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Article: Adopting Duplex Sequencing™ Technology for Genetic Toxicity Testing: A Proof-of-Concept Mutagenesis Experiment with N-Ethyl-N-Nitrosourea (ENU)-Exposed Rats.

Smith-Roe, Stephanie L / Hobbs, Cheryl A / Hull, Victoria / Auman, J Todd / Recio, Leslie / Streicker, Michael A / Rivas, Miriam V / Pratt, Gabriel A / Lo, Fang Yin / Higgins, Jacob E / Schmidt, Elizabeth K / Williams, Lindsey N / Nachmanson, Daniela / Valentine, Charles C / Salk, Jesse J / Witt, Kristine L

bioRxiv : the preprint server for biology

2023

Abstract: Duplex sequencing (DuplexSeq) is an error-corrected next-generation sequencing (ecNGS) method in which molecular barcodes informatically link PCR-copies back to their source DNA strands, enabling computational removal of errors by comparing grouped ... ...

Abstract	Duplex sequencing (DuplexSeq) is an error-corrected next-generation sequencing (ecNGS) method in which molecular barcodes informatically link PCR-copies back to their source DNA strands, enabling computational removal of errors by comparing grouped strand sequencing reads. The resulting background of less than one artifactual mutation per 10 Highlights: DuplexSeq is an ultra-accurate NGS technology that directly quantifies mutationsENU-dependent mutagenesis was detected 24 h post-exposure in proliferative tissuesMultiple tissues exhibited the canonical ENU mutation spectrum 7 d after exposureResults obtained with DuplexSeq were highly concordant between laboratoriesThe Rat-50 Mutagenesis Assay is promising for applications in genetic toxicology.
Language	English
Publishing date	2023-05-09
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.05.08.539833
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Article ; Online: Adopting duplex sequencing technology for genetic toxicity testing: A proof-of-concept mutagenesis experiment with N-ethyl-N-nitrosourea (ENU)-exposed rats.

Smith-Roe, Stephanie L / Hobbs, Cheryl A / Hull, Victoria / Todd Auman, J / Recio, Leslie / Streicker, Michael A / Rivas, Miriam V / Pratt, Gabriel A / Lo, Fang Yin / Higgins, Jacob E / Schmidt, Elizabeth K / Williams, Lindsey N / Nachmanson, Daniela / Valentine Iii, Charles C / Salk, Jesse J / Witt, Kristine L

Mutation research. Genetic toxicology and environmental mutagenesis

2023 Volume 891, Page(s) 503669

Abstract: Duplex sequencing (DS) is an error-corrected next-generation sequencing method in which molecular barcodes informatically link PCR-copies back to their source DNA strands, enabling computational removal of errors in consensus sequences. The resulting ... ...

Abstract	Duplex sequencing (DS) is an error-corrected next-generation sequencing method in which molecular barcodes informatically link PCR-copies back to their source DNA strands, enabling computational removal of errors in consensus sequences. The resulting background of less than one artifactual mutation per 10
MeSH term(s)	Rats ; Male ; Animals ; Ethylnitrosourea/toxicity ; Reproducibility of Results ; Rats, Sprague-Dawley ; Mutagenesis ; Mutation ; Nitrosourea Compounds ; Mutagens/toxicity
Chemical Substances	Ethylnitrosourea (P8M1T4190R) ; Nitrosourea Compounds ; Mutagens
Language	English
Publishing date	2023-08-03
Publishing country	Netherlands
Document type	Journal Article
ISSN	1879-3592
ISSN (online)	1879-3592
DOI	10.1016/j.mrgentox.2023.503669
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Article ; Online: Adherens junctional associated protein-1: a novel 1p36 tumor suppressor candidate in gliomas (Review).

