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Winter S, Coimbra RTF, Helsen P, Janke A. A chromosome-scale genome assembly of the okapi (Okapia johnstoni). J Hered 2022; 113:568-576. [PMID: 35788365 PMCID: PMC9584810 DOI: 10.1093/jhered/esac033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/30/2022] [Indexed: 12/05/2022] Open
Abstract
The okapi (Okapia johnstoni), or forest giraffe, is the only species in its genus and the only extant sister group of the giraffe within the family Giraffidae. The species is one of the remaining large vertebrates surrounded by mystery because of its elusive behavior as well as the armed conflicts in the region where it occurs, making it difficult to study. Deforestation puts the okapi under constant anthropogenic pressure, and it is currently listed as “Endangered” on the IUCN Red List. Here, we present the first annotated de novo okapi genome assembly based on PacBio continuous long reads, polished with short reads, and anchored into chromosome-scale scaffolds using Hi-C proximity ligation sequencing. The final assembly (TBG_Okapi_asm_v1) has a length of 2.39 Gbp, of which 98% are represented by 28 scaffolds > 3.9 Mbp. The contig N50 of 61 Mbp and scaffold N50 of 102 Mbp, together with a BUSCO score of 94.7%, and 23 412 annotated genes, underline the high quality of the assembly. This chromosome-scale genome assembly is a valuable resource for future conservation of the species and comparative genomic studies among the giraffids and other ruminants.
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Affiliation(s)
- Sven Winter
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage, Frankfurt am Main, Germany.,Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße, Vienna, Austria
| | - Raphael T F Coimbra
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage, Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße, Frankfurt am Main, Germany
| | - Philippe Helsen
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein, Antwerp, Belgium
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage, Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße, Frankfurt am Main, Germany
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2
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Kearsley L, Ranc N, Meier CM, Pacheco CM, Henriques P, Elias G, Poot M, Williams A, Costa LT, Helsen P, Hufkens K. The aeroecology of atmospheric convergence zones: the case of pallid swifts. OIKOS 2022. [DOI: 10.1111/oik.08594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lyndon Kearsley
- Belgian Ornithological Research Association Temse Belgium
- BlueGreen Labs Melsele Belgium
| | - Nathan Ranc
- Univ. de Toulouse, INRAE, CEFS Castanet‐Tolosan France
| | | | - Carlos Miguel Pacheco
- Research Center in Biodiversity and Genetic Resources, Univ. do Porto Vairão Portugal
| | | | | | - Martin Poot
- Martin Poot Ecology Culemborg the Netherlands
| | | | | | - Philippe Helsen
- Centre for Research and Conservation, Royal Zoological Society of Antwerp Antwerp Belgium
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3
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Leeflang HL, Van Dongen S, Helsen P. Mother’s curse on conservation: assessing the role of mtDNA in sex‐specific survival differences in ex‐situ breeding programs. Anim Conserv 2021. [DOI: 10.1111/acv.12740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- H. L. Leeflang
- Centre for Research and Conservation Royal Zoological Society of Antwerp Antwerp Belgium
| | - S. Van Dongen
- Department of Biology Evolutionary Ecology Group University of Antwerp Wilrijk Belgium
| | - P. Helsen
- Centre for Research and Conservation Royal Zoological Society of Antwerp Antwerp Belgium
- Department of Biology Evolutionary Ecology Group University of Antwerp Wilrijk Belgium
- Department of Biology Ghent University Ghent Belgium
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4
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Staes N, Guevara EE, Helsen P, Eens M, Stevens JMG. The Pan social brain: An evolutionary history of neurochemical receptor genes and their potential impact on sociocognitive differences. J Hum Evol 2021; 152:102949. [PMID: 33578304 DOI: 10.1016/j.jhevol.2021.102949] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 12/21/2022]
Abstract
