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Nieto-Blázquez ME, Gómez-Suárez M, Pfenninger M, Koch K. Impact of feralization on evolutionary trajectories in the genomes of feral cat island populations. PLoS One 2024; 19:e0308724. [PMID: 39137187 PMCID: PMC11321585 DOI: 10.1371/journal.pone.0308724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 07/29/2024] [Indexed: 08/15/2024] Open
Abstract
Feralization is the process of domesticated animals returning to the wild and it is considered the counterpart of domestication. Molecular genetic changes are well documented in domesticated organisms but understudied in feral populations. In this study, the genetic differentiation between domestic and feral cats was inferred by analysing whole-genome sequencing data of two geographically distant feral cat island populations, Dirk Hartog Island (Australia) and Kaho'olawe (Hawaii) as well as domestic cats and European wildcats. The study investigated population structure, genetic differentiation, genetic diversity, highly differentiated genes, and recombination rates. Genetic structure analyses linked both feral cat populations to North American domestic and European cat populations. Recombination rates in feral cats were lower than in domestic cats but higher than in wildcats. For Australian and Hawaiian feral cats, 105 and 94 highly differentiated genes compared to domestic cats respectively, were identified. Annotated genes had similar functions, with almost 30% of the divergent genes related to nervous system development in both feral groups. Twenty mutually highly differentiated genes were found in both feral populations. Evolution of highly differentiated genes was likely driven by specific demographic histories, the relaxation of the selective pressures associated with domestication, and adaptation to novel environments to a minor extent. Random drift was the prevailing force driving highly divergent regions, with relaxed selection in feral populations also playing a significant role in differentiation from domestic cats. The study demonstrates that feralization is an independent process that brings feral cats on a unique evolutionary trajectory.
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Affiliation(s)
- María Esther Nieto-Blázquez
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Manuela Gómez-Suárez
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Markus Pfenninger
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Katrin Koch
- Department of Biodiversity, Conservation and Attractions, Former, Biodiversity and Conservation Science, Woodvale, Australia
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2
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Wu ZY, Chapman MA, Liu J, Milne RI, Zhao Y, Luo YH, Zhu GF, Cadotte MW, Luan MB, Fan PZ, Monro AK, Li ZP, Corlett RT, Li DZ. Genomic variation, environmental adaptation, and feralization in ramie, an ancient fiber crop. PLANT COMMUNICATIONS 2024; 5:100942. [PMID: 38720463 DOI: 10.1016/j.xplc.2024.100942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/20/2023] [Accepted: 05/06/2024] [Indexed: 06/29/2024]
Abstract
Feralization is an important evolutionary process, but the mechanisms behind it remain poorly understood. Here, we use the ancient fiber crop ramie (Boehmeria nivea (L.) Gaudich.) as a model to investigate genomic changes associated with both domestication and feralization. We first produced a chromosome-scale de novo genome assembly of feral ramie and investigated structural variations between feral and domesticated ramie genomes. Next, we gathered 915 accessions from 23 countries, comprising cultivars, major landraces, feral populations, and the wild progenitor. Based on whole-genome resequencing of these accessions, we constructed the most comprehensive ramie genomic variation map to date. Phylogenetic, demographic, and admixture signal detection analyses indicated that feral ramie is of exoferal or exo-endo origin, i.e., descended from hybridization between domesticated ramie and the wild progenitor or ancient landraces. Feral ramie has higher genetic diversity than wild or domesticated ramie, and genomic regions affected by natural selection during feralization differ from those under selection during domestication. Ecological analyses showed that feral and domesticated ramie have similar ecological niches that differ substantially from the niche of the wild progenitor, and three environmental variables are associated with habitat-specific adaptation in feral ramie. These findings advance our understanding of feralization, providing a scientific basis for the excavation of new crop germplasm resources and offering novel insights into the evolution of feralization in nature.
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Affiliation(s)
- Zeng-Yuan Wu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Mark A Chapman
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Jie Liu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Richard I Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, UK
| | - Ying Zhao
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Guang-Fu Zhu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Marc W Cadotte
- Department of Biological Sciences, University of Toronto-Scarborough, Toronto, Ontario, Canada
| | - Ming-Bao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan 410205, China.
