Scholars@Duke
Erich David Jarvis

Erich David Jarvis

Adjunct Professor in the Department of Neurobiology
Neurobiology
jarvis@neuro.duke.edu
Box 3209 Med Ctr, Durham, NC 27710
the Rockefeller University, Box 54, 1230 York Avenue, New York, NY 10065

Selected Publications

Single-cell long-read sequencing-based mapping reveals specialized splicing patterns in developing and adult mouse and human brain.

Journal Article Nat Neurosci · June 2024 RNA isoforms influence cell identity and function. However, a comprehensive brain isoform map was lacking. We analyze single-cell RNA isoforms across brain regions, cell subtypes, developmental time points and species. For 72% of genes, full-length isoform ... Full text Link to item Cite

A genomic basis of vocal rhythm in birds.

Journal Article Nat Commun · April 23, 2024 Vocal rhythm plays a fundamental role in sexual selection and species recognition in birds, but little is known of its genetic basis due to the confounding effect of vocal learning in model systems. Uncovering its genetic basis could facilitate identifying ... Full text Link to item Cite

A region of suppressed recombination misleads neoavian phylogenomics.

Journal Article Proc Natl Acad Sci U S A · April 9, 2024 Genomes are typically mosaics of regions with different evolutionary histories. When speciation events are closely spaced in time, recombination makes the regions sharing the same history small, and the evolutionary history changes rapidly as we move along ... Full text Link to item Cite

Pangenome graph construction from genome alignments with Minigraph-Cactus.

Journal Article Nat Biotechnol · April 2024 Pangenome references address biases of reference genomes by storing a representative set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles determined by variant callers can be used to construct pangenome graphs, but advances ... Full text Link to item Cite

Problem-solving skills are predicted by technical innovations in the wild and brain size in passerines.

Journal Article Nat Ecol Evol · April 2024 Behavioural innovations can provide key advantages for animals in the wild, especially when ecological conditions change rapidly and unexpectedly. Innovation rates can be compared across taxa by compiling field reports of novel behaviours. Large-scale anal ... Full text Link to item Cite

A chromosome-level genome assembly for the dugong (Dugong dugon).

Journal Article J Hered · March 13, 2024 The dugong (Dugong dugon) is a marine mammal widely distributed throughout the Indo-Pacific and the Red Sea, with a Vulnerable conservation status, and little is known about many of the more peripheral populations, some of which are thought to be close to ... Full text Link to item Cite

A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography.

Journal Article Mol Biol Evol · March 1, 2024 The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-rea ... Full text Link to item Cite

Chromosome level genome assembly of the Etruscan shrew Suncus etruscus.

Journal Article Sci Data · February 7, 2024 Suncus etruscus is one of the world's smallest mammals, with an average body mass of about 2 grams. The Etruscan shrew's small body is accompanied by a very high energy demand and numerous metabolic adaptations. Here we report a chromosome-level genome ass ... Full text Link to item Cite

Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean.

Journal Article Sci Data · December 8, 2023 Chub mackerels (Scomber japonicus) are a migratory marine fish widely distributed in the Indo-Pacific Ocean. They are globally consumed for their high Omega-3 content, but their population is declining due to global warming. Here, we generated the first ch ... Full text Link to item Cite

A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants.

Journal Article BMC Biol · November 22, 2023 BACKGROUND: The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the ... Full text Link to item Cite

Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks.

Journal Article Nat Commun · October 19, 2023 Sharks occupy diverse ecological niches and play critical roles in marine ecosystems, often acting as apex predators. They are considered a slow-evolving lineage and have been suggested to exhibit exceptionally low cancer rates. These two features could be ... Full text Link to item Cite

The admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes.

Journal Article Nat Commun · October 17, 2023 Combining genome assembly with population and functional genomics can provide valuable insights to development and evolution, as well as tools for species management. Here, we present a chromosome-level genome assembly of the common brushtail possum (Trich ... Full text Link to item Cite

Species-wide genomics of kākāpō provides tools to accelerate recovery.

Journal Article Nat Ecol Evol · October 2023 The kākāpō is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand. We generated and analysed whole-genome sequence data for nearly all individuals living in early 2018 (169 individuals) to generate a hi ... Full text Link to item Cite

Prioritizing Endangered Species in Genome Sequencing: Conservation Genomics in Action with the First Platinum-Standard Reference-Quality Genome of the Critically Endangered European Mink Mustela lutreola L., 1761.

Journal Article Int J Mol Sci · October 1, 2023 The European mink Mustela lutreola (Mustelidae) ranks among the most endangered mammalian species globally, experiencing a rapid and severe decline in population size, density, and distribution. Given the critical need for effective conservation strategies ... Full text Link to item Cite

Songbird species that display more-complex vocal learning are better problem-solvers and have larger brains.

Journal Article Science · September 15, 2023 Complex vocal learning, a critical component of human spoken language, has been assumed to be associated with more-advanced cognitive abilities. Tests of this hypothesis between individuals within a species have been inconclusive and have not been done acr ... Full text Link to item Cite

A Chromosome-Level Reference Genome for the Black-Legged Kittiwake (Rissa tridactyla), a Declining Circumpolar Seabird.

Journal Article Genome Biol Evol · August 1, 2023 Amidst the current biodiversity crisis, the availability of genomic resources for declining species can provide important insights into the factors driving population decline. In the early 1990s, the black-legged kittiwake (Rissa tridactyla), a pelagic gul ... Full text Link to item Cite

A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta).

Journal Article G3 (Bethesda) · July 5, 2023 The Rock Ptarmigan (Lagopus muta) is a cold-adapted, largely sedentary, game bird with a Holarctic distribution. The species represents an important example of an organism likely to be affected by ongoing climatic shifts across a disparate range. We provid ... Full text Link to item Cite

How genomics can help biodiversity conservation.

Journal Article Trends Genet · July 2023 The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in bi ... Full text Link to item Cite

Increased mutation and gene conversion within human segmental duplications.

Journal Article Nature · May 2023 Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations of mapping short-read sequencing data1,2. Here we constructed 1:1 unambiguous alignments spanning high-identity SDs across 10 ... Full text Link to item Cite

Recombination between heterologous human acrocentric chromosomes.

Journal Article Nature · May 2023 The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats and extended segmental duplications1,2. Although the resolution of these regions in the first complete assembl ... Full text Link to item Cite

A high-quality reference genome for the critically endangered Aeolian wall lizard, Podarcis raffonei.

Journal Article The Journal of heredity · May 2023 The Aeolian wall lizard, Podarcis raffonei, is an endangered species endemic to the Aeolian archipelago, Italy, where it is present only in 3 tiny islets and a narrow promontory of a larger island. Because of the extremely limited area of occupancy, severe ... Full text Cite

An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes.

Journal Article Cell Rep · March 28, 2023 Programmed DNA loss is a gene silencing mechanism that is employed by several vertebrate and nonvertebrate lineages, including all living jawless vertebrates and songbirds. Reconstructing the evolution of somatically eliminated (germline-specific) sequence ... Full text Link to item Cite

Three amphioxus reference genomes reveal gene and chromosome evolution of chordates.

Journal Article Proc Natl Acad Sci U S A · March 7, 2023 The slow-evolving invertebrate amphioxus has an irreplaceable role in advancing our understanding of the vertebrate origin and innovations. Here we resolve the nearly complete chromosomal genomes of three amphioxus species, one of which best recapitulates ... Full text Link to item Cite

Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Journal Article Proceedings of the National Academy of Sciences of the United States of America · February 14, 2023 Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains lar ... Full text Cite

Birdsong neuroscience and the evolutionary substrates of learned vocalization.

Journal Article Trends Neurosci · February 2023 Oscine songbirds have served as a model for speech and its evolution since the discovery that birds in this clade learn to produce their songs by imitating conspecifics. We discuss the initial characterization of neural substrates for song learning and hig ... Full text Link to item Cite

A chromosome-level reference genome and pangenome for barn swallow population genomics.

Journal Article Cell Rep · January 31, 2023 Insights into the evolution of non-model organisms are limited by the lack of reference genomes of high accuracy, completeness, and contiguity. Here, we present a chromosome-level, karyotype-validated reference genome and pangenome for the barn swallow (Hi ... Full text Link to item Cite

Sex-specific changes in autosomal methylation rate in ageing common terns

Journal Article Frontiers in Ecology and Evolution · January 30, 2023 Senescence, an age-related decline in survival and/or reproductive performance, occurs in species across the tree of life. Molecular mechanisms underlying this within-individual phenomenon are still largely unknown, but DNA methylation changes with age are ... Full text Cite

The swan genome and transcriptome, it is not all black and white.

