A5076531032- dental development and anomalies
- Developmental Biology and Gene Regulation
- Genetic diversity and population structure
- Congenital heart defects research
- Cancer-related gene regulation
- Ichthyology and Marine Biology
- Fish Ecology and Management Studies
- Animal Genetics and Reproduction
- Chromosomal and Genetic Variations
- Animal Behavior and Reproduction
- Cancer-related molecular mechanisms research
- Zebrafish Biomedical Research Applications
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- interferon and immune responses
- CRISPR and Genetic Engineering
- Physiological and biochemical adaptations
- Genomics and Phylogenetic Studies
- Proteoglycans and glycosaminoglycans research
- Genetic and phenotypic traits in livestock
- Evolution and Genetic Dynamics
- Cellular Mechanics and Interactions
- Fish biology, ecology, and behavior
- Microtubule and mitosis dynamics
- Dental Trauma and Treatments
- Genomics and Chromatin Dynamics
University of California, Berkeley
2014-2023
Stanford University
2003-2014
Howard Hughes Medical Institute
2007-2014
University of Oregon
1997-2007
Marine stickleback fish have colonized and adapted to thousands of streams lakes formed since the last ice age, providing an exceptional opportunity characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing genomes twenty additional individuals from global set marine freshwater populations, identify genome-wide loci that are consistently associated with...
Understanding how developmental systems evolve after genome amplification is important for discerning the origins of vertebrate novelties, including neural crest, placodes, cartilage and bone. Sox9 development these features, zebrafish has two co-orthologs tetrapod SOX9 stemming from an ancient duplication event in lineage ray-fin fish. We have used a genotype-driven screen to isolate mutation deleting sox9b function, investigated its phenotype genetic interactions with sox9a null mutation....
The molecular genetic mechanisms of cartilage construction are incompletely understood. Zebrafish embryos homozygous for jellyfish (jef)mutations show craniofacial defects and lack elements the neurocranium, pharyngeal arches, pectoral girdle similar to humans with campomelic dysplasia. We that two alleles jef contain mutations in sox9a, one zebrafish orthologs human transcription factor SOX9. A mutation induced by ethyl nitrosourea changed a conserved nucleotide at splice junction severely...
The distribution of effect sizes genes underlying adaptation is unknown (Orr 2005). Are suites traits that diverged under natural selection controlled by a few pleiotropic large (major model), many independently acting small (infinitesimal or combination, with frequency inversely related to size (geometric model)? To address this we carried out quantitative trait loci (QTL) study suite 54 position describing body shapes two threespine stickleback species: an ancestral Pacific marine form and...
ABSTRACT Mutation of sucker (suc) disrupts development the lower jaw and other ventral cartilages in pharyngeal segments zebrafish head. Our sequencing, cosegregation rescue results indicate that suc encodes an Endothelin-1 (Et-1). Like mouse chick Et-1, suc/et-1 is expressed a central core arch paraxial mesoderm epithelia, both surface ectoderm endoderm, but not skeletogenic neural crest. Long before chondrogenesis, mutant embryos have severe defects crest expression dHAND, dlx2, msxE, gsc,...
A conserved endothelin 1 signaling pathway patterns the jaw and other pharyngeal skeletal elements in mice, chicks zebrafish. In zebrafish,endothelin (edn1 or sucker) is required for formation of ventral cartilages joints anterior arches young larvae. Here we present genetic analyses zebrafish twoedn1 downstream targets, bHLH transcription factor Hand2 homeobox Bapx1, that mediate dorsoventral (DV) patterning arches. First show edn1-expressing cells first (mandibular)and second (hyoid) arch...
Understanding the genetic architecture of evolutionary change remains a long-standing goal in biology. In vertebrates, skeletal evolution has contributed greatly to adaptation body form and function response changing ecological variables like diet predation. Here we use genome-wide linkage mapping threespine stickleback fish investigate evolved changes many armor trophic traits. We identify >100 quantitative trait loci (QTL) controlling pattern serially repeating elements, including gill...
