonomy and Phylogenetics
- Plant Molecular Biology Research
- Interdisciplinary Research and Collaboration
- scientometrics and bibliometrics research
- Genomics and Chromatin Dynamics
University of British Columbia
2012-2025
University of Arizona
2006-2011
Universidade do Porto
2005-2010
Consejo Superior de Investigaciones Científicas
2006
Centro de Investigação em Biodiversidade e Recursos Genéticos
2006
Flax (Linum usitatissimum) is an ancient crop that widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate improvement, we performed whole-genome shotgun sequencing the nuclear genome flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using Illumina analyzer. A de novo assembly, comprised exclusively deep-coverage (approximately 94× raw, approximately 69× filtered) short-sequence reads (44-100 bp), produced set scaffolds...
Summary P opulus trichocarpa is widespread across western North America spanning extensive variation in photoperiod, growing season and climate. We investigated trait . using over 2000 trees from a common garden at V ancouver, C anada, representing replicate plantings of 461 genotypes originating 136 provenance localities. measured 40 traits encompassing phenological events, biomass accumulation, growth rates, leaf, isotope gas exchange‐based ecophysiology traits. With replicated 29 354...
Abstract Patterns of genetic differentiation among taxa at early stages divergence provide an opportunity to make inferences about the history speciation. Here, we conduct a survey DNA‐sequence polymorphism and loci on autosomes, X chromosome, Y chromosome mitochondrial DNA in samples Mus domesticus, M. musculus castaneus . We analyzed our data under with gene flow model estimate that effective population size is 200 000–400 000, domesticus 100 000–200 000 60 000–120 000. These also suggest...
Summary In order to uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions black cottonwood ( Populus trichocarpa ) from much its range in western North America. Extensive data large‐scale phenotyping (with spatial and temporal replications within a common garden) genotyping 34 K single nucleotide polymorphism SNP array) all were for gene discovery genome‐wide association study GWAS ). We performed with 40 biomass, ecophysiology phenology traits 29 355...
See also the Commentary by Lexer and Stölting
Abstract All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin this trait. Despite some empirical counter examples, theory suggests that nonrecombining sex‐linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole‐genome scans sex‐associated region in trichocarpa is small and much younger than age genus. This indicates sex determination highly labile poplar, consistent with recent evidence...
In the early stages of reproductive isolation, genomic regions reduced recombination are expected to show greater levels differentiation, either because gene flow between species is in these or effects selection at linked sites within enhanced regions. Here, we study patterns DNA sequence variation 27 autosomal loci among populations Mus musculus musculus, M. m. domesticus, and castaneus, three subspecies house mice with collinear genomes. We found that some exhibit considerable shared...
Understanding the genetic structure of domestic species provides a window into process domestication and motivates design studies aimed at making links between genotype phenotype. Rabbits exhibit exceptional phenotypic diversity, are great commercial value, serve as important animal models in biomedical research. Here, we provide first comprehensive survey nucleotide polymorphism linkage disequilibrium (LD) within among rabbit breeds. We resequenced 16 genomic regions population samples both...
Populus trichocarpa is an ecologically important tree across western North America. We used a large population sample of 498 accessions over wide geographical area genotyped with 34K SNP array to quantify patterns genetic variation in this species (landscape genomics). present evidence that three processes contribute the observed patterns: (1) introgression from sister P. balsamifera, (2) isolation by distance (IBD), and (3) natural selection. Introgression was detected only at margins...
Abstract The western black cottonwood ( Populus trichocarpa ) was the first tree to have its genome fully sequenced and has emerged as model species for study of secondary growth wood formation. It is also a good candidate production lignocellulosic biofuels. Here, we present make available research community results sequencing transcriptome developing xylem in 20 accessions with high‐throughput next generation technology. We found over 0.5 million putative single nucleotide polymorphisms...
Abstract The house mouse is a well-established model organism, particularly for studying the genetics of complex traits. However, most studies mice use classical inbred strains, whose genomes derive from multiple species. Relatively little known about distribution genetic variation among these species or how strains relates to in wild. We sequenced intronic regions five X-linked loci large samples wild Mus domesticus and M. musculus, we found low levels nucleotide diversity both compared...
Abstract Genetic mapping of quantitative traits requires genotypic data for large numbers markers in many individuals. For such studies, the use single nucleotide polymorphism ( SNP ) genotyping arrays still offers most cost‐effective solution. Herein we report on design and performance a array Populus trichocarpa (black cottonwood). This was designed with s pre‐ascertained 34 wild accessions covering species latitudinal range. We adopted candidate gene approach to that resulted selection...