Journal Article Genome Biol · January 23, 2023 BACKGROUND: The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune r ... Full text Link to item Cite

Analysis of Mouse Vocal Communication (AMVOC): a deep, unsupervised method for rapid detection, analysis and classification of ultrasonic vocalisations

Journal Article Bioacoustics · January 1, 2023 Some aspects of the neural mechanisms underlying mouse ultrasonic vocalisations (USVs) are a useful model for the neurobiology of human speech and speech-related disorders. Much of the research on vocalisations and USVs is limited to offline methods and su ... Full text Cite

Unsupervised Temporal Analysis of Mouse Vocalizations

Conference CIBCB 2023 - 20th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology · January 1, 2023 Mice communicate using ultrasonic vocalizations (USVs) that vary according to parameters such as sex, genetic background, and environmental stimuli. The study of USVs production provides useful models of the underlying neurobiology mechanisms of human spee ... Full text Cite

A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes.

Journal Article BMC Biol · November 8, 2022 BACKGROUND: The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to human ... Full text Link to item Cite

Semi-automated assembly of high-quality diploid human reference genomes.

Journal Article Nature · November 2022 The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of ... Full text Link to item Cite

False gene and chromosome losses in genome assemblies caused by GC content variation and repeats.

Journal Article Genome Biol · September 27, 2022 BACKGROUND: Many short-read genome assemblies have been found to be incomplete and contain mis-assemblies. The Vertebrate Genomes Project has been producing new reference genome assemblies with an emphasis on being as complete and error-free as possible, w ... Full text Link to item Cite

Widespread false gene gains caused by duplication errors in genome assemblies.

Journal Article Genome Biol · September 27, 2022 BACKGROUND: False duplications in genome assemblies lead to false biological conclusions. We quantified false duplications in popularly used previous genome assemblies for platypus, zebra finch, and Anna's Hummingbird, and their new counterparts of the sam ... Full text Link to item Cite

Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs.

Journal Article Bioinformatics · September 2, 2022 MOTIVATION: With the current pace at which reference genomes are being produced, the availability of tools that can reliably and efficiently generate genome assembly summary statistics has become critical. Additionally, with the emergence of new algorithms ... Full text Link to item Cite

Haplotype-resolved assembly of diploid genomes without parental data.

Journal Article Nat Biotechnol · September 2022 Routine haplotype-resolved genome assembly from single samples remains an unresolved problem. Here we describe an algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction data to produce a haplotype-resolved assembly without the sequencing ... Full text Link to item Cite

Forebrain nuclei linked to woodpecker territorial drum displays mirror those that enable vocal learning in songbirds.

Journal Article PLoS Biol · September 2022 Vocal learning is thought to have evolved in 3 orders of birds (songbirds, parrots, and hummingbirds), with each showing similar brain regions that have comparable gene expression specializations relative to the surrounding forebrain motor circuitry. Here, ... Full text Link to item Cite

Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing.

Journal Article Gigascience · August 10, 2022 BACKGROUND: Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome as ... Full text Link to item Cite

The kākāpō (Strigops habroptilus).

Journal Article Trends Genet · August 2022 Full text Link to item Cite

Oxytocin and vasotocin receptor variation and the evolution of human prosociality

Journal Article Comprehensive Psychoneuroendocrinology · August 1, 2022 Modern human lifestyle strongly depends on complex social traits like empathy, tolerance and cooperation. These diverse facets of social cognition have been associated with variation in the oxytocin receptor (OTR) and its sister genes, the vasotocin/vasopr ... Full text Cite

Reference genomes for conservation.

Journal Article Science · July 22, 2022 High-quality reference genomes for non-model species can benefit conservation. ... Full text Link to item Cite

Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue.

Journal Article Nature biotechnology · July 2022 Single-nuclei RNA sequencing characterizes cell types at the gene level. However, compared to single-cell approaches, many single-nuclei cDNAs are purely intronic, lack barcodes and hinder the study of isoforms. Here we present single-nuclei isoform RNA se ... Full text Cite

Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation.

Journal Article Nat Methods · June 2022 Variant calling has been widely used for genotyping and for improving the consensus accuracy of long-read assemblies. Variant calls are commonly hard-filtered with user-defined cutoffs. However, it is impossible to define a single set of optimal cutoffs, a ... Full text Link to item Cite

The complete sequence of a human genome.

Journal Article Science · April 2022 Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortiu ... Full text Link to item Cite

A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta).

Journal Article Gigascience · April 1, 2022 BACKGROUND: The ring-tailed lemur (Lemur catta) is a charismatic strepsirrhine primate endemic to Madagascar. These lemurs are of particular interest, given their status as a flagship species and widespread publicity in the popular media. Unfortunately, a ... Full text Link to item Cite

The Human Pangenome Project: a global resource to map genomic diversity.

Journal Article Nature · April 2022 The human reference genome is the most widely used resource in human genetics and is due for a major update. Its current structure is a linear composite of merged haplotypes from more than 20 people, with a single individual comprising most of the sequence ... Full text Link to item Cite

Induction of an immortalized songbird cell line allows for gene characterization and knockout by CRISPR-Cas9.

Journal Article Sci Rep · March 14, 2022 The zebra finch is one of the most commonly studied songbirds in biology, particularly in genomics, neuroscience and vocal communication. However, this species lacks a robust cell line for molecular biology research and reagent optimization. We generated a ... Full text Link to item Cite

The era of reference genomes in conservation genomics.

Journal Article Trends Ecol Evol · March 2022 Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity an ... Full text Link to item Cite

Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19

Journal Article iScience · February 18, 2022 Impressive global efforts have identified both rare and common gene variants associated with severe COVID-19 using sequencing technologies. However, these studies lack the sensitivity to accurately detect several classes of variants, especially large struc ... Full text Cite

Oxytocin variation and brain region-specific gene expression in a domesticated avian species.

Journal Article Genes Brain Behav · February 2022 The Bengalese finch was domesticated more than 250 years ago from the wild white-rumped munia (WRM). Similar to other domesticated species, Bengalese finches show a reduced fear response and have lower corticosterone levels, compared to WRMs. Bengalese fin ... Full text Link to item Cite

The Earth BioGenome Project 2020: Starting the clock.

Journal Article Proc Natl Acad Sci U S A · January 25, 2022 Full text Link to item Cite

Why sequence all eukaryotes?

Journal Article Proc Natl Acad Sci U S A · January 25, 2022 Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have the ... Full text Link to item Cite

Darwinian genomics and diversity in the tree of life.

Journal Article Proc Natl Acad Sci U S A · January 25, 2022 Genomics encompasses the entire tree of life, both extinct and extant, and the evolutionary processes that shape this diversity. To date, genomic research has focused on humans, a small number of agricultural species, and established laboratory models. Few ... Full text Link to item Cite

Standards recommendations for the Earth BioGenome Project.

Journal Article Proc Natl Acad Sci U S A · January 25, 2022 A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technica ... Full text Link to item Cite

A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck).

Journal Article Gigascience · December 20, 2021 BACKGROUND: The tufted duck is a non-model organism that experiences high mortality in highly pathogenic avian influenza outbreaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian ... Full text Link to item Cite

Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans.

Journal Article Genome Res · November 2021 Vocal learning, the ability to imitate sounds from conspecifics and the environment, is a key component of human spoken language and learned song in three independently evolved avian groups-oscine songbirds, parrots, and hummingbirds. Humans and each of th ... Full text Link to item Cite

Population genomics of the critically endangered kākāpō.

Journal Article Cell Genom · October 13, 2021 The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a hi ... Full text Link to item Cite

Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution.

Journal Article Mol Ecol Resour · October 2021 With the advent of chromatin-interaction maps, chromosome-level genome assemblies have become a reality for a wide range of organisms. Scaffolding quality is, however, difficult to judge. To explore this gap, we generated multiple chromosome-scale genome a ... Full text Link to item Cite

Controlling for activity-dependent genes and behavioral states is critical for determining brain relationships within and across species.

Journal Article J Comp Neurol · August 2021 The genetic profile of vertebrate pallia has long driven debate on homology across distantly related clades. Based on an expression profile of the orphan nuclear receptor NR4A2 in mouse and chicken brains, Puelles et al. (The Journal of Comparative Neurolo ... Full text Link to item Cite

As above, so below: Whole transcriptome profiling demonstrates strong molecular similarities between avian dorsal and ventral pallial subdivisions.

Journal Article J Comp Neurol · August 2021 Over the last two decades, beginning with the Avian Brain Nomenclature Forum in 2000, major revisions have been made to our understanding of the organization and nomenclature of the avian brain. However, there are still unresolved questions on avian pallia ... Full text Link to item Cite

Variation in predicted COVID-19 risk among lemurs and lorises.

Journal Article Am J Primatol · June 2021 The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 2 million fatalities since it first emerged in late 2019. As we write, infection rates are at their highest point globally and are r ... Full text Link to item Cite

The role of sex chromosomes and sex hormones in vocal learning systems.

Journal Article Horm Behav · June 2021 Vocal learning is the ability to imitate and modify sounds through auditory experience, a rare trait found in only a few lineages of mammals and birds. It is a critical component of human spoken language, allowing us to verbally transmit speech repertoires ... Full text Link to item Cite

Evolutionary and biomedical insights from a marmoset diploid genome assembly.

Journal Article Nature · June 2021 The accurate and complete assembly of both haplotype sequences of a diploid organism is essential to understanding the role of variation in genome functions, phenotypes and diseases1. Here, using a trio-binning approach, we present a high-quality, diploid ... Full text Link to item Cite

Balanced imitation sustains song culture in zebra finches.