Humans have unique cognitive capacities that, compared with apes, are not only simply expressed as a higher level of general intelligence, but also as a quantitative difference in sociocognitive skills. Humans' closest living relatives, bonobos (Pan paniscus), and chimpanzees (Pan troglodytes), show key between-species differences in social cognition despite their close phylogenetic relatedness, with bonobos arguably showing greater similarities to humans. To better understand the evolution of these traits, we investigate the neurochemical mechanisms underlying sociocognitive skills by focusing on variation in genes encoding proteins with well-documented roles in mammalian social cognition: the receptors for vasopressin (AVPR1A), oxytocin (OXTR), serotonin (HTR1A), and dopamine (DRD2). Although these genes have been well studied in humans, little is known about variation in these genes that may underlie differences in social behavior and cognition in apes. We comparatively analyzed sequence data for 33 bonobos and 57 chimpanzees, together with orthologous sequence data for other apes. In all four genes, we describe genetic variants that alter the amino acid sequence of the respective receptors, raising the possibility that ligand binding or signal transduction may be impacted. Overall, bonobos show 57% more fixed substitutions than chimpanzees compared with the ancestral Pan lineage. Chimpanzees, show 31% more polymorphic coding variation, in line with their larger historical effective population size estimates and current wider distribution. An extensive literature review comparing allelic changes in Pan with known human behavioral variants revealed evidence of homologous evolution in bonobos and humans (OXTR rs4686301(T) and rs237897(A)), while humans and chimpanzees shared OXTR rs2228485(A), DRD2 rs6277(A), and DRD2 rs11214613(A) to the exclusion of bonobos. Our results offer the first in-depth comparison of neurochemical receptor gene variation in Pan and put forward new variants for future behavior-genotype association studies in apes, which can increase our understanding of the evolution of social cognition in modern humans.
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Affiliation(s)
- Nicky Staes
- Behavioral Ecology and Ecophysiology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium; Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein 26, 2018, Antwerp, Belgium.
| | - Elaine E Guevara
- Evolutionary Anthropology, Duke University, 130 Science Dr, Durham, NC, 27708, USA
| | - Philippe Helsen
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein 26, 2018, Antwerp, Belgium
| | - Marcel Eens
- Behavioral Ecology and Ecophysiology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Jeroen M G Stevens
- Behavioral Ecology and Ecophysiology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
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5
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Abstract
Common chimpanzees (Pan troglodytes) experienced a selective sweep, probably caused by a SIV-like virus, which targeted their MHC class I repertoire. Based on MHC class I intron 2 data analyses, this selective sweep took place about 2-3 million years ago. As a consequence, common chimpanzees have a skewed MHC class I repertoire that is enriched for allotypes that are able to recognise conserved regions of the SIV proteome. The bonobo (Pan paniscus) shared an ancestor with common chimpanzees approximately 1.5 to 2 million years ago. To investigate whether the signature of this selective sweep is also detectable in bonobos, the MHC class I gene repertoire of two bonobo panels comprising in total 29 animals was investigated by Sanger sequencing. We identified 14 Papa-A, 20 Papa-B and 11 Papa-C alleles, of which eight, five and eight alleles, respectively, have not been reported previously. Within this pool of MHC class I variation, we recovered only 2 Papa-A, 3 Papa-B and 6 Papa-C intron 2 sequences. As compared to humans, bonobos appear to have an even more diminished MHC class I intron 2 lineage repertoire than common chimpanzees. This supports the notion that the selective sweep may have predated the speciation of common chimpanzees and bonobos. The further reduction of the MHC class I intron 2 lineage repertoire observed in bonobos as compared to the common chimpanzee may be explained by a founding effect or other subsequent selective processes.
