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He K, Liang CH, Zhu Y, Dunn P, Zhao A, Minias P. Reconstructing Macroevolutionary Patterns in Avian MHC Architecture With Genomic Data. Front Genet 2022; 13:823686. [PMID: 35251132 PMCID: PMC8893315 DOI: 10.3389/fgene.2022.823686] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/25/2022] [Indexed: 12/28/2022] Open
Abstract
The Major Histocompatibility Complex (MHC) is a hyper-polymorphic genomic region, which forms a part of the vertebrate adaptive immune system and is crucial for intra- and extra-cellular pathogen recognition (MHC-I and MHC-IIA/B, respectively). Although recent advancements in high-throughput sequencing methods sparked research on the MHC in non-model species, the evolutionary history of MHC gene structure is still poorly understood in birds. Here, to explore macroevolutionary patterns in the avian MHC architecture, we retrieved contigs with antigen-presenting MHC and MHC-related genes from available genomes based on third-generation sequencing. We identified: 1) an ancestral avian MHC architecture with compact size and tight linkage between MHC-I, MHC-IIA/IIB and MHC-related genes; 2) three major patterns of MHC-IIA/IIB unit organization in different avian lineages; and 3) lineage-specific gene translocation events (e.g., separation of the antigen-processing TAP genes from the MHC-I region in passerines), and 4) the presence of a single MHC-IIA gene copy in most taxa, showing evidence of strong purifying selection (low dN/dS ratio and low number of positively selected sites). Our study reveals long-term macroevolutionary patterns in the avian MHC architecture and provides the first evidence of important transitions in the genomic arrangement of the MHC region over the last 100 million years of bird evolution.
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Affiliation(s)
- Ke He
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
- *Correspondence: Ke He, ; Piotr Minias,
| | - Chun-hong Liang
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
| | - Ying Zhu
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Peter Dunn
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
| | - Ayong Zhao
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
| | - Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łodz, Łódź, Poland
- *Correspondence: Ke He, ; Piotr Minias,
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Minucci MS, Issa JPM, Yokoyama FY, Dias FJ, Iyomasa DM, Guimarães EADBB, Watanabe IS, Iyomasa MM. Angioarchitecture and morphology of temporomandibular joint of Monodelphis domestica. Microsc Res Tech 2016; 79:806-13. [PMID: 27324400 DOI: 10.1002/jemt.22702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/25/2016] [Accepted: 06/03/2016] [Indexed: 11/08/2022]
Abstract
The opossum Monodelphis domestica presents movement of the temporomandibular joint (TMJ) reflecting adaptation to eating habits similar to movement in humans, but the structure of the TMJ is not yet known. Thus, nine young M. domestica, of both sexes were weighed, anesthetized with xylazine (10 mg kg(-1) ), and ketamine (70 mg kg(-1) ) and processed for: 1. The analyses of the macroscopic angioarchitecture after latex injection, as well as the topography of the TMJ; 2. The analysis of microvascularization after injection of Mercox resin and corrosion of soft tissue with NaOH using scanning electron microscopy and; 3. The histological evaluation of the TMJ with an optical microscope. Macroscopic analysis of the latex injected vessels revealed the distribution of the arteries from the common carotid artery, receiving branches of the superficial temporal and maxillary arteries. The mandibular condyle has the long axis in the lateral-lateral direction, and is convex in the anterior-posterior direction. Its topography was determined in relation to the eye and external acoustic meatus. With scanning electron microscopy, microvascularization consists of arterioles of varying diameter (85-15 µm) of the meandering capillary network in the retrodiscal region, and a network of straight capillaries in the TMJ anterior region. Via light microscopy the TMJ has similar histological features to those of humans. These macroscopic, microscopic and ultrastructural data from TMJ of the M. domestica could be a suitable model for TMJ physiology and pathophysiology studies for then speculate on possible human studies. Microsc. Res. Tech. 79:806-813, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Matheus Silvestre Minucci
- Department of Morphology, Physiology, and Basic Pathology, Ribeirao Preto Dentistry Faculty, University of São Paulo, Ribeirao Preto, SP, 14040-904, Brazil
| | - João Paulo Mardegan Issa
- Department of Morphology, Physiology, and Basic Pathology, Ribeirao Preto Dentistry Faculty, University of São Paulo, Ribeirao Preto, SP, 14040-904, Brazil
| | - Fernando Yukio Yokoyama
- Department of Morphology, Physiology, and Basic Pathology, Ribeirao Preto Dentistry Faculty, University of São Paulo, Ribeirao Preto, SP, 14040-904, Brazil
| | - Fernando José Dias
- CICO Research Centre, Dental School, Universidad De La Frontera, Temuco, Chile
| | - Daniela Mizusaki Iyomasa
- Department of Morphology, Physiology, and Basic Pathology, Ribeirao Preto Dentistry Faculty, University of São Paulo, Ribeirao Preto, SP, 14040-904, Brazil
| | | | - Ii-Sei Watanabe
- Department of Anatomy, Institute of Biomedical Sciences, University of Sao Paulo, 2415 Avenida Professor Lineu Prestes, Sao Paulo, SP, 05508-900, Brazil
| | - Mamie Mizusaki Iyomasa