Journal Article Nat Commun · May 7, 2021 Songbirds acquire songs by imitation, as humans do speech. Although imitation should drive convergence within a group and divergence through drift between groups, zebra finch songs sustain high diversity within a colony, but mild variation across colonies. ... Full text Link to item Cite

Reference genome and demographic history of the most endangered marine mammal, the vaquita.

Journal Article Mol Ecol Resour · May 2021 The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline for more than 20 years resulting from inadvertent deaths due to the increasing use of larg ... Full text Link to item Cite

Complete vertebrate mitogenomes reveal widespread repeats and gene duplications.

Journal Article Genome Biol · April 29, 2021 BACKGROUND: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. RESULTS: As part of the Vertebrate Genomes Project ... Full text Link to item Cite

Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C.

Journal Article Nat Commun · April 28, 2021 Haplotype-resolved genome assemblies are important for understanding how combinations of variants impact phenotypes. To date, these assemblies have been best created with complex protocols, such as cultured cells that contain a single-haplotype (haploid) g ... Full text Link to item Cite

Platypus and echidna genomes reveal mammalian biology and evolution.

Journal Article Nature · April 2021 Egg-laying mammals (monotremes) are the only extant mammalian outgroup to therians (marsupial and eutherian animals) and provide key insights into mammalian evolution1,2. Here we generate and analyse reference genomes of the platypus (Ornithorhynchus anati ... Full text Link to item Cite

Universal nomenclature for oxytocin-vasotocin ligand and receptor families.

Journal Article Nature · April 2021 Oxytocin (OXT; hereafter OT) and arginine vasopressin or vasotocin (AVP or VT; hereafter VT) are neurotransmitter ligands that function through specific receptors to control diverse functions1,2. Here we performed genomic analyses on 35 species that span a ... Full text Link to item Cite

At the beginning of speciation.

Journal Article Science · March 26, 2021 Full text Link to item Cite

Estrogen and sex-dependent loss of the vocal learning system in female zebra finches.

Journal Article Horm Behav · March 2021 Sex hormones alter the organization of the brain during early development and coordinate various behaviors throughout life. In zebra finches, song learning is limited to males, with the associated song learning brain pathways only maturing in males and atr ... Full text Link to item Cite

A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes.

Journal Article Genome Res · March 2021 Emu and other ratites are more informative than any other birds in reconstructing the evolution of the ancestral avian or vertebrate karyotype because of their much slower rate of genome evolution. Here, we generated a new chromosome-level genome assembly ... Full text Link to item Cite

A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain.

Journal Article Nat Commun · January 19, 2021 Splicing varies across brain regions, but the single-cell resolution of regional variation is unclear. We present a single-cell investigation of differential isoform expression (DIE) between brain regions using single-cell long-read sequencing in mouse hip ... Full text Link to item Cite

A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals.

Journal Article Gigascience · January 6, 2021 BACKGROUND: Ducks have a typical avian karyotype that consists of macro- and microchromosomes, but a pair of much less differentiated ZW sex chromosomes compared to chickens. To elucidate the evolution of chromosome architectures between ducks and chickens ... Full text Link to item Cite

Birdsong Learning and Culture: Analogies with Human Spoken Language

Journal Article Annual Review of Linguistics · January 4, 2021 Unlike many species, song learning birds and humans have independently evolved the ability to communicate via learned vocalizations. Both birdsong and spoken language are culturally transmitted across generations, within species-specific constraints that l ... Full text Cite

A Relationship between the Characteristics of the Oval Nucleus of the Mesopallium and Parrot Vocal Response to Playback.

Journal Article Brain Behav Evol · 2021 Correlations between differences in animal behavior and brain structures have been used to infer function of those structures. Brain region size has especially been suggested to be important for an animal's behavioral capability, controlled by specific bra ... Full text Link to item Cite

The genome sequence of the brown trout, Salmo trutta Linnaeus 1758

Journal Article Wellcome Open Research · January 1, 2021 We present a genome assembly from an individual female Salmo trutta (the brown trout; Chordata; Actinopteri; Salmoniformes; Salmonidae). The genome sequence is 2.37 gigabases in span. The majority of the assembly is scaffolded into 40 chromosomal pseudomol ... Full text Cite

Progressive Cactus is a multiple-genome aligner for the thousand-genome era.

Journal Article Nature · November 2020 New genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements in third-generation sequencing technologies1-3. For example, the number of vertebrate genome assemblies currently in the NCBI (N ... Full text Link to item Cite

Six reference-quality genomes reveal evolution of bat adaptations.

Journal Article Nature · July 2020 Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity and unique immunity. High-quality genomes are crucial for understanding the molecular basis and evolution of these traits. Here we incorporated long-read sequencing a ... Full text Link to item Cite

Tempo and Pattern of Avian Brain Size Evolution.

Journal Article Curr Biol · June 8, 2020 Relative brain sizes in birds can rival those of primates, but large-scale patterns and drivers of avian brain evolution remain elusive. Here, we explore the evolution of the fundamental brain-body scaling relationship across the origin and evolution of bi ... Full text Link to item Cite

Adaptive Radiation Genomics of Two Ecologically Divergent Hawai'ian Honeycreepers: The 'akiapōlā'au and the Hawai'i 'amakihi.

Journal Article J Hered · February 5, 2020 The Hawai'ian honeycreepers (drepanids) are a classic example of adaptive radiation: they adapted to a variety of novel dietary niches, evolving a wide range of bill morphologies. Here we investigated genomic diversity, demographic history, and genes invol ... Full text Link to item Cite

A draft genome sequence of the elusive giant squid, Architeuthis dux.

Journal Article Gigascience · January 1, 2020 BACKGROUND: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. T ... Full text Link to item Cite

The genome sequence of the Eurasian red squirrel, Sciurus vulgaris Linnaeus 1758

Journal Article Wellcome Open Research · January 1, 2020 We present a genome assembly from an individual male Sciurus vulgaris (the Eurasian red squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.88 gigabases in span. The majority of the assembly is scaffolded into 21 chromo ... Full text Cite

Identification and characterization of primordial germ cells in a vocal learning Neoaves species, the zebra finch.

Journal Article FASEB J · December 2019 The zebra finch has been used as a valuable vocal learning animal model for human spoken language. It is representative of vocal learning songbirds specifically, which comprise half of all bird species, and of Neoaves broadly, which comprise 95% of all bir ... Full text Link to item Cite

Evolution of vocal learning and spoken language.

Journal Article Science · October 4, 2019 Although language, and therefore spoken language or speech, is often considered unique to humans, the past several decades have seen a surge in nonhuman animal studies that inform us about human spoken language. Here, I present a modern, evolution-based sy ... Full text Link to item Cite

The vertebrate TLR supergene family evolved dynamically by gene gain/loss and positive selection revealing a host-pathogen arms race in birds

Journal Article Diversity · August 1, 2019 The vertebrate toll-like receptor (TLRs) supergene family is a first-line immune defense against viral and non-viral pathogens. Here, comparative evolutionary-genomics of 79 vertebrate species (8 mammals, 48 birds, 11 reptiles, 1 amphibian, and 11 fishes) ... Full text Cite

Avian Binocularity and Adaptation to Nocturnal Environments: Genomic Insights from a Highly Derived Visual Phenotype.

Journal Article Genome Biol Evol · August 1, 2019 Typical avian eyes are phenotypically engineered for photopic vision (daylight). In contrast, the highly derived eyes of the barn owl (Tyto alba) are adapted for scotopic vision (dim light). The dramatic modifications distinguishing barn owl eyes from othe ... Full text Link to item Cite

Parrot Genomes and the Evolution of Heightened Longevity and Cognition.

Journal Article Curr Biol · December 17, 2018 Parrots are one of the most distinct and intriguing groups of birds, with highly expanded brains [1], highly developed cognitive [2] and vocal communication [3] skills, and a long lifespan compared to other similar-sized birds [4]. Yet the genetic basis of ... Full text Link to item Cite

Bayesian Semiparametric Mixed Effects Markov Models With Application to Vocalization Syntax

Journal Article Journal of the American Statistical Association · October 2, 2018 Studying the neurological, genetic, and evolutionary basis of human vocal communication mechanisms using animal vocalization models is an important field of neuroscience. The datasets typically comprise structured sequences of syllables or “songs” produced ... Full text Cite

Earth BioGenome Project: Sequencing life for the future of life.

Journal Article Proc Natl Acad Sci U S A · April 24, 2018 Increasing our understanding of Earth's biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evoluti ... Full text Link to item Cite

Divergence in problem-solving skills is associated with differential expression of glutamate receptors in wild finches.

Journal Article Sci Adv · March 2018 Problem solving and innovation are key components of intelligence. We compare wild-caught individuals from two species that are close relatives of Darwin's finches, the innovative Loxigilla barbadensis, and its most closely related species in Barbados, the ... Full text Link to item Cite

Axon guidance pathways served as common targets for human speech/language evolution and related disorders.