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Affiliation(s)
- Natasja G de Groot
- Biomedical Primate Research Centre, Department of Comparative Genetics & Refinement, Rijswijk, The Netherlands.
| | - Corrine M C Heijmans
- Biomedical Primate Research Centre, Department of Comparative Genetics & Refinement, Rijswijk, The Netherlands
| | - Philippe Helsen
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Nel Otting
- Biomedical Primate Research Centre, Department of Comparative Genetics & Refinement, Rijswijk, The Netherlands
| | - Zjef Pereboom
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Jeroen M G Stevens
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium.,Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Ronald E Bontrop
- Biomedical Primate Research Centre, Department of Comparative Genetics & Refinement, Rijswijk, The Netherlands.,Department of Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH, Utrecht, The Netherlands
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6
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Staes N, Weiss A, Helsen P, Korody M, Eens M, Stevens JMG. Bonobo personality traits are heritable and associated with vasopressin receptor gene 1a variation. Sci Rep 2016; 6:38193. [PMID: 27910885 PMCID: PMC5133571 DOI: 10.1038/srep38193] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 11/04/2016] [Indexed: 11/30/2022] Open
Abstract
Despite being closely related, bonobos and chimpanzees show remarkable behavioral differences, the proximate origins of which remain unknown. This study examined the link between behavioral variation and variation in the vasopressin 1a receptor gene (Avpr1a) in bonobos. Chimpanzees are polymorphic for a ~360 bp deletion (DupB), which includes a microsatellite (RS3) in the 5′ promoter region of Avpr1a. In chimpanzees, the DupB deletion has been linked to lower sociability, lower social sensitivity, and higher anxiety. Chimpanzees and bonobos differ on these traits, leading some to believe that the absence of the DupB deletion in bonobos may be partly responsible for these differences, and to the prediction that similar associations between Avpr1a genotypes and personality traits should be present in bonobos. We identified bonobo personality dimensions using behavioral measures (SociabilityB, BoldnessB, OpennessB, ActivityB) and trait ratings (AssertivenessR, ConscientiousnessR, OpennessR, AgreeablenessR, AttentivenessR, ExtraversionR). In the present study we found that all 10 dimensions have nonzero heritabilities, indicating there is a genetic basis to personality, and that bonobos homozygous for shorter RS3 alleles were lower in AttentivenessR and higher in OpennessB. These results suggest that variations in Avpr1a genotypes explain both within and between species differences in personality traits of bonobos and chimpanzees.
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Affiliation(s)
- Nicky Staes
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium.,Behavioural Ecology &Ecophysiology Group, Department of Biology, University of Antwerp, Antwerp, Belgium.,Center for Advanced Study of Human Paleobiology, Department of Anthropology, George Washington University, Washington DC, United States of America
| | - Alexander Weiss
- Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, United Kingdom.,The Scottish Primate Research Group, United Kingdom
| | - Philippe Helsen
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium.,Behavioural Ecology &Ecophysiology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Marisa Korody
- San Diego Zoo Institute for Conservation Research, California, United States of America
| | - Marcel Eens
- Behavioural Ecology &Ecophysiology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Jeroen M G Stevens
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium.,Behavioural Ecology &Ecophysiology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
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7
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Bruford MW, Ginja C, Hoffmann I, Joost S, Orozco-terWengel P, Alberto FJ, Amaral AJ, Barbato M, Biscarini F, Colli L, Costa M, Curik I, Duruz S, Ferenčaković M, Fischer D, Fitak R, Groeneveld LF, Hall SJG, Hanotte O, Hassan FU, Helsen P, Iacolina L, Kantanen J, Leempoel K, Lenstra JA, Ajmone-Marsan P, Masembe C, Megens HJ, Miele M, Neuditschko M, Nicolazzi EL, Pompanon F, Roosen J, Sevane N, Smetko A, Štambuk A, Streeter I, Stucki S, Supakorn C, Telo Da Gama L, Tixier-Boichard M, Wegmann D, Zhan X. Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025. Front Genet 2015; 6:314. [PMID: 26539210 PMCID: PMC4612686 DOI: 10.3389/fgene.2015.00314] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 10/05/2015] [Indexed: 12/20/2022] Open
Abstract
Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that “…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity.” However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are societal in origin and are predicated on the value (e.g., socio-economic and cultural) of these resources to farmers, rural communities and society as a whole. The overall conclusion is that despite the fact that the livestock sector has been relatively well-organized in the application of genetic methodologies to date, there is still a large gap between the current state-of-the-art in the use of tools to characterize genomic resources and its application to many non-commercial and local breeds, hampering the consistent utilization of genetic and genomic data as indicators of genetic erosion and diversity. The livestock genomic sector therefore needs to make a concerted effort in the coming decade to enable to the democratization of the powerful tools that are now at its disposal, and to ensure that they are applied in the context of breed conservation as well as development.
