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Bayramov AV, Yastrebov SA, Mednikov DN, Araslanova KR, Ermakova GV, Zaraisky AG. Paired fins in vertebrate evolution and ontogeny. Evol Dev 2024; 26:e12478. [PMID: 38650470 DOI: 10.1111/ede.12478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 02/28/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
The origin of paired appendages became one of the most important adaptations of vertebrates, allowing them to lead active lifestyles and explore a wide range of ecological niches. The basic form of paired appendages in evolution is the fins of fishes. The problem of paired appendages has attracted the attention of researchers for more than 150 years. During this time, a number of theories have been proposed, mainly based on morphological data, two of which, the Balfour-Thacher-Mivart lateral fold theory and Gegenbaur's gill arch theory, have not lost their relevance. So far, however, none of the proposed ideas has been supported by decisive evidence. The study of the evolutionary history of the appearance and development of paired appendages lies at the intersection of several disciplines and involves the synthesis of paleontological, morphological, embryological, and genetic data. In this review, we attempt to summarize and discuss the results accumulated in these fields and to analyze the theories put forward regarding the prerequisites and mechanisms that gave rise to paired fins and limbs in vertebrates.
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Affiliation(s)
- Andrey V Bayramov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sergey A Yastrebov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry N Mednikov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Karina R Araslanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Galina V Ermakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Andrey G Zaraisky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Department of Regenerative Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
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Minhas R, Paterek A, Łapiński M, Bazała M, Korzh V, Winata CL. A novel conserved enhancer at zebrafish zic3 and zic6 loci drives neural expression. Dev Dyn 2019; 248:837-849. [PMID: 31194899 PMCID: PMC6771876 DOI: 10.1002/dvdy.69] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 05/28/2019] [Accepted: 06/07/2019] [Indexed: 01/15/2023] Open
Abstract
Background Identifying enhancers and deciphering their putative roles represent a major step to better understand the mechanism of metazoan gene regulation, development, and the role of regulatory elements in disease. Comparative genomics and transgenic assays have been used with some success to identify critical regions that are involved in regulating the spatiotemporal expression of genes during embryogenesis. Results We identified two novel tetrapod‐teleost conserved noncoding elements within the vicinity of the zic3 and zic6 loci in the zebrafish genome and demonstrated their ability to drive tissue‐specific expression in a transgenic zebrafish assay. The syntenic analysis and robust green fluorescent expression in the developing habenula in the stable transgenic line were correlated with known sites of endogenous zic3 and zic6 expression. Conclusion This transgenic line that expresses green fluorescent protein in the habenula is a valuable resource for studying a specific population of cells in the zebrafish central nervous system. Our observations indicate that a genomic sequence that is conserved between humans and zebrafish acts as an enhancer that likely controls zic3 and zic6 expression. Identified a novel enhancer near zebrafish zic3/zic6 locus. The novel enhancer drives tissue‐specific expression in the habenula. Zebrafish transgenic line generated in this study can be a useful resource for studying development of habenula.
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Affiliation(s)
- Rashid Minhas
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Randall Centre of Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Aleksandra Paterek
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Department of Clinical Physiology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Maciej Łapiński
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Michał Bazała
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Vladimir Korzh
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Cecilia L Winata
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
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Vassalli QA, Anishchenko E, Caputi L, Sordino P, D'Aniello S, Locascio A. Regulatory elements retained during chordate evolution: Coming across tunicates. Genesis 2014; 53:66-81. [DOI: 10.1002/dvg.22838] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 11/06/2014] [Accepted: 11/11/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Quirino Attilio Vassalli
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Evgeniya Anishchenko
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Luigi Caputi
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Paolo Sordino
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
- CNR ISAFOM, Institute for Agricultural and Forest Systems in the Mediterranean, Unitá organizzativa di supporto; Catania Italy
| | - Salvatore D'Aniello
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Annamaria Locascio
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
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Heude É, Shaikho S, Ekker M. The dlx5a/dlx6a genes play essential roles in the early development of zebrafish median fin and pectoral structures. PLoS One 2014; 9:e98505. [PMID: 24858471 PMCID: PMC4032342 DOI: 10.1371/journal.pone.0098505] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 05/02/2014] [Indexed: 11/18/2022] Open
Abstract
The Dlx5 and Dlx6 genes encode homeodomain transcription factors essential for the proper development of limbs in mammalian species. However, the role of their teleost counterparts in fin development has received little attention. Here, we show that dlx5a is an early marker of apical ectodermal cells of the pectoral fin buds and of the median fin fold, but also of cleithrum precursor cells during pectoral girdle development. We propose that early median fin fold establishment results from the medial convergence of dlx5a-expressing cells at the lateral edges of the neural keel. Expression analysis also shows involvement of dlx5a during appendage skeletogenesis. Using morpholino-mediated knock down, we demonstrate that disrupted dlx5a/6a function results in pectoral fin agenesis associated with misexpression of bmp4, fgf8a, and1 and msx genes. In contrast, the median fin fold presents defects in mesenchymal cell migration and actinotrichia formation, whereas the initial specification seems to occur normally. Our results demonstrate that the dlx5a/6a genes are essential for the induction of pectoral fin outgrowth, but are not required during median fin fold specification. The dlx5a/6a knock down also causes a failure of cleithrum formation associated with a drastic loss of runx2b and col10a1 expression. The data indicate distinct requirements for dlx5a/6a during median and pectoral fin development suggesting that initiation of unpaired and paired fin formation are not directed through the same molecular mechanisms. Our results refocus arguments on the mechanistic basis of paired appendage genesis during vertebrate evolution.