| | - Peng-Zhen Fan
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Alex K Monro
- Royal Botanic Gardens Kew, Richmond, Surrey TW9 3AE, UK
| | - Zhi-Peng Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Richard T Corlett
- Royal Botanic Gardens Kew, Richmond, Surrey TW9 3AE, UK; Center for Integrative Conservation and Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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3
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Andrade P, Alves JM, Pereira P, Rubin CJ, Silva E, Sprehn CG, Enbody E, Afonso S, Faria R, Zhang Y, Bonino N, Duckworth JA, Garreau H, Letnic M, Strive T, Thulin CG, Queney G, Villafuerte R, Jiggins FM, Ferrand N, Andersson L, Carneiro M. Selection against domestication alleles in introduced rabbit populations. Nat Ecol Evol 2024; 8:1543-1555. [PMID: 38907020 DOI: 10.1038/s41559-024-02443-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
Humans have moved domestic animals around the globe for thousands of years. These have occasionally established feral populations in nature, often with devastating ecological consequences. To understand how natural selection shapes re-adaptation into the wild, we investigated one of the most successful colonizers in history, the European rabbit. By sequencing the genomes of 297 rabbits across three continents, we show that introduced populations exhibit a mixed wild-domestic ancestry. We show that alleles that increased in frequency during domestication were preferentially selected against in novel natural environments. Interestingly, causative mutations for common domestication traits sometimes segregate at considerable frequencies if associated with less drastic phenotypes (for example, coat colour dilution), whereas mutations that are probably strongly maladaptive in nature are absent. Whereas natural selection largely targeted different genomic regions in each introduced population, some of the strongest signals of parallelism overlap genes associated with neuronal or brain function. This limited parallelism is probably explained by extensive standing genetic variation resulting from domestication together with the complex mixed ancestry of introduced populations. Our findings shed light on the selective and molecular mechanisms that enable domestic animals to re-adapt to the wild and provide important insights for the mitigation and management of invasive populations.
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Affiliation(s)
- Pedro Andrade
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
| | - Joel M Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Palaeogenomics and Bio-Archaeology Research Network Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Paulo Pereira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Institute of Marine Research, Bergen, Norway
| | - Eugénio Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - C Grace Sprehn
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Erik Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Yexin Zhang
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Never Bonino
- Estación Experimental Bariloche, Instituto Nacional de Tecnología Agropecuaria, Casilla de Correo Bariloche, Argentina
| | - Janine A Duckworth
- Wildlife Ecology and Management Group, Manaaki Whenua - Landcare Research, Lincoln, New Zealand
- Invasive Animals Cooperative Research Centre, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Hervé Garreau
- GenPhySE, Université de Toulouse, Castanet-Tolosan, France
| | - Mike Letnic
- Centre for Ecosystem Science, School of BEES, University of New South Wales, Sydney, New South Wales, Australia
- Evolution and Ecology Research Centre, School of BEES, University of New South Wales, Sydney, New South Wales, Australia
| | - Tanja Strive
- Centre for Invasive Species Solutions, University of Canberra, Bruce, Australian Capital Territory, Australia
- Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
| | - Carl-Gustaf Thulin
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Guillaume Queney
- ANTAGENE, Wildlife Genetics Laboratory, La Tour de Salvagny, France
| | | | | | - Nuno Ferrand
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, South Africa
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
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4
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Gautier M, Micol T, Camus L, Moazami-Goudarzi K, Naves M, Guéret E, Engelen S, Lemainque A, Colas F, Flori L, Druet T. Genomic Reconstruction of the Successful Establishment of a Feralized Bovine Population on the Subantarctic Island of Amsterdam. Mol Biol Evol 2024; 41:msae121. [PMID: 38889245 PMCID: PMC11339654 DOI: 10.1093/molbev/msae121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 05/13/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
The feral cattle of the subantarctic island of Amsterdam provide an outstanding case study of a large mammalian population that was established by a handful of founders and thrived within a few generations in a seemingly inhospitable environment. Here, we investigated the genetic history and composition of this population using genotyping and sequencing data. Our inference showed an intense but brief founding bottleneck around the late 19th century and revealed contributions from European taurine and Indian Ocean Zebu in the founder ancestry. Comparative analysis of whole-genome sequences further revealed a moderate reduction in genetic diversity despite high levels of inbreeding. The brief and intense bottleneck was associated with high levels of drift, a flattening of the site frequency spectrum and a slight relaxation of purifying selection on mildly deleterious variants. Unlike some populations that have experienced prolonged reductions in effective population size, we did not observe any significant purging of highly deleterious variants. Interestingly, the population's success in the harsh environment can be attributed to preadaptation from their European taurine ancestry, suggesting no strong bioclimatic challenge, and also contradicting evidence for insular dwarfism. Genome scan for footprints of selection uncovered a majority of candidate genes related to nervous system function, likely reflecting rapid feralization driven by behavioral changes and complex social restructuring. The Amsterdam Island cattle offers valuable insights into rapid population establishment, feralization, and genetic adaptation in challenging environments. It also sheds light on the unique genetic legacies of feral populations, raising ethical questions according to conservation efforts.