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Affiliation(s)
- Michael W Bruford
- School of Biosciences, Cardiff University Cardiff, UK ; Sustainable Places Research Institute, Cardiff University Cardiff, UK
| | - Catarina Ginja
- Faculdade de Ciências, Centro de Ecologia, Evolução e Alterações Ambientais (CE3C), Universidade de Lisboa Lisboa, Portugal ; Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Universidade do Porto, Campus Agrário de Vairão Portugal
| | - Irene Hoffmann
- Food and Agriculture Organization of the United Nations, Animal Genetic Resources Branch, Animal Production and Health Division Rome, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Florian J Alberto
- Laboratoire d'Ecologie Alpine, Université Grenoble Alpes Grenoble, France
| | - Andreia J Amaral
- Faculty of Sciences, BioISI- Biosystems and Integrative Sciences Institute, University of Lisbon Campo Grande, Portugal
| | - Mario Barbato
- School of Biosciences, Cardiff University Cardiff, UK
| | | | - Licia Colli
- BioDNA Centro di Ricerca sulla Biodiversità a sul DNA Antico, Istituto di Zootecnica, Università Cattolica del Sacro Cuore di Piacenza Italy
| | - Mafalda Costa
- School of Biosciences, Cardiff University Cardiff, UK
| | - Ino Curik
- Faculty of Agriculture, University of Zagreb Zagreb, Croatia
| | - Solange Duruz
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Daniel Fischer
- Natural Resources Institute Finland (Luke), Green Technology Jokioinen, Finland
| | - Robert Fitak
- Institut für Populationsgenetik Vetmeduni, Vienna, Austria
| | | | | | - Olivier Hanotte
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - Faiz-Ul Hassan
- School of Life Sciences, University of Nottingham Nottingham, UK ; Department of Animal Breeding and Genetics, University of Agriculture Faisalabad, Pakistan
| | - Philippe Helsen
- Centre for Research and Conservation, Royal Zoological Society of Antwerp Antwerp, Belgium
| | - Laura Iacolina
- Department of Chemistry and Bioscience, Aalborg University Aalborg, Denmark
| | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Green Technology Jokioinen, Finland ; Department of Biology, University of Eastern Finland Kuopio, Finland
| | - Kevin Leempoel
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Paolo Ajmone-Marsan
- BioDNA Centro di Ricerca sulla Biodiversità a sul DNA Antico, Istituto di Zootecnica, Università Cattolica del Sacro Cuore di Piacenza Italy
| | - Charles Masembe
- Institute of the Environment and Natural Resources, Makerere University Kampala, Uganda
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics Centre, Wageningen University Wageningen, Netherlands
| | - Mara Miele
- School of Planning and Geography, Cardiff University Cardiff, UK
| | | | | | - François Pompanon
- Laboratoire d'Ecologie Alpine, Université Grenoble Alpes Grenoble, France
| | - Jutta Roosen
- TUM School of Management, Technische Universität München Munich, Germany
| | - Natalia Sevane
- Department of Animal Production, Veterinary Faculty, Universidad Complutense de Madrid Madrid, Spain
| | | | - Anamaria Štambuk
- Department of Biology, Faculty of Science, University of Zagreb Zagreb, Croatia
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, UK
| | - Sylvie Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - China Supakorn
- School of Life Sciences, University of Nottingham Nottingham, UK ; School of Agricultural Technology, Walailak University Tha Sala, Thailand
| | - Luis Telo Da Gama
- Centre of Research in Animal Health (CIISA) - Faculty of Veterinary Medicine, University of Lisbon Lisbon, Portugal
| | | | - Daniel Wegmann
- Department of Biology, University of Fribourg Fribourg, Switzerland
| | - Xiangjiang Zhan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Beijing, China ; Cardiff University - Institute of Zoology, Joint Laboratory for Biocomplexity Research Beijing, China
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8
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Staes N, Koski SE, Helsen P, Fransen E, Eens M, Stevens JMG. Chimpanzee sociability is associated with vasopressin (Avpr1a) but not oxytocin receptor gene (OXTR) variation. Horm Behav 2015; 75:84-90. [PMID: 26299644 DOI: 10.1016/j.yhbeh.2015.08.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 06/16/2015] [Accepted: 08/14/2015] [Indexed: 11/25/2022]
Abstract