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Affiliation(s)
- Églantine Heude
- Centre for Advanced Research in Environmental Genomics, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Sarah Shaikho
- Centre for Advanced Research in Environmental Genomics, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Marc Ekker
- Centre for Advanced Research in Environmental Genomics, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
- * E-mail:
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Awruch CA. Reproductive endocrinology in chondrichthyans: the present and the future. Gen Comp Endocrinol 2013; 192:60-70. [PMID: 23763870 DOI: 10.1016/j.ygcen.2013.05.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Revised: 05/22/2013] [Accepted: 05/29/2013] [Indexed: 12/21/2022]
Abstract
The class Chondrichthyes, that includes Elasmobranchii and Holocephali, is a diverse group of fish occupying a key position at the base of vertebrate evolution. Their evolutionary success is greatly attributed to their wide range of reproductive strategies controlled by different endocrine mechanics. As in other vertebrates, hormonal control of reproduction in chondrichthyans is mediated by the neuropeptide gonadotropin-releasing hormone (GnRH) that regulates the brain control of gonadal activity via a hypothalamus-pituitary-gonadal (HPG) axis. Chondrichthyans lack of a direct vascular supply from the hypothalamus to the zone of the pituitary where the gonadotropic activity resides, thus transport between these two zones likely occurs via the general circulation. In the brain of elasmobranchs, two groups of GnRH, GnRH-I and GnRH-II were identified, and the presence of two immunoreactive gonadotropins similar to the luteinising (LH) and follicle stimulating (FSH) hormones was identified in the pituitary. In holocephalans, only GnRH-II has been confirmed, and while gonadotropin activity has been found in the buccal pituitary lobe, the presence of gonadotropin receptors in the gonads remains unknowns. The diversity of reproductive strategies display by chondrichthyans makes it difficult to generalize the control of gametogenesis and steroidogenesis; however, some general patterns emerge. In both sexes, androgens and estrogens are the main steroids during gonadal growth; while progestins have maturational activity. Androgens also form the precursors for estrogen steroid production. Estrogens stimulate the hepatic synthesis of yolk and stimulate the development of different part of the reproductive tract in females. The role of other gonadal steroids may play in chondrichthyan reproduction remains largely unknown. Future work should concentrate in filling the gaps into the current knowledge of the HPG axis regulation, and the use of reproductive endocrinology as a non-lethal technique for management of chondrichthyan populations.
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Affiliation(s)
- C A Awruch
- School of Zoology, University of Tasmania, Private Bag 5, Hobart, Tasmania 7001, Australia; CENPAT (Patagonian National Centre) - CONICET, Puerto Madryn, Chubut, Argentina.
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Debiais-Thibaud M, Metcalfe CJ, Pollack J, Germon I, Ekker M, Depew M, Laurenti P, Borday-Birraux V, Casane D. Heterogeneous conservation of Dlx paralog co-expression in jawed vertebrates. PLoS One 2013; 8:e68182. [PMID: 23840829 PMCID: PMC3695995 DOI: 10.1371/journal.pone.0068182] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 05/27/2013] [Indexed: 01/10/2023] Open
Abstract
Background The Dlx gene family encodes transcription factors involved in the development of a wide variety of morphological innovations that first evolved at the origins of vertebrates or of the jawed vertebrates. This gene family expanded with the two rounds of genome duplications that occurred before jawed vertebrates diversified. It includes at least three bigene pairs sharing conserved regulatory sequences in tetrapods and teleost fish, but has been only partially characterized in chondrichthyans, the third major group of jawed vertebrates. Here we take advantage of developmental and molecular tools applied to the shark Scyliorhinus canicula to fill in the gap and provide an overview of the evolution of the Dlx family in the jawed vertebrates. These results are analyzed in the theoretical framework of the DDC (Duplication-Degeneration-Complementation) model. Results The genomic organisation of the catshark Dlx genes is similar to that previously described for tetrapods. Conserved non-coding elements identified in bony fish were also identified in catshark Dlx clusters and showed regulatory activity in transgenic zebrafish. Gene expression patterns in the catshark showed that there are some expression sites with high conservation of the expressed paralog(s) and other expression sites with events of paralog sub-functionalization during jawed vertebrate diversification, resulting in a wide variety of evolutionary scenarios within this gene family. Conclusion Dlx gene expression patterns in the catshark show that there has been little neo-functionalization in Dlx genes over gnathostome evolution. In most cases, one tandem duplication and two rounds of vertebrate genome duplication have led to at least six Dlx coding sequences with redundant expression patterns followed by some instances of paralog sub-functionalization. Regulatory constraints such as shared enhancers, and functional constraints including gene pleiotropy, may have contributed to the evolutionary inertia leading to high redundancy between gene expression patterns.