Journal Article Brain Lang · November 2017 Human and several nonhuman species share the rare ability of modifying acoustic and/or syntactic features of sounds produced, i.e. vocal learning, which is the important neurobiological and behavioral substrate of human speech/language. This convergent tra ... Full text Link to item Cite

De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads.

Journal Article Gigascience · October 1, 2017 Reference-quality genomes are expected to provide a resource for studying gene structure, function, and evolution. However, often genes of interest are not completely or accurately assembled, leading to unknown errors in analyses or additional cloning effo ... Full text Link to item Cite

A hypothesis on a role of oxytocin in the social mechanisms of speech and vocal learning.

Journal Article Proc Biol Sci · August 30, 2017 Language acquisition in humans and song learning in songbirds naturally happen as a social learning experience, providing an excellent opportunity to reveal social motivation and reward mechanisms that boost sensorimotor learning. Our knowledge about the m ... Full text Link to item Cite

Eliciting and Analyzing Male Mouse Ultrasonic Vocalization (USV) Songs.

Journal Article J Vis Exp · May 9, 2017 Mice produce ultrasonic vocalizations (USVs) in a variety of social contexts throughout development and adulthood. These USVs are used for mother-pup retrieval1, juvenile interactions2, opposite and same sex interactions3,4,5, and territorial interactions6 ... Full text Link to item Cite

Overexpression of human NR2B receptor subunit in LMAN causes stuttering and song sequence changes in adult zebra finches.

Journal Article Sci Rep · April 21, 2017 Zebra finches (Taeniopygia guttata) learn to produce songs in a manner reminiscent of spoken language development in humans. One candidate gene implicated in influencing learning is the N-methyl-D-aspartate (NMDA) subtype 2B glutamate receptor (NR2B). Cons ... Full text Link to item Cite

Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles.

Journal Article Genome Biol Evol · August 25, 2016 Homologous synteny blocks (HSBs) and evolutionary breakpoint regions (EBRs) in mammalian chromosomes are enriched for distinct DNA features, contributing to distinct phenotypes. To reveal HSB and EBR roles in avian evolution, we performed a sequence-based ... Full text Link to item Cite

Bone-associated gene evolution and the origin of flight in birds.

Journal Article BMC Genomics · May 18, 2016 BACKGROUND: Bones have been subjected to considerable selective pressure throughout vertebrate evolution, such as occurred during the adaptations associated with the development of powered flight. Powered flight evolved independently in two extant clades o ... Full text Link to item Cite

Whole-Genome Identification, Phylogeny, and Evolution of the Cytochrome P450 Family 2 (CYP2) Subfamilies in Birds.

Journal Article Genome Biol Evol · April 13, 2016 The cytochrome P450 (CYP) superfamily defends organisms from endogenous and noxious environmental compounds, and thus is crucial for survival. However, beyond mammals the molecular evolution of CYP2 subfamilies is poorly understood. Here, we characterized ... Full text Link to item Cite

Perspectives from the Avian Phylogenomics Project: Questions that Can Be Answered with Sequencing All Genomes of a Vertebrate Class.

Journal Article Annu Rev Anim Biosci · 2016 The rapid pace of advances in genome technology, with concomitant reductions in cost, makes it feasible that one day in our lifetime we will have available extant genomes of entire classes of species, including vertebrates. I recently helped cocoordinate t ... Full text Link to item Cite

A Foxp2 Mutation Implicated in Human Speech Deficits Alters Sequencing of Ultrasonic Vocalizations in Adult Male Mice.

Journal Article Front Behav Neurosci · 2016 Development of proficient spoken language skills is disrupted by mutations of the FOXP2 transcription factor. A heterozygous missense mutation in the KE family causes speech apraxia, involving difficulty producing words with complex learned sequences of sy ... Full text Open Access Link to item Cite

Brain evolution by brain pathway duplication.

Journal Article Philos Trans R Soc Lond B Biol Sci · December 19, 2015 Understanding the mechanisms of evolution of brain pathways for complex behaviours is still in its infancy. Making further advances requires a deeper understanding of brain homologies, novelties and analogies. It also requires an understanding of how adapt ... Full text Open Access Link to item Cite

Olfactory Receptor Subgenomes Linked with Broad Ecological Adaptations in Sauropsida.

Journal Article Mol Biol Evol · November 2015 Olfactory receptors (ORs) govern a prime sensory function. Extant birds have distinct olfactory abilities, but the molecular mechanisms underlining diversification and specialization remain mostly unknown. We explored OR diversity in 48 phylogenetic and ec ... Full text Open Access Link to item Cite

Surviving as an underrepresented minority scientist in a majority environment.

Journal Article Mol Biol Cell · November 1, 2015 I believe the evidence will show that the science we conduct and discoveries we make are influenced by our cultural experience, whether they be positive, negative, or neutral. I grew up as a person of color in the United States of America, faced with chall ... Full text Open Access Link to item Cite

Listening in.

Journal Article Elife · October 21, 2015 Zebra finches communicate with each other in ways that are more complex than previously thought. ... Full text Open Access Link to item Cite

Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds.

Journal Article BMC Genomics · October 6, 2015 BACKGROUND: The wide range of complex photic systems observed in birds exemplifies one of their key evolutionary adaptions, a well-developed visual system. However, genomic approaches have yet to be used to disentangle the evolutionary mechanisms that gove ... Full text Open Access Link to item Cite

The Origin and Diversification of Birds.

Journal Article Curr Biol · October 5, 2015 Birds are one of the most recognizable and diverse groups of modern vertebrates. Over the past two decades, a wealth of new fossil discoveries and phylogenetic and macroevolutionary studies has transformed our understanding of how birds originated and beca ... Full text Open Access Link to item Cite

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".

Journal Article Science · September 25, 2015 Mitchell et al. argue that divergence-time estimates for our avian phylogeny were too young because of an "inappropriate" maximum age constraint for the most recent common ancestor of modern birds and that, as a result, most modern bird orders diverged bef ... Full text Open Access Link to item Cite

Transsynaptic Tracing from Peripheral Targets with Pseudorabies Virus Followed by Cholera Toxin and Biotinylated Dextran Amines Double Labeling.

Journal Article J Vis Exp · September 14, 2015 Transsynaptic tracing has become a powerful tool used to analyze central efferents that regulate peripheral targets through multi-synaptic circuits. This approach has been most extensively used in the brain by utilizing the swine pathogen pseudorabies viru ... Full text Open Access Link to item Cite

A refined model of the genomic basis for phenotypic variation in vertebrate hemostasis.

Journal Article BMC Evol Biol · June 30, 2015 BACKGROUND: Hemostasis is a defense mechanism that enhances an organism's survival by minimizing blood loss upon vascular injury. In vertebrates, hemostasis has been evolving with the cardio-vascular and hemodynamic systems over the last 450 million years. ... Full text Open Access Link to item Cite

Convergent differential regulation of SLIT-ROBO axon guidance genes in the brains of vocal learners.

Journal Article J Comp Neurol · April 15, 2015 Only a few distantly related mammals and birds have the trait of complex vocal learning, which is the ability to imitate novel sounds. This ability is critical for speech acquisition and production in humans, and is attributed to specialized forebrain voca ... Full text Open Access Link to item Cite

Avianbase: a community resource for bird genomics.

Journal Article Genome Biol · January 29, 2015 Giving access to sequence and annotation data for genome assemblies is important because, while facilitating research, it places both assembly and annotation quality under scrutiny, resulting in improvements to both. Therefore we announce Avianbase, a reso ... Full text Open Access Link to item Cite

Phylogenomic analyses data of the avian phylogenomics project.

Journal Article Gigascience · 2015 BACKGROUND: Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most ... Full text Open Access Link to item Cite

Male mice song syntax depends on social contexts and influences female preferences.

Journal Article Front Behav Neurosci · 2015 In 2005, Holy and Guo advanced the idea that male mice produce ultrasonic vocalizations (USV) with some features similar to courtship songs of songbirds. Since then, studies showed that male mice emit USV songs in different contexts (sexual and other) and ... Full text Open Access Link to item Cite

Core and Shell Song Systems Unique to the Parrot Brain.

Journal Article PLoS One · 2015 The ability to imitate complex sounds is rare, and among birds has been found only in parrots, songbirds, and hummingbirds. Parrots exhibit the most advanced vocal mimicry among non-human animals. A few studies have noted differences in connectivity, brain ... Full text Open Access Link to item Cite

Identification of dopamine receptors across the extant avian family tree and analysis with other clades uncovers a polyploid expansion among vertebrates.

Journal Article Front Neurosci · 2015 Dopamine is an important central nervous system transmitter that functions through two classes of receptors (D1 and D2) to influence a diverse range of biological processes in vertebrates. With roles in regulating neural activity, behavior, and gene expres ... Full text Open Access Link to item Cite

The Genome 10K Project: a way forward.

Journal Article Annu Rev Anim Biosci · 2015 The Genome 10K Project was established in 2009 by a consortium of biologists and genome scientists determined to facilitate the sequencing and analysis of the complete genomes of 10,000 vertebrate species. Since then the number of selected and initiated sp ... Full text Link to item Cite

Comparative genomics reveals molecular features unique to the songbird lineage.