The importance of genes in regulating phenotypic variation of personality traits in humans and animals is becoming increasingly apparent in recent studies. Here we focus on variation in the vasopressin receptor gene 1a (Avpr1a) and oxytocin receptor gene (OXTR) and their effects on social personality traits in chimpanzees. We combine newly available genetic data on Avpr1a and OXTR allelic variation of 62 captive chimpanzees with individual variation in personality, based on behavioral assessments. Our study provides support for the positive association of the Avpr1a promoter region, in particular the presence of DupB, and sociability in chimpanzees. This complements findings of previous studies on adolescent chimpanzees and studies that assessed personality using questionnaire data. In contrast, no significant associations were found for the single nucleotide polymorphism (SNP) ss1388116472 of the OXTR and any of the personality components. Most importantly, our study provides additional evidence for the regulatory function of the 5' promoter region of Avpr1a on social behavior and its evolutionary stable effect across species, including rodents, chimpanzees and humans. Although it is generally accepted that complex social behavior is regulated by a combination of genes, the environment and their interaction, our findings highlight the importance of candidate genes with large effects on behavioral variation.
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Affiliation(s)
- Nicky Staes
- University of Antwerp, Department of Biology, B-2610 Antwerp, Belgium; Centre for Research and Conservation, Royal Zoological Society of Antwerp, B-2018 Antwerp, Belgium.
| | - Sonja E Koski
- Helsinki University, Finnish Centre of Excellence in Intersubjectivity in Interaction, FI-00014 Helsinki, Finland.
| | - Philippe Helsen
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, B-2018 Antwerp, Belgium; University of Antwerp, Department of Biology, B-2610 Antwerp, Belgium.
| | - Erik Fransen
- University of Antwerp, Statua Center for Statistics, B-2000 Antwerp, Belgium.
| | - Marcel Eens
- University of Antwerp, Department of Biology, B-2610 Antwerp, Belgium.
| | - Jeroen M G Stevens
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, B-2018 Antwerp, Belgium; University of Antwerp, Department of Biology, B-2610 Antwerp, Belgium.
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9
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Staes N, Stevens JMG, Helsen P, Hillyer M, Korody M, Eens M. Oxytocin and vasopressin receptor gene variation as a proximate base for inter- and intraspecific behavioral differences in bonobos and chimpanzees. PLoS One 2014; 9:e113364. [PMID: 25405348 PMCID: PMC4236177 DOI: 10.1371/journal.pone.0113364] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 10/22/2014] [Indexed: 01/08/2023] Open
Abstract
Recent literature has revealed the importance of variation in neuropeptide receptor gene sequences in the regulation of behavioral phenotypic variation. Here we focus on polymorphisms in the oxytocin receptor gene (OXTR) and vasopressin receptor gene 1a (Avpr1a) in chimpanzees and bonobos. In humans, a single nucleotide polymorphism (SNP) in the third intron of OXTR (rs53576 SNP (A/G)) is linked with social behavior, with the risk allele (A) carriers showing reduced levels of empathy and prosociality. Bonobos and chimpanzees differ in these same traits, therefore we hypothesized that these differences might be reflected in variation at the rs53576 position. We sequenced a 320 bp region surrounding rs53576 but found no indications of this SNP in the genus Pan. However, we identified previously unreported SNP variation in the chimpanzee OXTR sequence that differs from both humans and bonobos. Humans and bonobos have previously been shown to have a more similar 5′ promoter region of Avpr1a when compared to chimpanzees, who are polymorphic for the deletion of ∼360 bp in this region (+/− DupB) which includes a microsatellite (RS3). RS3 has been linked with variation in levels of social bonding, potentially explaining part of the interspecies behavioral differences found in bonobos, chimpanzees and humans. To date, results for bonobos have been based on small sample sizes. Our results confirmed that there is no DupB deletion in bonobos with a sample size comprising approximately 90% of the captive founder population, whereas in chimpanzees the deletion of DupB had the highest frequency. Because of the higher frequency of DupB alleles in our bonobo population, we suggest that the presence of this microsatellite may partly reflect documented differences in levels of sociability found in bonobos and chimpanzees.