- Department of Morphology, Physiology, and Basic Pathology, Ribeirao Preto Dentistry Faculty, University of São Paulo, Ribeirao Preto, SP, 14040-904, Brazil
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Abstract
Marsupial immune responses were previously touted as ‘primitive’ but we now know that the marsupial immune system is complex and on par with that of eutherian mammals. In this manuscript we review the field of marsupial immunology, focusing on basic anatomy, developmental immunology, immunogenetics and evolution. We concentrate on advances to our understanding of marsupial immune gene architecture, made possible by the recent sequencing of the opossum, tammar wallaby and Tasmanian devil genomes. Characterisation of immune gene sequences now paves the way for the development of immunological assays that will allow us to more accurately study health and disease in marsupials.
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Brinkmeyer-Langford CL, Murphy WJ, Childers CP, Skow LC. A conserved segmental duplication within ELA. Anim Genet 2010; 41 Suppl 2:186-95. [DOI: 10.1111/j.1365-2052.2010.02137.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Husbandry of Monodelphis domestica in the study of mammalian embryogenesis. Lab Anim (NY) 2010; 39:219-26. [DOI: 10.1038/laban0710-219] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Accepted: 03/08/2010] [Indexed: 01/23/2023]
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Abstract
The strategic importance of the genome sequence of the gray, short-tailed opossum, Monodelphis domestica, accrues from both the unique phylogenetic position of metatherian (marsupial) mammals and the fundamental biologic characteristics of metatherians that distinguish them from other mammalian species. Metatherian and eutherian (placental) mammals are more closely related to one another than to other vertebrate groups, and owing to this close relationship they share fundamentally similar genetic structures and molecular processes. However, during their long evolutionary separation these alternative mammals have developed distinctive anatomical, physiologic, and genetic features that hold tremendous potential for examining relationships between the molecular structures of mammalian genomes and the functional attributes of their components. Comparative analyses using the opossum genome have already provided a wealth of new evidence regarding the importance of noncoding elements in the evolution of mammalian genomes, the role of transposable elements in driving genomic innovation, and the relationships between recombination rate, nucleotide composition, and the genomic distributions of repetitive elements. The genome sequence is also beginning to enlarge our understanding of the evolution and function of the vertebrate immune system, and it provides an alternative model for investigating mechanisms of genomic imprinting. Equally important, availability of the genome sequence is fostering the development of new research tools for physical and functional genomic analyses of M. domestica that are expanding its versatility as an experimental system for a broad range of research applications in basic biology and biomedically oriented research.
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Meyer-Lucht Y, Otten C, Püttker T, Sommer S. Selection, diversity and evolutionary patterns of the MHC class II DAB in free-ranging Neotropical marsupials. BMC Genet 2008; 9:39. [PMID: 18534008 PMCID: PMC2442840 DOI: 10.1186/1471-2156-9-39] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Accepted: 06/05/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Research on the genetic architecture and diversity of the MHC has focused mainly on eutherian mammals, birds and fish. So far, studies on model marsupials used in laboratory investigations indicated very little or even no variation in MHC class II genes. However, natural levels of diversity and selection are unknown in marsupials as studies on wild populations are virtually absent. We used two endemic South American mouse opossums, Gracilinanus microtarsus and Marmosops incanus, to investigate characteristic features of MHC selection. This study is the first investigation of MHC selection in free-ranging Neotropical marsupials. In addition, the evolutionary history of MHC lineages within the group of marsupials was examined. RESULTS G. microtarsus showed extensive levels of MHC diversity within and among individuals as 47 MHC-DAB alleles and high levels of sequence divergence were detected at a minimum of four loci. Positively selected codon sites were identified, of which most were congruent with human antigen binding sites. The diversity in M. incanus was rather low with only eight observed alleles at presumably two loci. However, these alleles also revealed high sequence divergence. Again, positive selection was identified on specific codon sites, all congruent with human ABS and with positively selected sites observed in G. microtarsus. In a phylogenetic comparison alleles of M. incanus interspersed widely within alleles of G. microtarsus with four alleles being present in both species. CONCLUSION Our investigations revealed extensive MHC class II polymorphism in a natural marsupial population, contrary to previous assumptions. Furthermore, our study confirms for the first time in marsupials the presence of three characteristic features common at MHC loci of eutherian mammals, birds and fish: large allelic sequence divergence, positive selection on specific sites and trans-specific polymorphism.