Zeng, Liang / Fee, Brian E / Rivas, Miriam V / Lin, James / Adamson, David Cory

International journal of oncology

2014 Volume 45, Issue 1, Page(s) 13–17

Abstract: In a broad range of human cancers 1p36 has been a mutational hotspot which strongly suggests that the loss of tumor suppressor activity maps to this genomic region during tumorigenesis. Adherens junctional associated protein-1 (AJAP1; also known as ... ...

Abstract	In a broad range of human cancers 1p36 has been a mutational hotspot which strongly suggests that the loss of tumor suppressor activity maps to this genomic region during tumorigenesis. Adherens junctional associated protein-1 (AJAP1; also known as Shrew1) was initially discovered as a novel transmembrane protein of adherent junctions in epithelial cells. Gene profiling showed AJAP1 on 1p36 is frequently lost or epigenetically silenced. AJAP1 may affect cell motility, migration, invasion and proliferation by unclear mechanisms. AJAP1 may be translocated to the nucleus, via its interaction with β-catenin complexes, where it can regulate gene transcription, then possibly have a potent impact on cell cycling and apoptosis. Significantly, loss of AJAP1 expression predicts poor clinical outcome of patients with malignant gliomas such as GBM and it may serve as a promising tumor suppressor-related target. In this review, we summarize and discuss current knowledge that may identify AJAP1 as a tumor suppressor in gliomas.
MeSH term(s)	Cell Adhesion Molecules/genetics ; Cell Adhesion Molecules/metabolism ; Chromosomes, Human, Pair 1/metabolism ; Epigenesis, Genetic ; Gene Deletion ; Gene Silencing ; Glioma/genetics ; Glioma/pathology ; Humans ; Mutation ; Tumor Suppressor Proteins/genetics ; Tumor Suppressor Proteins/metabolism
Chemical Substances	AJAP1 protein, human ; Cell Adhesion Molecules ; Tumor Suppressor Proteins
Language	English
Publishing date	2014-07
Publishing country	Greece
Document type	Journal Article ; Review
ZDB-ID	1154403-x
ISSN	1791-2423 ; 1019-6439
ISSN (online)	1791-2423
ISSN	1019-6439
DOI	10.3892/ijo.2014.2425
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Article ; Online: Convergent differential regulation of parvalbumin in the brains of vocal learners.

Hara, Erina / Rivas, Miriam V / Ward, James M / Okanoya, Kazuo / Jarvis, Erich D

PloS one

2012 Volume 7, Issue 1, Page(s) e29457

Abstract: 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 ... ...

Abstract	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 learners show convergent behaviors and associated brain pathways for vocal communication. However, it is not clear whether this behavioral and anatomical convergence is associated with molecular convergence. Here we used oligo microarrays to screen for genes differentially regulated in brain nuclei necessary for producing learned vocalizations relative to adjacent brain areas that control other behaviors in avian vocal learners versus vocal non-learners. A top candidate gene in our screen was a calcium-binding protein, parvalbumin (PV). In situ hybridization verification revealed that PV was expressed significantly higher throughout the song motor pathway, including brainstem vocal motor neurons relative to the surrounding brain regions of all distantly related avian vocal learners. This differential expression was specific to PV and vocal learners, as it was not found in avian vocal non-learners nor for control genes in learners and non-learners. Similar to the vocal learning birds, higher PV up-regulation was found in the brainstem tongue motor neurons used for speech production in humans relative to a non-human primate, macaques. These results suggest repeated convergent evolution of differential PV up-regulation in the brains of vocal learners separated by more than 65-300 million years from a common ancestor and that the specialized behaviors of learned song and speech may require extra calcium buffering and signaling.
MeSH term(s)	Animals ; Birds/anatomy & histology ; Birds/genetics ; Birds/metabolism ; Birds/physiology ; Brain/anatomy & histology ; Brain/metabolism ; Brain/physiology ; Brain Mapping/veterinary ; Gene Expression Regulation ; Humans ; Learning/physiology ; Macaca/anatomy & histology ; Macaca/genetics ; Macaca/metabolism ; Microarray Analysis ; Models, Biological ; Parrots/anatomy & histology ; Parrots/genetics ; Parrots/metabolism ; Parvalbumins/genetics ; Parvalbumins/metabolism ; Phylogeny ; Quail/anatomy & histology ; Quail/genetics ; Quail/metabolism ; Songbirds/anatomy & histology ; Songbirds/genetics ; Songbirds/metabolism ; Vocalization, Animal/physiology
Chemical Substances	Parvalbumins
Language	English
Publishing date	2012-01-06
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0029457
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Article ; Online: The dusp1 immediate early gene is regulated by natural stimuli predominantly in sensory input neurons.