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Affiliation(s)
- Nicky Staes
- University of Antwerp, Department of Biology, Ethology research group, 2610, Antwerp, Belgium
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, 2018, Antwerp, Belgium
- * E-mail:
| | - Jeroen M. G. Stevens
- University of Antwerp, Department of Biology, Ethology research group, 2610, Antwerp, Belgium
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, 2018, Antwerp, Belgium
| | - Philippe Helsen
- University of Antwerp, Department of Biology, Ethology research group, 2610, Antwerp, Belgium
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, 2018, Antwerp, Belgium
| | - Mia Hillyer
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, 2018, Antwerp, Belgium
- Molecular Systematics Unit, Western Australian Museum, Perth, WA 6106, Australia
| | - Marisa Korody
- San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, United States of America
| | - Marcel Eens
- University of Antwerp, Department of Biology, Ethology research group, 2610, Antwerp, Belgium
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10
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Stanton DWG, Hart J, Galbusera P, Helsen P, Shephard J, Kümpel NF, Wang J, Ewen JG, Bruford MW. Distinct and diverse: range-wide phylogeography reveals ancient lineages and high genetic variation in the endangered okapi (Okapia johnstoni). PLoS One 2014; 9:e101081. [PMID: 25007188 PMCID: PMC4090074 DOI: 10.1371/journal.pone.0101081] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 06/02/2014] [Indexed: 11/22/2022] Open
Abstract
The okapi is an endangered, evolutionarily distinctive even-toed ungulate classified within the giraffidae family that is endemic to the Democratic Republic of Congo. The okapi is currently under major anthropogenic threat, yet to date nothing is known about its genetic structure and evolutionary history, information important for conservation management given the species' current plight. The distribution of the okapi, being confined to the Congo Basin and yet spanning the Congo River, also makes it an important species for testing general biogeographic hypotheses for Congo Basin fauna, a currently understudied area of research. Here we describe the evolutionary history and genetic structure of okapi, in the context of other African ungulates including the giraffe, and use this information to shed light on the biogeographic history of Congo Basin fauna in general. Using nuclear and mitochondrial DNA sequence analysis of mainly non-invasively collected samples, we show that the okapi is both highly genetically distinct and highly genetically diverse, an unusual combination of genetic traits for an endangered species, and feature a complex evolutionary history. Genetic data are consistent with repeated climatic cycles leading to multiple Plio-Pleistocene refugia in isolated forests in the Congo catchment but also imply historic gene flow across the Congo River.