The increasing ecological and economical importance of Populus species hybrids has stimulated research into the investigation natural variation estimation extent genetic control over its wood quality traits for traditional forestry activities as well emerging bioenergy sector. A realized kinship matrix based on informative, high-density, biallelic single nucleotide polymorphism (SNP) markers was constructed to estimate trait variance components, heritabilities, phenotypic correlations....
Hybrid zones provide an excellent opportunity for studying the consequences of genetic changes between closely related taxa. Here we investigate patterns variability and gene flow at four X-linked loci within two subspecies European rabbit (Oryctolagus cuniculus O. c. algirus). Two these genes are located near centromere telomeres. We observed a deep split in genealogy each with root along deepest branch case, consistent evolution allopatry. The centromeric showed low levels variability,...
ABSTRACT Haploblocks are regions of the genome that coalesce to an ancestor as a single unit. Differentiated haplotypes in these can result from accumulation mutational differences low‐recombination chromosomal regions, especially when selective sweeps occur within geographically structured populations. We introduce method identify large well‐differentiated haploblock (LHBRs), based on variance standardised heterozygosity (ViSHet) nucleotide polymorphism (SNP) genotypes among individuals,...
Abstract The role of the Y chromosome in speciation is unclear. Hybrid zones provide natural arenas for studying speciation, as differential introgression markers may reveal selection acting against incompatibilities. Two subspecies European rabbit ( Oryctolagus cuniculus ) form a hybrid zone Iberian Peninsula. Previous work on mitochondrial DNA (mtDNA), Y‐ and X‐linked loci revealed existence two divergent lineages genome that these are largely subspecies‐specific mtDNA loci. Here we...
A 'genes-to-ecosystems' approach has been proposed as a novel avenue for integrating the consequences of intraspecific genetic variation with underlying architecture species to shed light on relationships among hierarchies ecological organization (genes → individuals communities ecosystems). However, attempts identify genes major effect structure and/or ecosystem processes have limited and comprehensive test this yet emerge. Here, we present an interdisciplinary field study that integrated...
Abstract Hybridization between divergent lineages can result in losses of distinct evolutionary taxa. Alternatively, hybridization lead to increased genetic variability that may fuel local adaptation and the generation novel traits and/or Here, we examined single‐nucleotide polymorphisms generated using genotyping‐by‐sequencing a population Dolly Varden char (Pisces: Salmonidae) is highly admixed within contact zone two subspecies ( Salvelinus malma , Northern [NDV] S. m. lordi Southern...
Summary We have sequenced 2388 bp of the European rabbit sex determining region Y ( SRY ) gene. These data provide a 10‐fold increase in coverage chromosome this species, including entire open reading frame , polyadenylation signal, and two repetitive sequences 5′ ‐region. A survey 2021 gene eight domestic breeds four wild individuals revealed total nine single nucleotide polymorphisms one indel, defining deeply divergent lineages. The resulting estimation diversity π = 1.34 × 10 −3 is very...
The human Y chromosome consists of ampliconic genes, which are located in palindromes and undergo frequent gene conversion, single-copy genes including the primary sex-determining locus, SRY. Here, we demonstrate that SRY is duplicated a large palindrome European rabbit (Oryctolagus cuniculus). Furthermore, show through comparative sequencing orthologous arms have diverged 0.40% between subspecies over at least 2 My, but paralogous remained nearly identical. This provides clear evidence...
Abstract Accurate knowledge of geographic ranges and genetic relationships among populations is important when managing a species or population conservation concern. Along the western coast Canada, subspecies northern goshawk ( Accipiter gentilis laingi ) legally designated as Threatened. The range distinctness this form, in comparison with broadly distributed North American atricapillus ), unclear. Given morphological uncertainty, we analyzed genomic thousands single nucleotide...
Abstract In this work we report the genetic polymorphism of a 7-bp insertion in 3' untranslated region rabbit SRY gene. The polymorphic GAATTAA motif was found exclusively one two divergent Y-chromosomal lineages, suggesting that its origin is more recent than separation O. c. algirus and cuniculus Y-chromosomes. addition, remarkable observation haplotypes exhibiting 0, 1 2 inserts essentially all populations suggests gene duplicated evolving under concerted evolution.
All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin this trait. Theory suggests that non-recombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole genome scans sex-associated region in P. trichocarpa is small and much younger than age genus. This indicates sex-determination highly labile poplar, consistent with recent evidence “turnover” sex determination animals. We performed...