Horita, Haruhito / Wada, Kazuhiro / Rivas, Miriam V / Hara, Erina / Jarvis, Erich D

The Journal of comparative neurology

2010 Volume 518, Issue 14, Page(s) 2873–2901

Abstract: 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 ... ...

Abstract	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 thalamic sensory input neurons themselves. Here, we report the first such gene, dual specificity phosphatase 1 (dusp1). Dusp1 is an inactivator of mitogen-activated protein kinase (MAPK), and MAPK activates expression of egr1, one of the most commonly studied IEGs, as determined in cultured cells. We found that in the brain of naturally behaving songbirds and other avian species, hearing song, seeing visual stimuli, or performing motor behavior caused high dusp1 upregulation, respectively, in auditory, visual, and somatosensory input cell populations of the thalamus and thalamic-recipient sensory neurons of the telencephalic pallium, whereas high egr1 upregulation occurred only in subsequently connected secondary and tertiary sensory neuronal populations of these same pathways. Motor behavior did not induce high levels of dusp1 expression in the motor-associated areas adjacent to song nuclei, where egr1 is upregulated in response to movement. Our analysis of dusp1 expression in mouse brain suggests similar regulation in the sensory input neurons of the thalamus and thalamic-recipient layer IV and VI neurons of the cortex. These findings suggest that dusp1 has specialized regulation to sensory input neurons of the thalamus and telencephalon; they further suggest that this regulation may serve to attenuate stimulus-induced expression of egr1 and other IEGs, leading to unique molecular properties of forebrain sensory input neurons.
MeSH term(s)	Animals ; Auditory Perception/physiology ; Avian Proteins/genetics ; Avian Proteins/metabolism ; Brain/metabolism ; Columbidae ; Dual Specificity Phosphatase 1/genetics ; Dual Specificity Phosphatase 1/metabolism ; Early Growth Response Protein 1/genetics ; Early Growth Response Protein 1/metabolism ; Gene Expression Regulation ; Male ; Melopsittacus ; Mice ; Motor Activity/physiology ; Neurons, Afferent/metabolism ; Songbirds ; Species Specificity ; Telencephalon/metabolism ; Thalamus/metabolism ; Visual Perception/physiology
Chemical Substances	Avian Proteins ; Early Growth Response Protein 1 ; Dual Specificity Phosphatase 1 (EC 3.1.3.48) ; Dusp1 protein, mouse (EC 3.1.3.48)
Language	English
Publishing date	2010-05-27
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	3086-7
ISSN	1096-9861 ; 0021-9967 ; 0092-7317
ISSN (online)	1096-9861
ISSN	0021-9967 ; 0092-7317
DOI	10.1002/cne.22370
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Article ; Online: Convergent differential regulation of SLIT-ROBO axon guidance genes in the brains of vocal learners.

Wang, Rui / Chen, Chun-Chun / Hara, Erina / Rivas, Miriam V / Roulhac, Petra L / Howard, Jason T / Chakraborty, Mukta / Audet, Jean-Nicolas / Jarvis, Erich D

The Journal of comparative neurology

2014 Volume 523, Issue 6, Page(s) 892–906

Abstract: 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 ... ...