Journal Article BMC Genomics · December 13, 2014 BACKGROUND: Songbirds (oscine Passeriformes) are among the most diverse and successful vertebrate groups, comprising almost half of all known bird species. Identifying the genomic innovations that might be associated with this success, as well as with char ... Full text Open Access Link to item Cite

Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles.

Journal Article BMC Evol Biol · December 12, 2014 BACKGROUND: Vertebrate skin appendages are constructed of keratins produced by multigene families. Alpha (α) keratins are found in all vertebrates, while beta (β) keratins are found exclusively in reptiles and birds. We have studied the molecular evolution ... Full text Open Access Link to item Cite

Comparative genomics reveals insights into avian genome evolution and adaptation.

Journal Article Science · December 12, 2014 Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principall ... Full text Open Access Link to item Cite

Whole-genome analyses resolve early branches in the tree of life of modern birds.

Journal Article Science · December 12, 2014 To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that con ... Full text Open Access Link to item Cite

Complex evolutionary trajectories of sex chromosomes across bird taxa.

Journal Article Science · December 12, 2014 Sex-specific chromosomes, like the W of most female birds and the Y of male mammals, usually have lost most genes owing to a lack of recombination. We analyze newly available genomes of 17 bird species representing the avian phylogenetic range, and find th ... Full text Open Access Link to item Cite

Convergent transcriptional specializations in the brains of humans and song-learning birds.

Journal Article Science · December 12, 2014 Song-learning birds and humans share independently evolved similarities in brain pathways for vocal learning that are essential for song and speech and are not found in most other species. Comparisons of brain transcriptomes of song-learning birds and huma ... Full text Open Access Link to item Cite

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

Journal Article Science · December 12, 2014 To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater c ... Full text Open Access Link to item Cite

Core and region-enriched networks of behaviorally regulated genes and the singing genome.

Journal Article Science · December 12, 2014 Songbirds represent an important model organism for elucidating molecular mechanisms that link genes with complex behaviors, in part because they have discrete vocal learning circuits that have parallels with those that mediate human speech. We found that ... Full text Open Access Link to item Cite

Evidence for a single loss of mineralized teeth in the common avian ancestor.

Journal Article Science · December 12, 2014 Edentulism, the absence of teeth, has evolved convergently among vertebrates, including birds, turtles, and several lineages of mammals. Instead of teeth, modern birds (Neornithes) use a horny beak (rhamphotheca) and a muscular gizzard to acquire and proce ... Full text Open Access Link to item Cite

Genomic resources for the endangered Hawaiian honeycreepers.

Journal Article BMC Genomics · December 12, 2014 BACKGROUND: The Hawaiian honeycreepers are an avian adaptive radiation containing many endangered and extinct species. They display a dramatic range of phenotypic variation and are a model system for studies of evolution, conservation, disease dynamics and ... Full text Open Access Link to item Cite

Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor.

Journal Article BMC Genomics · December 11, 2014 BACKGROUND: The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype an ... Full text Open Access Link to item Cite

The basal ganglia within a cognitive system in birds and mammals.

Journal Article Behav Brain Sci · December 2014 The primate basal ganglia are fundamental to Ackermann et al.'s proposal. However, primates and rodents are models for human cognitive functions involving basal ganglia circuits, and links between striatal function and vocal communication come from songbir ... Full text Link to item Cite

Basal ganglia function, stuttering, sequencing, and repair in adult songbirds.

Journal Article Sci Rep · October 13, 2014 A pallial-basal-ganglia-thalamic-pallial loop in songbirds is involved in vocal motor learning. Damage to its basal ganglia part, Area X, in adult zebra finches has been noted to have no strong effects on song and its function is unclear. Here we report th ... Full text Open Access Link to item Cite

NSF workshop report: discovering general principles of nervous system organization by comparing brain maps across species.

Journal Article J Comp Neurol · May 1, 2014 Efforts to understand nervous system structure and function have received new impetus from the federal Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative. Comparative analyses can contribute to this effort by leading to the di ... Full text Open Access Link to item Cite

NSF workshop report: discovering general principles of nervous system organization by comparing brain maps across species.

Journal Article Brain Behav Evol · 2014 Efforts to understand nervous system structure and function have received new impetus from the federal Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative. Comparative analyses can contribute to this effort by leading to the di ... Full text Open Access Link to item Cite

High-coverage sequencing and annotated assemblies of the budgerigar genome.

Journal Article Gigascience · 2014 BACKGROUND: Parrots belong to a group of behaviorally advanced vertebrates and have an advanced ability of vocal learning relative to other vocal-learning birds. They can imitate human speech, synchronize their body movements to a rhythmic beat, and unders ... Full text Open Access Link to item Cite

Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition.

Journal Article Genome Biol · 2014 BACKGROUND: While effective population size (Ne) and life history traits such as generation time are known to impact substitution rates, their potential effects on base composition evolution are less well understood. GC content increases with decreasing bo ... Full text Open Access Link to item Cite

Low frequency of paleoviral infiltration across the avian phylogeny.

Journal Article Genome Biol · 2014 BACKGROUND: Mammalian genomes commonly harbor endogenous viral elements. Due to a lack of comparable genome-scale sequence data, far less is known about endogenous viral elements in avian species, even though their small genomes may enable important insigh ... Full text Open Access Link to item Cite

Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species.

Journal Article Genome Biol · 2014 BACKGROUND: Nearly one-quarter of all avian species is either threatened or nearly threatened. Of these, 73 species are currently being rescued from going extinct in wildlife sanctuaries. One of the previously most critically-endangered is the crested ibis ... Full text Open Access Link to item Cite

Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment.

Journal Article Gigascience · 2014 BACKGROUND: Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the host ... Full text Open Access Link to item Cite

Comparative genomic data of the Avian Phylogenomics Project.

Dataset · 2014 BACKGROUND: The evolutionary relationships of modern birds are among the most challenging to understand in systematic biology and have been debated for centuries. To address this challenge, we assembled or collected the genomes of 48 avian species spanning ... Full text Open Access Link to item Cite

Evolutionary genomics and adaptive evolution of the Hedgehog gene family (Shh, Ihh and Dhh) in vertebrates.

Journal Article PLoS One · 2014 The Hedgehog (Hh) gene family codes for a class of secreted proteins composed of two active domains that act as signalling molecules during embryo development, namely for the development of the nervous and skeletal systems and the formation of the testis c ... Full text Open Access Link to item Cite

Maintenance and neuronal differentiation of chicken induced pluripotent stem-like cells.

Journal Article Stem Cells Int · 2014 Pluripotent stem cells have the potential to become any cell in the adult body, including neurons and glia. Avian stem cells could be used to study questions, like vocal learning, that would be difficult to examine with traditional mouse models. Induced pl ... Full text Open Access Link to item Cite

Molecular profiling of the developing avian telencephalon: regional timing and brain subdivision continuities.

Journal Article J Comp Neurol · November 2013 In our companion study (Jarvis et al. [2013] J Comp Neurol. doi: 10.1002/cne.23404) we used quantitative brain molecular profiling to discover that distinct subdivisions in the avian pallium above and below the ventricle and the associated mesopallium lami ... Full text Open Access Link to item Cite

Global view of the functional molecular organization of the avian cerebrum: mirror images and functional columns.

Journal Article J Comp Neurol · November 2013 Based on quantitative cluster analyses of 52 constitutively expressed or behaviorally regulated genes in 23 brain regions, we present a global view of telencephalic organization of birds. The patterns of constitutively expressed genes revealed a partial mi ... Full text Open Access Link to item Cite

Different mechanisms are responsible for dishabituation of electrophysiological auditory responses to a change in acoustic identity than to a change in stimulus location.

Journal Article Neurobiol Learn Mem · November 2013 Repeated exposure to an auditory stimulus leads to habituation of the electrophysiological and immediate-early-gene (IEG) expression response in the auditory system. A novel auditory stimulus reinstates this response in a form of dishabituation. This has b ... Full text Open Access Link to item Cite

Global view of the functional molecular organization of the avian cerebrum: mirror images and functional columns.

Journal Article J Comp Neurol · November 2013 Based on quantitative cluster analyses of 52 constitutively expressed or behaviorally regulated genes in 23 brain regions, we present a global view of telencephalic organization of birds. The patterns of constitutively expressed genes revealed a partial mi ... Full text Link to item Cite

Mammalian genes induce partially reprogrammed pluripotent stem cells in non-mammalian vertebrate and invertebrate species.

Journal Article Elife · September 3, 2013 Cells are fundamental units of life, but little is known about evolution of cell states. Induced pluripotent stem cells (iPSCs) are once differentiated cells that have been re-programmed to an embryonic stem cell-like state, providing a powerful platform f ... Full text Open Access Link to item Cite

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Journal Article Gigascience · July 22, 2013 BACKGROUND: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available ... Full text Open Access Link to item Cite

The genomic consequences of adaptive divergence and reproductive isolation between species of manakins.