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Affiliation(s)
- Mélanie Debiais-Thibaud
- Institut des Sciences de l’Evolution, Université de Montpellier II, UMR5554, Montpellier, France
- * E-mail:
| | - Cushla J. Metcalfe
- Laboratoire Evolution Génome et Spéciation UPR9034 CNRS, Gif-sur-Yvette, France
| | - Jacob Pollack
- Center for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Canada
| | - Isabelle Germon
- Laboratoire Evolution Génome et Spéciation UPR9034 CNRS, Gif-sur-Yvette, France
| | - Marc Ekker
- Center for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Canada
| | - Michael Depew
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, California, United States of America
| | - Patrick Laurenti
- Laboratoire Evolution Génome et Spéciation UPR9034 CNRS, Gif-sur-Yvette, France
- Université Paris Diderot, Paris, France
| | - Véronique Borday-Birraux
- Laboratoire Evolution Génome et Spéciation UPR9034 CNRS, Gif-sur-Yvette, France
- Université Paris Diderot, Paris, France
| | - Didier Casane
- Laboratoire Evolution Génome et Spéciation UPR9034 CNRS, Gif-sur-Yvette, France
- Université Paris Diderot, Paris, France
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MacDonald RB, Pollack JN, Debiais-Thibaud M, Heude E, Talbot JC, Ekker M. The ascl1a and dlx genes have a regulatory role in the development of GABAergic interneurons in the zebrafish diencephalon. Dev Biol 2013; 381:276-85. [PMID: 23747543 DOI: 10.1016/j.ydbio.2013.05.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 05/08/2013] [Accepted: 05/25/2013] [Indexed: 11/28/2022]
Abstract
During development of the mouse forebrain interneurons, the Dlx genes play a key role in a gene regulatory network (GRN) that leads to the GABAergic phenotype. Here, we have examined the regulatory relationships between the ascl1a, dlx, and gad1b genes in the zebrafish forebrain. Expression of ascl1a overlaps with dlx1a in the telencephalon and diencephalon during early forebrain development. The loss of Ascl1a function results in a loss of dlx expression, and subsequent losses of dlx5a and gad1b expression in the diencephalic prethalamus and hypothalamus. Loss of Dlx1a and Dlx2a function, and, to a lesser extent, of Dlx5a and Dlx6a, impairs gad1b expression in the prethalamus and hypothalamus. We conclude that dlx1a/2a act downstream of ascl1a but upstream of dlx5a/dlx6a and gad1b to activate GABAergic specification. This pathway is conserved in the diencephalon, but has diverged between mammals and teleosts in the telencephalon.
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Affiliation(s)
- Ryan B MacDonald
- Center for Advanced Research in Environmental Genomics, Department of Biology, University of Ottawa, Ottawa, ON, Canada, K1N 6N5
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Abstract
Holocephalans (ratfish, rabbitfish and chimaeras) figure with increasing prominence in studies of gnathostome evolutionary biology. Here, we provide the first complete description of the teeth and toothplates of one of the earliest known holocephalans, Chondrenchelys problematica, including the first unambiguous evidence of a gnathostome with an extra-mandibular dentition. We further demonstrate that holocephalan toothplate ontogeny differs fundamentally from all other extant gnathostome examples, and show how the conjunction of these teeth and toothplates challenges the monophyly of an extinct chondrichthyan clade, the Petalodontiformes. Chondrenchelys provides a novel perspective on the evolution of dentitions in shark-like fishes, expands the known repertoire of gnathostome dental morphologies and offers a glimpse of radically new chondrichthyan ecomorphs, now lost from the modern biota, following the end-Devonian extinctions.
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Affiliation(s)
- John A Finarelli
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA.