Abstract	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 vocal control circuits that have several unique connections relative to adjacent brain circuits. As a result, it has been hypothesized that there could exist convergent changes in genes involved in neural connectivity of vocal learning circuits. In support of this hypothesis, expanding on our related study (Pfenning et al. [2014] Science 346: 1256846), here we show that the forebrain part of this circuit that makes a relatively rare direct connection to brainstem vocal motor neurons in independent lineages of vocal learning birds (songbird, parrot, and hummingbird) has specialized regulation of axon guidance genes from the SLIT-ROBO molecular pathway. The SLIT1 ligand was differentially downregulated in the motor song output nucleus that makes the direct projection, whereas its receptor ROBO1 was developmentally upregulated during critical periods for vocal learning. Vocal nonlearning bird species and male mice, which have much more limited vocal plasticity and associated circuits, did not show comparable specialized regulation of SLIT-ROBO genes in their nonvocal motor cortical regions. These findings are consistent with SLIT and ROBO gene dysfunctions associated with autism, dyslexia, and speech sound language disorders and suggest that convergent evolution of vocal learning was associated with convergent changes in the SLIT-ROBO axon guidance pathway.
MeSH term(s)	Age Factors ; Animals ; Axons/physiology ; Birds/physiology ; Brain/anatomy & histology ; Female ; Gene Expression Regulation/physiology ; Glycoproteins/genetics ; Glycoproteins/metabolism ; Learning/physiology ; Male ; Mice ; Mice, Inbred C57BL ; Nerve Tissue Proteins/genetics ; Nerve Tissue Proteins/metabolism ; Neurons/cytology ; RNA, Messenger/metabolism ; Receptors, Immunologic/genetics ; Receptors, Immunologic/metabolism ; Vocalization, Animal/physiology ; Roundabout Proteins
Chemical Substances	Glycoproteins ; Nerve Tissue Proteins ; RNA, Messenger ; Receptors, Immunologic ; slit protein, vertebrate
Language	English
Publishing date	2014-12-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	3086-7
ISSN	1096-9861 ; 0021-9967 ; 0092-7317
ISSN (online)	1096-9861
ISSN	0021-9967 ; 0092-7317
DOI	10.1002/cne.23719
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Article ; Online: Convergent transcriptional specializations in the brains of humans and song-learning birds.

Pfenning, Andreas R / Hara, Erina / Whitney, Osceola / Rivas, Miriam V / Wang, Rui / Roulhac, Petra L / Howard, Jason T / Wirthlin, Morgan / Lovell, Peter V / Ganapathy, Ganeshkumar / Mouncastle, Jacquelyn / Moseley, M Arthur / Thompson, J Will / Soderblom, Erik J / Iriki, Atsushi / Kato, Masaki / Gilbert, M Thomas P / Zhang, Guojie / Bakken, Trygve /

Bongaarts, Angie / Bernard, Amy / Lein, Ed / Mello, Claudio V / Hartemink, Alexander J / Jarvis, Erich D

Science (New York, N.Y.)

2014 Volume 346, Issue 6215, Page(s) 1256846

Abstract: 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 ... ...

Abstract	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 humans relative to vocal nonlearners identified convergent gene expression specializations in specific song and speech brain regions of avian vocal learners and humans. The strongest shared profiles relate bird motor and striatal song-learning nuclei, respectively, with human laryngeal motor cortex and parts of the striatum that control speech production and learning. Most of the associated genes function in motor control and brain connectivity. Thus, convergent behavior and neural connectivity for a complex trait are associated with convergent specialized expression of multiple genes.
MeSH term(s)	Adult ; Animals ; Birds/genetics ; Birds/physiology ; Brain/anatomy & histology ; Brain/physiology ; Brain Mapping ; Corpus Striatum/anatomy & histology ; Corpus Striatum/physiology ; Evolution, Molecular ; Finches/genetics ; Finches/physiology ; Gene Expression Regulation ; Humans ; Learning ; Male ; Motor Cortex/anatomy & histology ; Motor Cortex/physiology ; Neural Pathways ; Species Specificity ; Speech ; Transcription, Genetic ; Transcriptome ; Vocalization, Animal
Language	English
Publishing date	2014-12-11
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.1256846
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Zs.A 27: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Global view of the functional molecular organization of the avian cerebrum: mirror images and functional columns.

