A5060807605- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Ichthyology and Marine Biology
- Genetic diversity and population structure
- melanin and skin pigmentation
- Developmental Biology and Gene Regulation
- Animal Genetics and Reproduction
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Fish biology, ecology, and behavior
- Biochemical Analysis and Sensing Techniques
- Aquaculture Nutrition and Growth
- Congenital heart defects research
- Physiological and biochemical adaptations
- Aquaculture disease management and microbiota
- interferon and immune responses
- Retinal Development and Disorders
- MicroRNA in disease regulation
- Fish Biology and Ecology Studies
- Regulation of Appetite and Obesity
- Invertebrate Immune Response Mechanisms
- Zebrafish Biomedical Research Applications
- Genomics and Chromatin Dynamics
- Paleontology and Evolutionary Biology
- Epigenetics and DNA Methylation
- Bone Metabolism and Diseases
Michigan State University
2016-2024
Michigan United
2023
University of Oregon
2011-2019
Integra (United States)
2018
National Research Council
2016-2017
Columbia University
2017
University of California, Berkeley
2016
University of Würzburg
2006-2013
Eugene Research Institute
2012
University of Konstanz
2001-2009
Through phylogeny reconstruction we identified 49 genes with a single copy in man, mouse, and chicken, one or two copies the tetraploid frog Xenopus laevis , zebrafish ( Danio rerio ). For 22 of these genes, both duplicates had orthologs pufferfish Takifugu rubripes another 20 found only ortholog but each case it was more closely related to than other. Forty-three pairs duplicated map 24 25 linkage groups they are not randomly distributed; 10 regions genome that contain between five sets...
The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage lobe-finned fish thought to have become extinct 70 million years ago. modern looks remarkably similar many its ancient relatives, and evolutionary proximity our own ancestors provides glimpse the that first walked on land. Here we report genome sequence African coelacanth, Latimeria chalumnae. Through phylogenomic analysis, conclude lungfish, not is closest relative tetrapods. Coelacanth protein-coding...
Ingo Braasch, John Postlethwait and colleagues report the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before duplication. Their data provide insights into evolution genes involved in immunity, mineralization development facilitate comparison cis-regulatory elements between humans. To connect human biology to fish biomedical models, we sequenced teleost duplication (TGD). The slowly evolving has conserved content size many entire chromosomes bony...
There are approximately 25 000 species in the division Teleostei and most believed to have arisen during a relatively short period of time ca. 200 Myr ago. The discovery ‘extra’ Hox gene clusters zebrafish ( Danio rerio ), medaka Oryzias latipes pufferfish Fugu rubripes has led hypothesis that genome duplication provided genetic raw material necessary for teleost radiation. We identified 27 groups orthologous genes which included one from man, mouse chicken, or two tetraploid Xenopus...
With more than 30,000 species, ray-finned fish represent approximately half of vertebrates. The evolution was impacted by several whole genome duplication (WGD) events including a teleost-specific WGD event (TGD) that occurred at the root teleost lineage about 350 million years ago (Mya) and recent in salmonids, carps, suckers others. In plants animals, are associated with adaptive radiations evolutionary innovations. WGD-spurred innovation may be especially relevant case fish, which...
Several attributes intuitively considered to be typical mammalian features, such as complex behavior, live birth and malignant disease cancer, also appeared several times independently in lower vertebrates. The genetic mechanisms underlying the evolution of these elaborate traits are poorly understood. platyfish, X. maculatus, offers a unique model better understand molecular biology traits. We report here sequencing platyfish genome. Integrating genome assembly with extensive maps...
Within vertebrates, major sex determining genes can differ among taxa and even within species. In zebrafish (Danio rerio), neither heteromorphic chromosomes nor single determination of large effect, like Sry in mammals, have yet been identified. Furthermore, environmental factors influence determination. Although progress has made understanding gonad differentiation (e.g. the germ cells on fate), primary genetic basis remains poorly understood. To identify loci associated with sex, we...
Abstract Sturgeons seem to be frozen in time. The archaic characteristics of this ancient fish lineage place it a key phylogenetic position at the base ~30,000 modern teleost species. Moreover, sturgeons are notoriously polyploid, providing unique opportunities investigate evolution polyploid genomes. We assembled high-quality chromosome-level reference genome for sterlet, Acipenser ruthenus . Our analysis revealed very low protein rate that is least as slow other deep branches vertebrate...