Journal Article Mol Ecol · June 2013 The processes of adaptation and speciation are expected to shape genomic variation within and between diverging species. Here we analyze genomic heterogeneity of genetic differentiation and introgression in a hybrid zone between two bird species (Manacus c ... Full text Open Access Link to item Cite

Detecting neural activity-dependent immediate early gene expression in the brain

Chapter · January 1, 2013 In this chapter, we present an in situ hybridization protocol with radioactive probe that has been successfully and easily used on detecting mRNA expression level and patterns, in multiple tissue types and developmental stages. To detect behaviorally regul ... Full text Cite

Mouse vocal communication system: are ultrasounds learned or innate?

Journal Article Brain Lang · January 2013 Mouse ultrasonic vocalizations (USVs) are often used as behavioral readouts of internal states, to measure effects of social and pharmacological manipulations, and for behavioral phenotyping of mouse models for neuropsychiatric and neurodegenerative disord ... Full text Open Access Link to item Cite

Rudimentary substrates for vocal learning in a suboscine.

Journal Article Nat Commun · 2013 Vocal learning has evolved in only a few groups of mammals and birds. The key neuroanatomical and behavioural links bridging vocal learners and non-learners are still unknown. Here we show that a non-vocal-learning suboscine, the eastern phoebe, expresses ... Full text Open Access Link to item Cite

Birds, primates, and spoken language origins: Behavioral phenotypes and neurobiological substrates

Journal Article Frontiers in Evolutionary Neuroscience · December 1, 2012 Vocal learners such as humans and songbirds can learn to produce elaborate patterns of structurally organized vocalizations, whereas many other vertebrates such as non-human primates and most other bird groups either cannot or do so to a very limited degre ... Full text Open Access Cite

Dopamine regulation of human speech and bird song: a critical review.

Journal Article Brain Lang · September 2012 To understand the neural basis of human speech control, extensive research has been done using a variety of methodologies in a range of experimental models. Nevertheless, several critical questions about learned vocal motor control still remain open. One o ... Full text Open Access Link to item Cite

Hybrid error correction and de novo assembly of single-molecule sequencing reads.

Journal Article Nat Biotechnol · July 1, 2012 Single-molecule sequencing instruments can generate multikilobase sequences with the potential to greatly improve genome and transcriptome assembly. However, the error rates of single-molecule reads are high, which has limited their use thus far to reseque ... Full text Open Access Link to item Cite

Radioactive in situ hybridization for detecting diverse gene expression patterns in tissue.

Journal Article J Vis Exp · April 27, 2012 Knowing the timing, level, cellular localization, and cell type that a gene is expressed in contributes to our understanding of the function of the gene. Each of these features can be accomplished with in situ hybridization to mRNAs within cells. Here we p ... Full text Open Access Link to item Cite

Radioactive in situ hybridization for detecting diverse gene expression patterns in tissue

Journal Article Journal of Visualized Experiments · April 27, 2012 Knowing the timing, level, cellular localization, and cell type that a gene is expressed in contributes to our understanding of the function of the gene. Each of these features can be accomplished with in situ hybridization to mRNAs within cells. Here we p ... Full text Cite

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes.

Journal Article Genome Biol · January 31, 2012 The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these proje ... Full text Open Access Link to item Cite

Of mice, birds, and men: the mouse ultrasonic song system has some features similar to humans and song-learning birds.

Journal Article PLoS One · 2012 Humans and song-learning birds communicate acoustically using learned vocalizations. The characteristic features of this social communication behavior include vocal control by forebrain motor areas, a direct cortical projection to brainstem vocal motor neu ... Full text Open Access Link to item Cite

Interspecies avian brain chimeras reveal that large brain size differences are influenced by cell-interdependent processes.

Journal Article PLoS One · 2012 Like humans, birds that exhibit vocal learning have relatively delayed telencephalon maturation, resulting in a disproportionately smaller brain prenatally but enlarged telencephalon in adulthood relative to vocal non-learning birds. To determine if this s ... Full text Open Access Link to item Cite

Specialized motor-driven dusp1 expression in the song systems of multiple lineages of vocal learning birds.

Journal Article PLoS One · 2012 Mechanisms for the evolution of convergent behavioral traits are largely unknown. Vocal learning is one such trait that evolved multiple times and is necessary in humans for the acquisition of spoken language. Among birds, vocal learning is evolved in song ... Full text Open Access Link to item Cite

Convergent differential regulation of parvalbumin in the brains of vocal learners.

Journal Article PLoS One · 2012 Spoken language and learned song are complex communication behaviors found in only a few species, including humans and three groups of distantly related birds--songbirds, parrots, and hummingbirds. Despite their large phylogenetic distances, these vocal le ... Full text Open Access Link to item Cite

Dynamic evolution of base composition: causes and consequences in avian phylogenomics.

Journal Article Mol Biol Evol · August 2011 Resolving the phylogenetic relationships among birds is a classical problem in systematics, and this is particularly so when it comes to understanding the relationships among Neoaves. Previous phylogenetic inference of birds has been limited to mitochondri ... Full text Open Access Link to item Cite

Empowering 21st century biology

Journal Article BioScience · December 1, 2010 Several lists of grand challenges in biology have been published recently, highlighting the strong need to answer fundamental questions about how life evolves and is governed, and how to apply this knowledge to solve the pressing problems of our times. To ... Full text Open Access Cite

Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny.

Journal Article Mol Phylogenet Evol · October 2010 Classically, the mitochondrial genome is sequenced by a series of amplicons using conserved PCR primers. Here we show how shot-gun transcriptome sequencing can be used to obtain the complete set of protein-coding genes from the mtDNA of four passerine bird ... Full text Open Access Link to item Cite

Night-time neuronal activation of Cluster N in a day- and night-migrating songbird.

Journal Article Eur J Neurosci · August 2010 Magnetic compass orientation in a night-migratory songbird requires that Cluster N, a cluster of forebrain regions, is functional. Cluster N, which receives input from the eyes via the thalamofugal pathway, shows high neuronal activity in night-migrants pe ... Full text Open Access Link to item Cite

The dusp1 immediate early gene is regulated by natural stimuli predominantly in sensory input neurons.

Journal Article J Comp Neurol · July 15, 2010 Many immediate early genes (IEGs) have activity-dependent induction in a subset of brain subdivisions or neuron types. However, none have been reported yet with regulation specific to thalamic-recipient sensory neurons of the telencephalon or in the thalam ... Full text Open Access Link to item Cite

The genome of a songbird.

Journal Article Nature · April 1, 2010 The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other a ... Full text Open Access Link to item Cite

Dopamine receptors in a songbird brain.

Journal Article J Comp Neurol · March 15, 2010 Dopamine is a key neuromodulatory transmitter in the brain. It acts through dopamine receptors to affect changes in neural activity, gene expression, and behavior. In songbirds, dopamine is released into the striatal song nucleus Area X, and the levels dep ... Full text Open Access Link to item Cite

Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.

Journal Article Mol Ecol · March 2010 Next-generation sequencing technology provides an attractive means to obtain large-scale sequence data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation and selection intensity across the avian genome, we perfor ... Full text Open Access Link to item Cite

Assessing visual requirements for social context-dependent activation of the songbird song system.

Journal Article Proc Biol Sci · January 22, 2009 Social context has been shown to have a profound influence on brain activation in a wide range of vertebrate species. Best studied in songbirds, when males sing undirected song, the level of neural activity and expression of immediate early genes (IEGs) in ... Full text Open Access Link to item Cite

Behaviorally regulated mRNA and protein expression in the songbird brain

Chapter · January 1, 2009 Most biological processes are the result of the regulated expression of genes into their protein products in a defined temporal and spatial manner. The study of these dynamic protein changes in the brain is called neuroproteomics. A class of proteins expre ... Cite

Bird song systems: Evolution

Journal Article · January 1, 2009 This article presents the vocal and auditory pathways of vocal-learning birds and a hypothesis about their evolution. These pathways control the ability to produce learned song in the few groups of birds that have vocal learning abilities, songbirds, parro ... Full text Open Access Cite

Bird Brain: Evolution

Journal Article · January 1, 2009 This article presents the classic and modern views of avian brain evolution in the context of vertebrate brain evolution. The classical view held that the avian cerebrum along with those of other vertebrates evolved in progressive dorsal-to-ventral stages ... Full text Open Access Cite

Early onset of deafening-induced song deterioration and differential requirements of the pallial-basal ganglia vocal pathway.

Journal Article Eur J Neurosci · December 2008 Similar to humans, songbirds rely on auditory feedback to maintain the acoustic and sequence structure of adult learned vocalizations. When songbirds are deafened, the learned features of song, such as syllable structure and sequencing, eventually deterior ... Full text Open Access Link to item Cite

Molecular mapping of movement-associated areas in the avian brain: a motor theory for vocal learning origin.

Journal Article PLoS One · March 12, 2008 Vocal learning is a critical behavioral substrate for spoken human language. It is a rare trait found in three distantly related groups of birds-songbirds, hummingbirds, and parrots. These avian groups have remarkably similar systems of cerebral vocal nucl ... Full text Open Access Link to item Cite

Profiling of experience-regulated proteins in the songbird auditory forebrain using quantitative proteomics.