Jarvis, Erich D / Yu, Jing / Rivas, Miriam V / Horita, Haruhito / Feenders, Gesa / Whitney, Osceola / Jarvis, Syrus C / Jarvis, Electra R / Kubikova, Lubica / Puck, Ana E P / Siang-Bakshi, Connie / Martin, Suzanne / McElroy, Michael / Hara, Erina / Howard, Jason / Pfenning, Andreas / Mouritsen, Henrik / Chen, Chun-Chun / Wada, Kazuhiro

The Journal of comparative neurology

2013 Volume 521, Issue 16, Page(s) 3614–3665

Abstract: 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 ... ...

Abstract	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 mirror image organization of three major cell populations that wrap above, around, and below the ventricle and adjacent lamina through the mesopallium. The patterns of behaviorally regulated genes revealed functional columns of activation across boundaries of these cell populations, reminiscent of columns through layers of the mammalian cortex. The avian functionally regulated columns were of two types: those above the ventricle and associated mesopallial lamina, formed by our revised dorsal mesopallium, hyperpallium, and intercalated hyperpallium; and those below the ventricle, formed by our revised ventral mesopallium, nidopallium, and intercalated nidopallium. Based on these findings and known connectivity, we propose that the avian pallium has four major cell populations similar to those in mammalian cortex and some parts of the amygdala: 1) a primary sensory input population (intercalated pallium); 2) a secondary intrapallial population (nidopallium/hyperpallium); 3) a tertiary intrapallial population (mesopallium); and 4) a quaternary output population (the arcopallium). Each population contributes portions to columns that control different sensory or motor systems. We suggest that this organization of cell groups forms by expansion of contiguous developmental cell domains that wrap around the lateral ventricle and its extension through the middle of the mesopallium. We believe that the position of the lateral ventricle and its associated mesopallium lamina has resulted in a conceptual barrier to recognizing related cell groups across its border, thereby confounding our understanding of homologies with mammals.
MeSH term(s)	Animals ; Birds/anatomy & histology ; Cell Count ; Cerebrum/anatomy & histology ; Cerebrum/metabolism ; Gene Expression ; Imaging, Three-Dimensional ; Nerve Tissue Proteins/genetics ; Nerve Tissue Proteins/metabolism ; Neuroimaging ; Neurons/metabolism ; Species Specificity
Chemical Substances	Nerve Tissue Proteins
Language	English
Publishing date	2013-07-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	3086-7
ISSN	1096-9861 ; 0021-9967 ; 0092-7317
ISSN (online)	1096-9861
ISSN	0021-9967 ; 0092-7317
DOI	10.1002/cne.23404
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Article: A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes.

Proceedings of the National Academy of Sciences of the United States of America

2006 Volume 103, Issue 41, Page(s) 15212–15217

Abstract: 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 ... ...

Abstract	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 overcome these limitations, we constructed 21 regular, normalized, and subtracted full-length cDNA libraries from brains of zebra finches in 57 developmental and behavioral conditions in an attempt to clone as much of the brain transcriptome as possible. From these libraries, approximately 14,000 transcripts were isolated, representing an estimated 4,738 genes. With the cDNAs, we created a hierarchically organized transcriptome database and a large-scale songbird brain cDNA microarray. We used the arrays to reveal a set of 33 genes that are regulated in forebrain vocal nuclei by singing behavior. These genes clustered into four anatomical and six temporal expression patterns. Their functions spanned a large range of cellular and molecular categories, from signal transduction, trafficking, and structural, to synaptically released molecules. With the full-length cDNAs and a lentiviral vector system, we were able to overexpress, in vocal nuclei, proteins of representative singing-regulated genes in the absence of singing. This publicly accessible resource http://songbirdtranscriptome.net can now be used to study molecular neuroethological mechanisms of behavior.
MeSH term(s)	Animals ; Behavior, Animal/physiology ; Chickens ; Ethology ; Female ; Finches/genetics ; Finches/physiology ; Gene Expression Profiling ; Gene Expression Regulation/physiology ; Humans ; Male ; Molecular Sequence Data ; Nervous System Physiological Phenomena ; Vocalization, Animal/physiology
Language	English
Publishing date	2006-10-03
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.0607098103
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Article ; Online: Comparative genomics reveals insights into avian genome evolution and adaptation.