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Affiliation(s)
| | - John Hart
- Lukuru Foundation, Projet Tshuapa-Lomami-Lualaba (TL2), Kinshasa, Democratic Republic of Congo
| | - Peter Galbusera
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Philippe Helsen
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Jill Shephard
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Noëlle F. Kümpel
- Conservation Programmes, Zoological Society of London, London, United Kingdom
| | - Jinliang Wang
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - John G. Ewen
- Institute of Zoology, Zoological Society of London, London, United Kingdom
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Jordaens K, Van Houtte N, Helsen P, Breugelmans K, Jaksons P, Backeljau T. Mixed breeding system in the hermaphroditic land slug Arion intermedius (Stylommatophora, Arionidae). Hereditas 2013; 150:45-52. [PMID: 24164457 DOI: 10.1111/j.1601-5223.2013.02272.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Theory suggests that hermaphroditic plants and animals should be either entirely outcrossing or entirely selfing. As such, very few hermaphroditic plants and basommatophoran snails have a mixed breeding system. However, reliable estimates of selfing rates are lacking for most hermaphroditic animals. This partly prevents to delineate the relative contributions of the selective factors that determine selfing and outcrossing rates in hermaphroditic animal taxa. Here, we studied the population genetic structure of, and breeding system in, 11 populations of the hermaphroditic land slug Arion intermedius using five polymorphic microsatellite loci. Moreover, genotype frequencies deviated significantly from Hardy-Weinberg equilibrium expectations for most of the loci in all populations suggesting some level of selfing. Estimates of the selfing level s, suggest moderate levels of outcrossing (mean s based on FIS = 0.84; mean s based on the two-locus heterozygosity disequilibrium = 0.20, or with a ML approach = 0.22). Our study therefore suggests that A. intermedius has a mixed breeding system. A re-analysis of allozyme data from another arionid slug ( subgenus Carinarion) indicates that mixed breeding may be more common in arionid slugs than hitherto was assumed. These results seem therefore at variance with current theoretical and empirical predictions and opens perspectives for the study on the evolutionary factors driving mixed breeding systems in animals.
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Affiliation(s)
- Kurt Jordaens
- Royal Museum for Central Africa, Tervuren, BelgiumUniversity of Antwerp, Antwerp, BelgiumRoyal Belgian Institute of Natural Sciences, Brussels, Belgium
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Tkint T, Verheyen E, De Kegel B, Helsen P, Adriaens D. Dealing with food and eggs in mouthbrooding cichlids: structural and functional trade-offs in fitness related traits. PLoS One 2012; 7:e31117. [PMID: 22348043 PMCID: PMC3279513 DOI: 10.1371/journal.pone.0031117] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 01/03/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND As in any vertebrate, heads of fishes are densely packed with functions. These functions often impose conflicting mechanical demands resulting in trade-offs in the species-specific phenotype. When phenotypical traits are linked to gender-specific parental behavior, we expect sexual differences in these trade-offs. This study aims to use mouthbrooding cichlids as an example to test hypotheses on evolutionary trade-offs between intricately linked traits that affect different aspects of fitness. We focused on the oral apparatus, which is not only equipped with features used to feed and breathe, but is also used for the incubation of eggs. We used this approach to study mouthbrooding as part of an integrated functional system with diverging performance requirements and to explore gender-specific selective environments within a species. METHODOLOGY/PRINCIPAL FINDINGS Because cichlids are morphologically very diverse, we hypothesize that the implications of the added constraint of mouthbrooding will primarily depend on the dominant mode of feeding of the studied species. To test this, we compared the trade-off for two maternal mouthbrooding cichlid species: a "suction feeder" (Haplochromis piceatus) and a "biter" (H. fischeri). The comparison of morphology and performance of both species revealed clear interspecific and intersex differences. Our observation that females have larger heads was interpreted as a possible consequence of the fact that in both the studied species mouthbrooding is done by females only. As hypothesized, the observed sexual dimorphism in head shape is inferred as being suboptimal for some aspects of the feeding performance in each of the studied species. Our comparison also demonstrated that the suction feeding species had smaller egg clutches and more elongated eggs. CONCLUSIONS/SIGNIFICANCE Our findings support the hypothesis that there is a trade-off between mouthbrooding and feeding performance in the two studied haplochromine cichlids, stressing the importance of including species-specific information at the gender level when addressing interspecific functional/morphological differences.
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Affiliation(s)
- Tim Tkint
- Department of Biology, Research Group Evolutionary Morphology of Vertebrates, Ghent University, Ghent, Belgium.
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