A5042165233- Animal Vocal Communication and Behavior
- Chromosomal and Genetic Variations
- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Animal Behavior and Reproduction
- Marine animal studies overview
- RNA and protein synthesis mechanisms
- Livestock and Poultry Management
- Genetic and phenotypic traits in livestock
- Animal Nutrition and Physiology
- Animal Genetics and Reproduction
- Bat Biology and Ecology Studies
- Neuroendocrine regulation and behavior
- Cancer-related molecular mechanisms research
- Cephalopods and Marine Biology
- Genomics and Chromatin Dynamics
- Forensic and Genetic Research
- Genetic Mapping and Diversity in Plants and Animals
- Plant Molecular Biology Research
- interferon and immune responses
- Evolution and Paleontology Studies
- Primate Behavior and Ecology
- Pleistocene-Era Hominins and Archaeology
University of California, Los Angeles
2022-2025
Rockefeller University
2017-2024
Howard Hughes Medical Institute
2022
New York Proton Center
2022
University of California, Davis
2020
Abstract High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, biodiversity conservation. However, such available only a few non-microbial species 1–4 . To address this issue, international Genome 10K (G10K) consortium 5,6 has worked over five-year period evaluate develop cost-effective methods assembling highly accurate nearly genomes. Here we present lessons learned from generating 16 that represent six major vertebrate...
Abstract Reference-quality genomes are expected to provide a resource for studying gene structure, function, and evolution. However, often genes of interest not completely or accurately assembled, leading unknown errors in analyses additional cloning efforts the correct sequences. A promising solution is long-read sequencing. Here we tested PacBio-based sequencing diploid assembly potential improvements Sanger-based intermediate-read zebra finch reference Illumina-based short-read Anna's...
Abstract High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, biodiversity conservation. However, such only available a few non-microbial species 1–4 . To address this issue, international Genome 10K (G10K) consortium 5,6 has worked over five-year period evaluate develop cost-effective methods assembling most accurate genomes date. Here we summarize these developments, introduce set quality standards, present lessons...
Oxytocin (OXT; hereafter OT) and arginine vasopressin or vasotocin (AVP VT; VT) are neurotransmitter ligands that function through specific receptors to control diverse functions1,2. Here we performed genomic analyses on 35 species span all major vertebrate lineages, including newly generated high-contiguity assemblies from the Vertebrate Genomes Project3,4. Our findings support claim5 OT (also known as OXT) VT AVP) adjacent paralogous genes have resulted a local duplication, which infer was...
Dire wolves (Aenocyon dirus) are extinct predators of Pleistocene North America. Although phenotypically similar to living (Canis lupus), dire have yet be placed confidently in the canid family tree. We generated 3.4x and 12.8x paleogenomes from two well-preserved dating > 13,000 72,000 years ago, estimated consensus species trees for these 10 species. Our results revealed that ~2/3 wolf ancestry is derived a lineage sister clade comprising gray wolf, coyote, dhole, remaining ~1/3 near...
Abstract Over the last two decades, beginning with Avian Brain Nomenclature Forum in 2000, major revisions have been made to our understanding of organization and nomenclature avian brain. However, there are still unresolved questions on pallial organization, particularly whether cells above vestigial ventricle represent distinct populations those below it or similar populations. To test these hypotheses, we profiled transcriptomes subdivisions dorsal ventral boundary using RNA sequencing a...
Low genomic diversity is generally indicative of small population size and considered detrimental by decreasing long-term adaptability.
Abstract Background Vocal learning is a rare, convergent trait that fundamental to both human speech and birdsong. The Forkhead Box P2 (FOXP2) transcription factor appears necessary for types of learned signals, as mutations in FOXP2 result deficits, disrupting its expression zebra finches impairs male-specific song learning. In juvenile adult male finches, striatal mRNA protein decline acutely within song-dedicated neurons during singing, indicating transcriptional targets are also...
Abstract Vocal learning, the ability to imitate sounds and a component of spoken language, is complex convergent trait observed in only few independent lineages mammals birds. Clear gene expression convergences have been found vocal learning brain regions among several learners, but amino acid remain an open question. Here, we investigated whether avian clades that could be related their specialized trait. We developed tool, Convergent Sequence Variant finder (CSV finder), applied alignment...
Abstract Vocal learning is a skilled motor behavior observed in several mammalian and avian species critical for human speech. While convergent gene expression patterns have highlighted similar primary striatal pathways vocal imitation songbirds humans, the extent of molecular circuit convergence remains unresolved. Here we profiled four principal song nuclei zebra finch (HVC, LMAN, RA, Area X) their surrounding brain regions using RNA-Seq compared them with specialized markers identified...
Abstract Reference quality genomes are expected to provide a resource for studying gene structure and function. However, often genes of interest not completely or accurately assembled, leading unknown errors in analyses additional cloning efforts the correct sequences. A promising solution this problem is long-read sequencing. Here we tested PacBio-based sequencing diploid assembly potential improvements Sanger-based intermediate-read zebra finch reference Illumina-based short-read Anna’s...
Abstract Background A thorough analysis of genome evolution is fundamental for biodiversity understanding. The iconic monotremes (platypus and echidna) feature extraordinary biology. However, they also exhibit rearrangements in several chromosomes, especially the sex chromosome chain. Therefore, lack a chromosome-level echidna has limited insights into monotremes, particular multiple chromosomes complex. Results Here, we present new long reads–based short-beaked (Tachyglossus aculeatus)...
Vocal learning is a rare, convergent trait that fundamental to both human speech and birdsong. The Forkhead Box P2 (FoxP2) transcription factor appears necessary for types of learned signals, as mutations in FoxP2 result deficits, disrupting its expression zebra finches impairs male-specific song learning. In juvenile adult male finches, striatal mRNA protein decline acutely within song-dedicated neurons during singing, indicating transcriptional targets are also behaviorally regulated....
Abstract Over the last two decades, beginning with Avian Brain Nomenclature Forum in 2000, major revisions have been made to our understanding of organization and nomenclature avian brain. However, there are still unresolved questions on pallial organization, particularly whether cells above ventricle represent different populations those below it. Concerns included limited number genes profiled, biased selection genes, potential independent origins cell types parts Here we test competing...
Abstract Motivation Genetic variants in noncoding regions can drive changes phenotype disrupting transcription factor binding site (TFBS) motifs. Other tools including motifbreakR have been developed to assess the impact of TFBS-disrupting variants. Here we introduce tfboot package for statistically evaluating TFBS disruption across a set upstream promoter regions. Results The builds on motifbreakR, plyranges, and GenomicRanges provide methods bootstrapping quantify gene sets interest...
The diversity of germ cell developmental strategies has been well documented across many vertebrate clades. However, much our understanding avian primordial (PGC) specification and differentiation derived from only one species, the chicken (Gallus gallus). Of three major classes birds, chickens belong to Galloanserae, representing less than 4% while nearly 95% extant bird species Neoaves. This represents a significant gap in knowledge development hampering efforts adapt genome editing...
Abstract Single amino acid variants (SAVs) may provide clues to understanding evolution of traits. A complex trait that has evolved convergently among species is vocal learning, the rare ability imitate sounds heard and an important component spoken-language. Here we assessed whether convergent learning bird have SAVs (CSAVs) could be associated with their specialized trait. We analyzed avian genomes identified CSAVs in learners, but also most combinations tested. The number was proportional...