Zhang, Guojie / Li, Cai / Li, Qiye / Li, Bo / Larkin, Denis M / Lee, Chul / Storz, Jay F / Antunes, Agostinho / Greenwold, Matthew J / Meredith, Robert W / Ödeen, Anders / Cui, Jie / Zhou, Qi / Xu, Luohao / Pan, Hailin / Wang, Zongji / Jin, Lijun / Zhang, Pei / Hu, Haofu /

Yang, Wei / Hu, Jiang / Xiao, Jin / Yang, Zhikai / Liu, Yang / Xie, Qiaolin / Yu, Hao / Lian, Jinmin / Wen, Ping / Zhang, Fang / Li, Hui / Zeng, Yongli / Xiong, Zijun / Liu, Shiping / Zhou, Long / Huang, Zhiyong / An, Na / Wang, Jie / Zheng, Qiumei / Xiong, Yingqi / Wang, Guangbiao / Wang, Bo / Wang, Jingjing / Fan, Yu / da Fonseca, Rute R / Alfaro-Núñez, Alonzo / Schubert, Mikkel / Orlando, Ludovic / Mourier, Tobias / Howard, Jason T / Ganapathy, Ganeshkumar / Pfenning, Andreas / Whitney, Osceola / Rivas, Miriam V / Hara, Erina / Smith, Julia / Farré, Marta / Narayan, Jitendra / Slavov, Gancho / Romanov, Michael N / Borges, Rui / Machado, João Paulo / Khan, Imran / Springer, Mark S / Gatesy, John / Hoffmann, Federico G / Opazo, Juan C / Håstad, Olle / Sawyer, Roger H / Kim, Heebal / Kim, Kyu-Won / Kim, Hyeon Jeong / Cho, Seoae / Li, Ning / Huang, Yinhua / Bruford, Michael W / Zhan, Xiangjiang / Dixon, Andrew / Bertelsen, Mads F / Derryberry, Elizabeth / Warren, Wesley / Wilson, Richard K / Li, Shengbin / Ray, David A / Green, Richard E / O'Brien, Stephen J / Griffin, Darren / Johnson, Warren E / Haussler, David / Ryder, Oliver A / Willerslev, Eske / Graves, Gary R / Alström, Per / Fjeldså, Jon / Mindell, David P / Edwards, Scott V / Braun, Edward L / Rahbek, Carsten / Burt, David W / Houde, Peter / Zhang, Yong / Yang, Huanming / Wang, Jian / Jarvis, Erich D / Gilbert, M Thomas P / Wang, Jun

Science (New York, N.Y.)

2014 Volume 346, Issue 6215, Page(s) 1311–1320

Abstract: 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 ... ...

Abstract	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 principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
MeSH term(s)	Adaptation, Physiological ; Animals ; Biodiversity ; Biological Evolution ; Birds/classification ; Birds/genetics ; Birds/physiology ; Conserved Sequence ; Diet ; Evolution, Molecular ; Female ; Flight, Animal ; Genes ; Genetic Variation ; Genome ; Genomics ; Male ; Molecular Sequence Annotation ; Phylogeny ; Reproduction/genetics ; Selection, Genetic ; Sequence Analysis, DNA ; Synteny ; Vision, Ocular/genetics ; Vocalization, Animal
Language	English
Publishing date	2014-12-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.1251385
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Zs.A 27: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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