Accurate species phylogenies are a prerequisite for all evolutionary research. Teleosts the largest and most diversified group of extant vertebrates, but relationships among their three oldest lineages remain unresolved. On basis seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited topology deepest branches teleost phylogeny using independent gene sequence chromosomal rearrangement phylogenomic approaches. These analyses converged to single scenario that...
Coloration and color patterning belong to the most diverse phenotypic traits in animals. Particularly, teleost fishes possess more pigment cell types than any other group of vertebrates. As result an ancient fish-specific genome duplication (FSGD), genomes might contain copies genes involved development tetrapods. No systematic genomic inventory allowing test this hypothesis has been drawn up so far for pigmentation fish, almost nothing is known about evolution these different fish lineages....
Significance The fossil record shows that the wrist and digits have an aquatic origin, becoming recognizable in a group of (mostly extinct) fish contained robust fins. Do fins living fishes equivalent these structures? Because comparisons fin limb morphology been inconclusive, we sought to investigate this question using developmental molecular data. By utilizing nonmodel (the spotted gar), find regulatory networks control “wrist digit”-building genes ( Hox ) are deeply conserved between...
The origin of novel phenotypic characters is a key component in organismal diversification; yet, the mechanisms underlying emergence such evolutionary novelties are largely unknown. Here we examine egg-spots, an innovation most species-rich group cichlids, haplochromines, where these conspicuous male fin colour markings involved mating. Applying combination RNAseq, comparative genomics and functional experiments, identify two pigmentation genes, fhl2a fhl2b, show that especially more rapidly...
<ns4:p><ns4:bold>Background</ns4:bold>: The telencephalon shows a remarkable structural diversity among vertebrates. In particular, the everted of ray-finned fishes has markedly different morphology compared to evaginated all other This difference in development hampered comparison between areas pallium and pallial nuclei Various models homology subdivisions tetrapods have been proposed based on connectional, neurochemical, gene expression functional data. However, no consensus reached so...
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...
Abstract The bowfin ( Amia calva ) is a ray-finned fish that possesses unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. phylogenetic position as representative neopterygian fishes, its archetypical body plan unduplicated slowly evolving genome make central species for the genomic exploration fishes. Here we present chromosome-level assembly enables gene-order analyses, settling long-debated relationships. We examine chromatin...
The study of sex determination and chromosome organization in nonmodel species has long been technically challenging, but new sequencing methodologies now enable precise high-throughput identification sex-specific genomic sequences. In particular, restriction site-associated DNA (RAD-Seq) is being extensively applied to explore systems many plant animal species. However, software specifically designed search for visualize sex-biased markers using RAD-Seq data lacking. Here, we present...
Whole-genome duplications (WGDs) have occurred repeatedly in the vertebrate lineage, but their evolutionary significance for phenotypic evolution remains elusive. Here, we investigated impact of fish-specific genome duplication (FSGD) on pigmentation pathways teleost fishes. Pigmentation and color patterning are among most diverse traits teleosts, pigmentary system is complex all groups. Using a comparative genomic approach including phylogenetic synteny analyses, 128 genes five genomes...
Control and coordination of eukaryotic gene expression rely on transcriptional posttranscriptional regulatory networks. Evolutionary innovations adaptations often require rapid changes such It has long been hypothesized that transposable elements (TE) might contribute to the rewiring interactions. More recently it emerged TEs bring in ready-to-use transcription factor binding sites create alterations promoters by which they were captured. A process where architecture is remarkable plasticity...
Abstract Background The exceptionally diverse species flocks of cichlid fishes in East Africa are prime examples parallel adaptive radiations. About 80% Africa's more than 1 800 endemic species, and all the Lakes Victoria Malawi, belong to a particularly rapidly evolving lineage, haplochromines. One characteristic feature haplochromines is their possession egg-dummies on males' anal fins. These egg-spots mimic real eggs play an important role mating system these maternal mouthbrooding fish....
In adaptating to perpetual darkness, cave species gradually lose eyes and body pigmentation evolve alternatives for exploring their environments. Although troglodyte features evolved independently many times in cavefish, we do not yet know whether independent evolution of these characters involves common genetic mechanisms. Surface-dwelling cave-dwelling make the freshwater teleost genus Sinocyclocheilus an excellent model studying adaptations life constant darkness. We compared mature...
Fishes of the genus Danio exhibit diverse pigment patterns that serve as useful models for understanding genes and cell behaviors underlying evolution adult form. Among these species, zebrafish D. rerio several dark stripes melanophores with sparse iridophores alternate light interstripes dense xanthophores. By contrast, closely related species nigrofasciatus has an attenuated pattern fewer melanophores, interstripes. Here we demonstrate differences in iridophore development presage fully...