Abstract Marine populations of the threespine stickleback (Gasterosteus aculeatus) have repeatedly colonized and rapidly adapted to freshwater habitats, providing a powerful system map genetic architecture evolved traits. Here, we developed applied binned genotyping-by-sequencing (GBS) method build dense genome-wide linkage maps sticklebacks using two large marine by F2 crosses more than 350 fish each. The resulting significantly improve genome assembly anchoring 78 new scaffolds...
Synovial joints are the lubricated connections between bones of our body that commonly affected in arthritis. It is assumed synovial first evolved as vertebrates came to land, with ray-finned fishes lacking joints. Here, we examine expression and function a critical lubricating protein mammalian joints, Prg4/Lubricin, diverse fishes. We find Prg4 homologs specifically enriched at jaw pectoral fin zebrafish, stickleback, gar, genetic deletion zebrafish prg4b gene resulting same age-related...
In vertebrate embryos, streams of cranial neural crest (CNC) cells migrate to form segmental pharyngeal arches and differentiate into segment-specific parts the facial skeleton. To identify genes involved in specifying identity head, we screened for mutations affecting cartilage patterning zebrafish larval pharynx. We present positional cloning initial phenotypic characterization a homeotic locus discovered this screen. show that ortholog human oncogenic histone acetyltransferase MOZ...
Significance How body pattern evolves in nature remains largely unknown. Although recent progress has been made on the molecular basis of losing morphological features during adaptation to new environments (regressive evolution), there are few well worked out examples how may be gained natural species (constructive evolution). Here we use genetic crosses study threespine stickleback fish have increased their tooth number a freshwater environment. Genetic mapping and gene expression...
Endothelin 1 (Edn1), a secreted peptide expressed ventrally in the primordia of zebrafish pharyngeal arches, is required for correct patterning cartilage development. We have studied mutants and morpholino-injected larvae to examine role Edn1 signal anterior arch bone development during first week after fertilization. observe remarkable variety phenotypic changes dermal bones arches reduction, including loss, size reduction expansion, fusion shape change. Notably, that occur appear relate...
Teeth are a classic model system of organogenesis, as repeated and reciprocal epithelial mesenchymal interactions pattern placode formation outgrowth. Less is known about the developmental genetic bases tooth development replacement in polyphyodonts, vertebrates with continual replacement. Here we leverage natural variation threespine stickleback fish Gasterosteus aculeatus to investigate We find that two derived freshwater populations have both convergently evolved more ventral pharyngeal...
We examined variability of oil-sac volume in fifth copepodites (C5) Calanus finmarchicus collected over and around Georges Bank during winter spring 1997. Volumes were estimated from video images taken live specimens. Maximum sac increases with prosome length volume, showing a progressively higher apparent maximum (AM) at greater length. In small C5 (prosome PL=1.9 mm, PV=0.31 mm 3 ) 28% body capacity was occupied by oil. large (PL=2.7 PV=1·1 the 50% capacity. Thus, appear to have...
Convergent evolution, the repeated evolution of similar phenotypes in independent lineages, provides natural replicates to study mechanisms evolution. Cases convergent might have same underlying developmental and genetic bases, implying that some evolutionary trajectories be predictable. In a classic example most freshwater populations threespine stickleback fish independently evolved reduction gill raker number adapt novel diets. Gill rakers are segmentally reiterated set dermal bones...
The extent to which convergent adaptation similar ecological niches occurs by a predictable genetic basis remains fundamental question in biology. Threespine stickleback fish have undergone an adaptive radiation ancestral oceanic populations repeatedly colonized and adapted freshwater habitats. In multiple lakes British Columbia, two different ecotypes evolved: deep-bodied benthic form forage near the lake substrate, narrow-bodied limnetic open water. Here, we use genome-wide linkage mapping...
Changes in developmental gene regulatory networks enable evolved changes morphology. These can be cis elements that act an allele-specific manner, or to the overall trans environment interacts with sequences. Here we address several questions about evolution of expression accompanying a convergently constructive morphological trait, increases tooth number two independently derived freshwater populations threespine stickleback fish (Gasterosteus aculeatus). Are and/or associated evolution? Do...