Journal Article Eur J Neurosci · March 2008 Auditory and perceptual processing of songs are required for a number of behaviors in songbirds such as vocal learning, territorial defense, mate selection and individual recognition. These neural processes are accompanied by increased expression of a few ... Full text Open Access Link to item Cite

Neural systems for vocal learning in birds and humans: a synopsis.

Journal Article J Ornithol · December 1, 2007 I present here a synopsis on a hypothesis that I derived on the similarities and differences of vocal learning systems in vocal learning birds for learned song and in humans for spoken language. This hypothesis states that vocal learning birds-songbirds, p ... Full text Open Access Link to item Cite

Role of the midbrain dopaminergic system in modulation of vocal brain activation by social context.

Journal Article Eur J Neurosci · June 2007 In a well-studied model of social behaviour, male zebra finches sing directed song to court females and undirected song, used possibly for practice or advertisement. Although the two song types are similar, the level of neural activity and expression of th ... Full text Open Access Link to item Cite

The pallial basal ganglia pathway modulates the behaviorally driven gene expression of the motor pathway.

Journal Article Eur J Neurosci · April 2007 The discrete neural network for songbird vocal communication provides an effective system to study neural mechanisms of learned motor behaviors in vertebrates. This system consists of two pathways--a vocal motor pathway used to produce learned vocalization ... Full text Open Access Link to item Cite

Lateralized activation of Cluster N in the brains of migratory songbirds.

Journal Article Eur J Neurosci · February 2007 Cluster N is a cluster of forebrain regions found in night-migratory songbirds that shows high activation of activity-dependent gene expression during night-time vision. We have suggested that Cluster N may function as a specialized night-vision area in ni ... Full text Open Access Link to item Cite

The evolution of vocal learning systems in birds and humans

Journal Article · January 1, 2007 Vocal learning is a rare trait found to date in only three groups of distantly related birds - parrots, hummingbirds, and songbirds - and four groups of distantly related mammals - humans, bats, cetaceans, and elephants. Remarkably, the three groups of bir ... Full text Cite

Computational inference of neural information flow networks.

Journal Article PLoS Comput Biol · November 24, 2006 Determining how information flows along anatomical brain pathways is a fundamental requirement for understanding how animals perceive their environments, learn, and behave. Attempts to reveal such neural information flow have been made using linear computa ... Full text Open Access Link to item Cite

A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes.

Journal Article Proc Natl Acad Sci U S A · October 10, 2006 Songbirds have one of the most accessible neural systems for the study of brain mechanisms of behavior. However, neuroethological studies in songbirds have been limited by the lack of high-throughput molecular resources and gene-manipulation tools. To over ... Full text Open Access Link to item Cite

VOCALIZATIONS AND ASSOCIATED BEHAVIORS OF THE SOMBRE HUMMINGBIRD (APHANTOCHROA CIRRHOCHLORIS) AND THE RUFOUS-BREASTED HERMIT (GLAUCIS HIRSUTUS).

Journal Article Auk · October 2006 Vocal behavior in tropical hummingbirds is a new area of study. Here, we present findings on the vocalizations and associated behaviors of two species: Sombre Hummingbird (Aphantochroa cirrhochloris) and Rufous-breasted Hermit (Glaucis hirsutus). These are ... Full text Open Access Link to item Cite

Social context-dependent singing-regulated dopamine.

Journal Article J Neurosci · August 30, 2006 Like the mammalian striatum, the songbird striatum receives dense dopaminergic input from the midbrain ventral tegmental area-substantia nigra pars compacta complex. The songbird striatum also contains a unique vocal nucleus, Area X, which has been implica ... Full text Open Access Link to item Cite

Selection for and against vocal learning in birds and mammals

Journal Article Ornithological Science · January 1, 2006 Vocal learning, the substrate for human language, is a rare trait found to date in only three distantly related groups of birds (parrots, hummingbirds, and songbirds) and four distantly related groups of mammals (humans, bats, cetaceans, and elephants). Br ... Full text Cite

Rapid behavioral and genomic responses to social opportunity.

Journal Article PLoS biology. · November 1, 2005 From primates to bees, social status regulates reproduction. In the cichlid fish Astatotilapia (Haplochromis) burtoni, subordinate males have reduced fertility and must become dominant to reproduce. This increase in sexual capacity is orchestrated by neuro ... Open Access Cite

Rapid behavioral and genomic responses to social opportunity.

Journal Article PLoS Biol · November 2005 From primates to bees, social status regulates reproduction. In the cichlid fish Astatotilapia (Haplochromis) burtoni, subordinate males have reduced fertility and must become dominant to reproduce. This increase in sexual capacity is orchestrated by neuro ... Full text Link to item Cite

Night-vision brain area in migratory songbirds.

Journal Article Proc Natl Acad Sci U S A · June 7, 2005 Twice each year, millions of night-migratory songbirds migrate thousands of kilometers. To find their way, they must process and integrate spatiotemporal information from a variety of cues including the Earth's magnetic field and the night-time starry sky. ... Full text Open Access Link to item Cite

Avian brains and a new understanding of vertebrate brain evolution.

Journal Article Nat Rev Neurosci · February 2005 We believe that names have a powerful influence on the experiments we do and the way in which we think. For this reason, and in the light of new evidence about the function and evolution of the vertebrate brain, an international consortium of neuroscientis ... Full text Open Access Link to item Cite

Advances to Bayesian network inference for generating causal networks from observational biological data.

Journal Article Bioinformatics · December 12, 2004 MOTIVATION: Network inference algorithms are powerful computational tools for identifying putative causal interactions among variables from observational data. Bayesian network inference algorithms hold particular promise in that they can capture linear, n ... Full text Open Access Link to item Cite

Differential expression of glutamate receptors in avian neural pathways for learned vocalization.

Journal Article J Comp Neurol · August 9, 2004 Learned vocalization, the substrate for human language, is a rare trait. It is found in three distantly related groups of birds-parrots, hummingbirds, and songbirds. These three groups contain cerebral vocal nuclei for learned vocalization not found in the ... Full text Open Access Link to item Cite

Songbirds and the revised avian brain nomenclature.

Journal Article Ann N Y Acad Sci · June 2004 It has become increasingly clear that the standard nomenclature for many telencephalic and related brainstem structures of the avian brain is based on flawed once-held assumptions of homology to mammalian brain structures, greatly hindering functional comp ... Full text Open Access Link to item Cite

Learned birdsong and the neurobiology of human language.

Journal Article Ann N Y Acad Sci · June 2004 Vocal learning, the substrate for human language, is a rare trait found to date in only three distantly related groups of mammals (humans, bats, and cetaceans) and three distantly related groups of birds (parrots, hummingbirds, and songbirds). Brain pathwa ... Full text Open Access Link to item Cite

Revised nomenclature for avian telencephalon and some related brainstem nuclei.

Journal Article J Comp Neurol · May 31, 2004 The standard nomenclature that has been used for many telencephalic and related brainstem structures in birds is based on flawed assumptions of homology to mammals. In particular, the outdated terminology implies that most of the avian telencephalon is a h ... Full text Open Access Link to item Cite

FoxP2 expression in avian vocal learners and non-learners.

Journal Article J Neurosci · March 31, 2004 Most vertebrates communicate acoustically, but few, among them humans, dolphins and whales, bats, and three orders of birds, learn this trait. FOXP2 is the first gene linked to human speech and has been the target of positive selection during recent primat ... Full text Open Access Link to item Cite

Brains and birdsong

Journal Article · January 1, 2004 Scientists have a come a long way in their studies of brains and birdsong. The discovery of new neurons in the adult brain has revolutionary implications for medical science. The molecular biology of vocal learning is helpful in understanding genetic mecha ... Full text Open Access Cite

Rapid response of the preoptic area to social opportunity

Conference INTEGRATIVE AND COMPARATIVE BIOLOGY · December 1, 2003 Link to item Cite

Analysis of the mouse transcriptome for genes involved in the function of the nervous system.

Journal Article Genome Res · June 2003 We analyzed the mouse Representative Transcript and Protein Set for molecules involved in brain function. We found full-length cDNAs of many known brain genes and discovered new members of known brain gene families, including Family 3 G-protein coupled rec ... Full text Open Access Link to item Cite

Influence of network topology and data collection on network inference.

Conference Pac Symp Biocomput · 2003 We recently developed an approach for testing the accuracy of network inference algorithms by applying them to biologically realistic simulations with known network topology. Here, we seek to determine the degree to which the network topology and data samp ... Open Access Link to item Cite

Induction of hippocampal long-term potentiation during waking leads to increased extrahippocampal zif-268 expression during ensuing rapid-eye-movement sleep.

Journal Article J Neurosci · December 15, 2002 Rapid-eye-movement (REM) sleep plays a key role in the consolidation of memories acquired during waking (WK). The search for mechanisms underlying that role has revealed significant correlations in the patterns of neuronal firing, regional blood flow, and ... Full text Open Access Link to item Cite

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

Journal Article Nature · December 5, 2002 Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physic ... Full text Open Access Link to item Cite

A framework for integrating the songbird brain.