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Affiliation(s)
- Yvonne Meyer-Lucht
- Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str, 17, D-10315 Berlin, Germany.
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Abstract
In many instances, there are large sex differences in mutation rates, recombination rates, selection, rates of gene flow, and genetic drift. Mutation rates are often higher in males, a difference that has been estimated both directly and indirectly. The higher male mutation rate appears related to the larger number of cell divisions in male lineages but mutation rates also appear gene- and organism-specific. When there is recombination in only one sex, it is always the homogametic sex. When there is recombination in both sexes, females often have higher recombination but there are many exceptions. There are a number of hypotheses to explain the sex differences in recombination. Sex-specific differences in selection may result in stable polymorphisms or for sex chromosomes, faster evolutionary change. In addition, sex-dependent selection may result in antagonistic pleiotropy or sexually antagonistic genes. There are many examples of sex-specific differences in gene flow (dispersal) and a number of adaptive explanations for these differences. The overall effective population size (genetic drift) is dominated by the lower sex-specific effective population size. The mean of the mutation, recombination, and gene flow rates over the two sexes can be used in a population genetics context unless there are sex-specific differences in selection or genetic drift. Sex-specific differences in these evolutionary factors appear to be unrelated to each other. The evolutionary explanations for sex-specific differences for each factor are multifaceted and, in addition, explanations may include chance, nonadaptive differences, or mechanistic, nonevolutionary factors.
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Affiliation(s)
- Philip W Hedrick
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501, USA.
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Baker ML, Miller RD. Evolution of mammalian CD1: marsupial CD1 is not orthologous to the eutherian isoforms and is a pseudogene in the opossum Monodelphis domestica. Immunology 2007; 121:113-21. [PMID: 17244156 PMCID: PMC2265927 DOI: 10.1111/j.1365-2567.2007.02545.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
CD1 is a member of the major histocompatibility complex (MHC) class I family of proteins that present lipid antigens to T cells and natural killer (NK) T cells; it is found in both eutherian mammals and birds. In eutherians, duplication of the CD1 gene has resulted in multiple isoforms. A marsupial CD1 homologue was identified in a set of expressed sequence tags from the thymus of the bandicoot Isoodon macrourus. Southern blot and genomic sequence analyses revealed that CD1 is a single copy gene in both I. macrourus and a distantly related marsupial, the opossum Monodelphis domestica, which is currently the only marsupial species for which a whole genome sequence is available. We found that the opossum CD1 is located in a genomic region with a high degree of conserved synteny to the chromosomal regions containing human and mouse CD1. A phylogenetic analysis of mammalian CD1 revealed that marsupial CD1 is not orthologous to the eutherian CD1 isoforms, consistent with the latter having emerged by duplication after the separation of marsupials and eutherians 170-180 million years ago. The I. macrourus CD1 gene is actively transcribed and appears to encode a functional protein. In contrast, transcription of the M. domestica CD1 was not detected in any tissue and the predicted CD1 gene sequence contains a number of deletions that appear to render the locus a pseudogene.
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Affiliation(s)
- Michelle L Baker
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque NM 87131, USA.
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Hornecker JL, Samollow PB, Robinson ES, VandeBerg JL, McCarrey JR. Meiotic sex chromosome inactivation in the marsupialMonodelphis domestica. Genesis 2007; 45:696-708. [DOI: 10.1002/dvg.20345] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Gouin N, Wright AM, Miska KB, Parra ZE, Samollow PB, Baker ML, Miller RD. Modo-UG, a marsupial nonclassical MHC class I locus. Immunogenetics 2006; 58:396-406. [PMID: 16738937 DOI: 10.1007/s00251-006-0115-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Accepted: 03/22/2006] [Indexed: 11/30/2022]
Abstract
Modo-UG is a class I gene located in the MHC of the marsupial Monodelphis domestica, the gray, short-tailed opossum. Modo-UG is expressed as three alternatively spliced mRNA forms, all of which encode a transmembrane form with a short cytoplasmic tail that lacks phosphorylation sites typically found in classical class I molecules. The three alternative mRNAs would encode a full-length form, an isoform lacking the alpha2 domain, and one lacking both alpha2 and alpha3 domains. Genotyping both captive-bred and wild M. domestica from different geographic regions revealed no variation in the residues that make up Modo-UG's peptide-binding groove. Modo-UG's low polymorphism is contrasting to that of a nearby class I locus, Modo-UA1, which has a highly polymorphic peptide-binding region. Absence of functional polymorphism in Modo-UG is therefore not a general feature of opossum class I genes but the result of negative selection. Modo-UG is the first MHC linked marsupial class I to be described that appears to clearly have nonclassical features.