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Yu M, Xi Y, Pollack J, Debiais‐Thibaud M, MacDonald RB, Ekker M. Activity of
dlx5a
/
dlx6a
regulatory elements during zebrafish GABAergic neuron development. Int J Dev Neurosci 2011; 29:681-91. [DOI: 10.1016/j.ijdevneu.2011.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 06/10/2011] [Accepted: 06/16/2011] [Indexed: 02/02/2023] Open
Affiliation(s)
- Man Yu
- Centre for Advanced Research in Environmental Genomics (CAREG)Department of BiologyUniversity of Ottawa20 Marie CurieOttawaONCanadaK1N 6N5
- Department of Cellular and Molecular MedicineUniversity of Ottawa451 Smyth RoadOttawaONCanadaK1H 8M5
| | - Yanwei Xi
- Centre for Advanced Research in Environmental Genomics (CAREG)Department of BiologyUniversity of Ottawa20 Marie CurieOttawaONCanadaK1N 6N5
| | - Jacob Pollack
- Centre for Advanced Research in Environmental Genomics (CAREG)Department of BiologyUniversity of Ottawa20 Marie CurieOttawaONCanadaK1N 6N5
| | - Mélanie Debiais‐Thibaud
- Centre for Advanced Research in Environmental Genomics (CAREG)Department of BiologyUniversity of Ottawa20 Marie CurieOttawaONCanadaK1N 6N5
| | - Ryan B. MacDonald
- Centre for Advanced Research in Environmental Genomics (CAREG)Department of BiologyUniversity of Ottawa20 Marie CurieOttawaONCanadaK1N 6N5
| | - Marc Ekker
- Centre for Advanced Research in Environmental Genomics (CAREG)Department of BiologyUniversity of Ottawa20 Marie CurieOttawaONCanadaK1N 6N5
- Department of Cellular and Molecular MedicineUniversity of Ottawa451 Smyth RoadOttawaONCanadaK1H 8M5
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Ancestral and derived attributes of the dlx gene repertoire, cluster structure and expression patterns in an African cichlid fish. EvoDevo 2011; 2:1. [PMID: 21205289 PMCID: PMC3024246 DOI: 10.1186/2041-9139-2-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Accepted: 01/04/2011] [Indexed: 01/03/2023] Open
Abstract
Background Cichlid fishes have undergone rapid, expansive evolutionary radiations that are manifested in the diversification of their trophic morphologies, tooth patterning and coloration. Understanding the molecular mechanisms that underlie the cichlids' unique patterns of evolution requires a thorough examination of genes that pattern the neural crest, from which these diverse phenotypes are derived. Among those genes, the homeobox-containing Dlx gene family is of particular interest since it is involved in the patterning of the brain, jaws and teeth. Results In this study, we characterized the dlx genes of an African cichlid fish, Astatotilapia burtoni, to provide a baseline to later allow cross-species comparison within Cichlidae. We identified seven dlx paralogs (dlx1a, -2a, -4a, -3b, -4b, -5a and -6a), whose orthologies were validated with molecular phylogenetic trees. The intergenic regions of three dlx gene clusters (dlx1a-2a, dlx3b-4b, and dlx5a-6a) were amplified with long PCR. Intensive cross-species comparison revealed a number of conserved non-coding elements (CNEs) that are shared with other percomorph fishes. This analysis highlighted additional lineage-specific gains/losses of CNEs in different teleost fish lineages and a novel CNE that had previously not been identified. Our gene expression analyses revealed overlapping but distinct expression of dlx orthologs in the developing brain and pharyngeal arches. Notably, four of the seven A. burtoni dlx genes, dlx2a, dlx3b, dlx4a and dlx5a, were expressed in the developing pharyngeal teeth. Conclusion This comparative study of the dlx genes of A. burtoni has deepened our knowledge of the diversity of the Dlx gene family, in terms of gene repertoire, expression patterns and non-coding elements. We have identified possible cichlid lineage-specific changes, including losses of a subset of dlx expression domains in the pharyngeal teeth, which will be the targets of future functional studies.
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Konopka G, Geschwind DH. Human brain evolution: harnessing the genomics (r)evolution to link genes, cognition, and behavior. Neuron 2010; 68:231-44. [PMID: 20955931 DOI: 10.1016/j.neuron.2010.10.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2010] [Indexed: 01/01/2023]
Abstract
The evolution of the human brain has resulted in numerous specialized features including higher cognitive processes such as language. Knowledge of whole-genome sequence and structural variation via high-throughput sequencing technology provides an unprecedented opportunity to view human evolution at high resolution. However, phenotype discovery is a critical component of these endeavors and the use of nontraditional model organisms will also be critical for piecing together a complete picture. Ultimately, the union of developmental studies of the brain with studies of unique phenotypes in a myriad of species will result in a more thorough model of the groundwork the human brain was built upon. Furthermore, these integrative approaches should provide important insights into human diseases.
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Affiliation(s)
- Genevieve Konopka
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA
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