Journal Article J Comp Physiol A Neuroethol Sens Neural Behav Physiol · December 2002 Featured Publication Biological systems by default involve complex components with complex relationships. To decipher how biological systems work, we assume that one needs to integrate information over multiple levels of complexity. The songbird vocal communication system is i ... Full text Open Access Link to item Cite

Evaluating functional network inference using simulations of complex biological systems.

Journal Article Bioinformatics · 2002 Featured Publication MOTIVATION: Although many network inference algorithms have been presented in the bioinformatics literature, no suitable approach has been formulated for evaluating their effectiveness at recovering models of complex biological systems from limited data. T ... Full text Open Access Link to item Cite

The importance of anatomical substrates

Journal Article Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technolgoy, CBGIST 2001 · December 1, 2001 At Duke University we have recently formed a Songbird Consortium, whose purpose is to utilize multi-level analysis to decipher how the brain learns and generates complex behavior. Songbirds share with humans the rare trait of vocal learning. This makes the ... Cite

A membrane-associated progesterone-binding protein, 25-Dx, is regulated by progesterone in brain regions involved in female reproductive behaviors.

Journal Article Proc Natl Acad Sci U S A · November 7, 2000 The ventromedial hypothalamus (VMH) plays a central role in the regulation of the female reproductive behavior lordosis, a behavior dependent upon the sequential activation of receptors for the ovarian steroid hormones estradiol (E) and progesterone (P). T ... Full text Open Access Link to item Cite

Behaviourally driven gene expression reveals song nuclei in hummingbird brain.

Journal Article Nature · August 10, 2000 Featured Publication Hummingbirds have developed a wealth of intriguing features, such as backwards flight, ultraviolet vision, extremely high metabolic rates, nocturnal hibernation, high brain-to-body size ratio and a remarkable species-specific diversity of vocalizations. Li ... Full text Open Access Link to item Cite

Site-specific retinoic acid production in the brain of adult songbirds.

Journal Article Neuron · August 2000 The song system of songbirds, a set of brain nuclei necessary for song learning and production, has distinctive morphological and functional properties. Utilizing differential display, we searched for molecular components involved in song system regulation ... Full text Open Access Link to item Cite

A relationship between behavior, neurotrophin expression, and new neuron survival.

Journal Article Proc Natl Acad Sci U S A · July 18, 2000 Featured Publication The high vocal center (HVC) controls song production in songbirds and sends a projection to the robust nucleus of the archistriatum (RA) of the descending vocal pathway. HVC receives new neurons in adulthood. Most of the new neurons project to RA and repla ... Full text Open Access Link to item Cite

Molecular mapping of brain areas involved in parrot vocal communication.

Journal Article J Comp Neurol · March 27, 2000 Featured Publication Auditory and vocal regulation of gene expression occurs in separate discrete regions of the songbird brain. Here we demonstrate that regulated gene expression also occurs during vocal communication in a parrot, belonging to an order whose ability to learn ... Full text Open Access Link to item Cite

Chapter 2.2.2 Applying differential display to brain research

Journal Article Techniques in the Behavioral and Neural Sciences · December 1, 1999 Full text Cite

Cooperative colonial patterning in the genus B acillus

Journal Article FASEB JOURNAL · April 23, 1999 Link to item Cite

The 70-kDa heat shock cognate protein (Hsc73) gene is enhanced by ovarian hormones in the ventromedial hypothalamus.

Journal Article Proc Natl Acad Sci U S A · February 16, 1999 Estrogen (E) and progesterone (P) orchestrate many cellular responses involved in female reproductive physiology, including reproductive behaviors. E- and P-binding neurons important for lordosis behavior have been located within the ventromedial hypothala ... Full text Open Access Link to item Cite

The name game

Other SCIENTIFIC AMERICAN · February 1, 1999 Link to item Cite

For whom the bird sings: context-dependent gene expression.

Journal Article Neuron · October 1998 Featured Publication Male zebra finches display two song behaviors: directed and undirected singing. The two differ little in the vocalizations produced but greatly in how song is delivered. "Directed" song is usually accompanied by a courtship dance and is addressed almost ex ... Full text Open Access Link to item Cite

Classification and genetic characterization of pattern-forming Bacilli.

Journal Article Mol Microbiol · February 1998 One of the more natural but less commonly studied forms of colonial bacterial growth is pattern formation. This type of growth is characterized by bacterial populations behaving in an organized manner to generate readily identifiable geometric and predicta ... Full text Open Access Link to item Cite

Selective expression of insulin-like growth factor II in the songbird brain.

Journal Article J Neurosci · September 15, 1997 Neuronal replacement occurs in the forebrain of juvenile and adult songbirds. To address the molecular processes that govern this replacement, we cloned the zebra finch insulin-like growth factor II (IGF-II) cDNA, a factor known to regulate neuronal develo ... Full text Open Access Link to item Cite

Brain gene regulation by territorial singing behavior in freely ranging songbirds.

Journal Article Neuroreport · May 27, 1997 To investigate the ecological relevance of brain gene regulation associated with singing behavior in songbirds, we challenged freely ranging song sparrows with conspecific song playbacks within their breeding territories. Males responded by approaching the ... Full text Open Access Link to item Cite

Motor-driven gene expression.

Journal Article Proc Natl Acad Sci U S A · April 15, 1997 Featured Publication There is increased neuronal firing in the high vocal center (a motor nucleus) and other song nuclei of canaries, Serinus canaria, and zebra finches, Taeniopygia guttata, whenever these songbirds sing or hear song. These observations suggested that song per ... Full text Open Access Link to item Cite

Identification of aberrantly regulated genes in diseased skin using the cDNA differential display technique.

Journal Article J Invest Dermatol · February 1997 It is hypothesized that psoriasis may be caused by aberrant gene expression. In an effort to identify and clone psoriasis-specific genes, we compared gene expression in normal, tape-stripped (wounded), and psoriatic skin using the cDNA differential display ... Full text Link to item Cite

Decrements in auditory responses to a repeated conspecific song are long-lasting and require two periods of protein synthesis in the songbird forebrain.

Journal Article Proc Natl Acad Sci U S A · April 11, 1995 Earlier work showed that playbacks of conspecific song induce expression of the immediate early gene ZENK in the caudo-medial neostriatum (NCM) of awake male zebra finches and that this response disappears with repeated presentations of the same stimulus. ... Full text Link to item Cite

Associative learning and stimulus novelty influence the song-induced expression of an immediate early gene in the canary forebrain.

Journal Article Learn Mem · 1995 To identify variables that affect immediate early gene (IEG) expression in the auditory telencephalon of songbirds, we developed a conditioning paradigm that trained adult male canaries to associate song with a mild shock. Learning of the association was m ... Full text Link to item Cite

Two tRNA gene clusters associated with rRNA operons rrnD and rrnE in Bacillus subtilis.

Journal Article J Bacteriol · January 1993 Sequence analysis of cloned rescued DNA fragments from a Bacillus subtilis strain with an inserted recombinant plasmid in ribosomal operon rrnE revealed the presence of two tRNA genes for Met and Asp at the 3' end of the operon. Probing chromosomal DNA fro ... Full text Link to item Cite

Genetic structure and DNA sequences at junctions involved in the rearrangements of Bacillus subtilis strains carrying the trpE26 mutation.

Journal Article Genetics · December 1990 Studies on the region upstream to ribosomal operon rrnD of Bacillus subtilis led to the characterization of two of the four chromosomal junctions involved in the rearrangements (a translocation and an inversion) of the strains carrying the trpE26 mutation. ... Full text Link to item Cite

The structure of the trpE, trpD and 5' trpC genes of Bacillus pumilus.

Journal Article Gene · March 1, 1990 The nucleotide (nt) sequences of the Bacillus pumilus trpE, trpD and 5' portions of trpC genes have been determined. Genetic analysis suggested the presence of an internal promoter upstream from the trpC gene, yet no typical consensus sequences were found. ... Full text Link to item Cite

Chromosomal organization of rRNA operons in Bacillus subtilis.

Journal Article Genetics · November 1988 Integrative mapping with vectors containing ribosomal DNA sequences were used to complete the mapping of the 10 rRNA gene sets in the endospore forming bacterium Bacillus subtilis. Southern hybridizations allowed the assignment of nine operons to distinct ... Full text Link to item Cite

Instability of rRNA operons in Bacillus subtilis.

Journal Article J Bacteriol · February 1988 Many laboratory strains of Bacillus subtilis contain 9 rather than 10 rRNA operons due to deletions occurring within the rrnJ-rrnW or rrnI-rrnH-rrnG gene cluster. These operons are members of two sets of closely spaced clusters located in the cysA-aroI reg ... Full text Link to item Cite

Mapping of rRNA genes with integrable plasmids in Bacillus subtilis.

Journal Article J Bacteriol · January 1986 Integrable plasmids pGR102 and pWR103 containing ribosomal sequences from within the transcriptional units for 16S and 23S were used to transform Bacillus subtilis. To date, these plasmids integrated into 7 of 10 known rrn operons. Two such events occurred ... Full text Link to item Cite