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Affiliation(s)
- Nicolas Gouin
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, TX, 78245, USA
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12
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Belov K, Deakin JE, Papenfuss AT, Baker ML, Melman SD, Siddle HV, Gouin N, Goode DL, Sargeant TJ, Robinson MD, Wakefield MJ, Mahony S, Cross JGR, Benos PV, Samollow PB, Speed TP, Graves JAM, Miller RD. Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. PLoS Biol 2006; 4:e46. [PMID: 16435885 PMCID: PMC1351924 DOI: 10.1371/journal.pbio.0040046] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Accepted: 12/12/2005] [Indexed: 11/19/2022] Open
Abstract
The first sequenced marsupial genome promises to reveal unparalleled insights into mammalian evolution. We have used the Monodelphis domestica (gray short-tailed opossum) sequence to construct the first map of a marsupial major histocompatibility complex (MHC). The MHC is the most gene-dense region of the mammalian genome and is critical to immunity and reproductive success. The marsupial MHC bridges the phylogenetic gap between the complex MHC of eutherian mammals and the minimal essential MHC of birds. Here we show that the opossum MHC is gene dense and complex, as in humans, but shares more organizational features with non-mammals. The Class I genes have amplified within the Class II region, resulting in a unique Class I/II region. We present a model of the organization of the MHC in ancestral mammals and its elaboration during mammalian evolution. The opossum genome, together with other extant genomes, reveals the existence of an ancestral "immune supercomplex" that contained genes of both types of natural killer receptors together with antigen processing genes and MHC genes.
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Affiliation(s)
- Katherine Belov
- 1Centre for Advanced Technologies in Animal Genetics and Reproduction, Faculty of Veterinary Science, The University of Sydney, Camden, Australia
| | - Janine E Deakin
- 2ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, Australia
| | - Anthony T Papenfuss
- 3The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Michelle L Baker
- 4Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Sandra D Melman
- 4Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Hannah V Siddle
- 1Centre for Advanced Technologies in Animal Genetics and Reproduction, Faculty of Veterinary Science, The University of Sydney, Camden, Australia
| | - Nicolas Gouin
- 5Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, Texas, United States of America
| | - David L Goode
- 3The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Tobias J Sargeant
- 3The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Mark D Robinson
- 3The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Matthew J Wakefield
- 3The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Shaun Mahony
- 6National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland
| | - Joseph G. R Cross
- 2ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, Australia
| | - Panayiotis V Benos
- 7Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Paul B Samollow
- 8Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Terence P Speed
- 3The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Jennifer A. Marshall Graves
- 2ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, Australia
| | - Robert D Miller
- 4Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
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Samollow PB. Status and applications of genomic resources for the gray, short-tailed opossum, Monodelphis domestica, an American marsupial model for comparative biology. AUST J ZOOL 2006. [DOI: 10.1071/zo05059] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Owing to its small size, favourable reproductive characteristics, and simple husbandry, the gray, short-tailed opossum, Monodelphis domestica, has become the most widely distributed and intensively utilised laboratory-bred research marsupial in the world today. This article provides an overview of the current state and future projections of genomic resources for this species and discusses the potential impact of this growing resource base on active research areas that use M. domestica as a model system. The resources discussed include: fully arrayed, bacterial artificial chromosome (BAC) libraries; an expanding linkage map; developing full-genome BAC-contig and chromosomal fluorescence in situ hybridisation maps; public websites providing access to the M. domestica whole-genome-shotgun sequence trace database and the whole-genome sequence assembly; and a new project underway to create an expressed-sequence database and microchip expression arrays for functional genomics applications. Major research areas discussed span a variety of genetic, evolutionary, physiologic, reproductive, developmental, and behavioural topics, including: comparative immunogenetics; genomic imprinting; reproductive biology; neurobiology; photobiology and carcinogenesis; genetics of lipoprotein metabolism; developmental and behavioural endocrinology; sexual differentiation and development; embryonic and fetal development; meiotic recombination; genome evolution; molecular evolution and phylogenetics; and more.
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