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Affiliation(s)
- Mathieu Gautier
- CBGP, INRAE, CIRAD, IRD, L’institut Agro, Université de Montpellier, Montpellier, France
| | | | - Louise Camus
- CBGP, INRAE, CIRAD, IRD, L’institut Agro, Université de Montpellier, Montpellier, France
| | | | | | - Elise Guéret
- MGX-Montpellier GenomiX, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Stefan Engelen
- Retired, CEA, Institut de biologie François-Jacob, Genoscope, Université Paris-Saclay, Evry, France
| | - Arnaud Lemainque
- Retired, CEA, Institut de biologie François-Jacob, Genoscope, Université Paris-Saclay, Evry, France
| | - François Colas
- Retired, Saint-Paul and Amsterdam District, Terres Australes et Antarctiques Françaises, France
| | - Laurence Flori
- SELMET, INRAE, CIRAD, L’institut Agro, Université de Montpellier, Montpellier, France
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
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5
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Chen R, Chen K, Yao X, Zhang X, Yang Y, Su X, Lyu M, Wang Q, Zhang G, Wang M, Li Y, Duan L, Xie T, Li H, Yang Y, Zhang H, Guo Y, Jia G, Ge X, Sarris PF, Lin T, Sun D. Genomic analyses reveal the stepwise domestication and genetic mechanism of curd biogenesis in cauliflower. Nat Genet 2024; 56:1235-1244. [PMID: 38714866 PMCID: PMC11176064 DOI: 10.1038/s41588-024-01744-4] [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: 03/02/2023] [Accepted: 04/04/2024] [Indexed: 05/12/2024]
Abstract
Cauliflower (Brassica oleracea L. var. botrytis) is a distinctive vegetable that supplies a nutrient-rich edible inflorescence meristem for the human diet. However, the genomic bases of its selective breeding have not been studied extensively. Herein, we present a high-quality reference genome assembly C-8 (V2) and a comprehensive genomic variation map consisting of 971 diverse accessions of cauliflower and its relatives. Genomic selection analysis and deep-mined divergences were used to explore a stepwise domestication process for cauliflower that initially evolved from broccoli (Curd-emergence and Curd-improvement), revealing that three MADS-box genes, CAULIFLOWER1 (CAL1), CAL2 and FRUITFULL (FUL2), could have essential roles during curd formation. Genome-wide association studies identified nine loci significantly associated with morphological and biological characters and demonstrated that a zinc-finger protein (BOB06G135460) positively regulates stem height in cauliflower. This study offers valuable genomic resources for better understanding the genetic bases of curd biogenesis and florescent development in crops.
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Affiliation(s)
- Rui Chen
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China.
| | - Ke Chen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
- Key Laboratory of Weed Control in Southern Farmland, Ministry of Agriculture and Rural Affairs, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xingwei Yao
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Xiaoli Zhang
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Yingxia Yang
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Xiao Su
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Mingjie Lyu
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Qian Wang
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Guan Zhang
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Mengmeng Wang
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Yanhao Li
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Lijin Duan
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Tianyu Xie
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Haichao Li
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China
- College of Life Sciences, Nankai University, Tianjin, China
| | - Yuyao Yang
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China
- College of Life Sciences, Nankai University, Tianjin, China
| | - Hong Zhang
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China
- College of Life Sciences, Nankai University, Tianjin, China
| | - Yutong Guo
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China
- College of Life Sciences, Nankai University, Tianjin, China
| | - Guiying Jia
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China
- College of Life Sciences, Nankai University, Tianjin, China
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Panagiotis F Sarris
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - Tao Lin
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China.
| | - Deling Sun
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China.
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6
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Barmentlo NWG, Meirmans PG, Stiver WH, Yarkovich JG, McCann BE, Piaggio AJ, Wright D, Smyser TJ, Bosse M. Natural selection on feralization genes contributed to the invasive spread of wild pigs throughout the United States. Mol Ecol 2024; 33:e17383. [PMID: 38747342 DOI: 10.1111/mec.17383] [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: 01/30/2024] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 06/07/2024]
Abstract
Despite a long presence in the contiguous United States (US), the distribution of invasive wild pigs (Sus scrofa × domesticus) has expanded rapidly since the 1980s, suggesting a more recent evolutionary shift towards greater invasiveness. Contemporary populations of wild pigs represent exoferal hybrid descendants of domestic pigs and European wild boar, with such hybridization expected to enrich genetic diversity and increase the adaptive potential of populations. Our objective was to characterize how genetic enrichment through hybridization increases the invasiveness of populations by identifying signals of selection and the ancestral origins of selected loci. Our study focused on invasive wild pigs within Great Smoky Mountains National Park, which represents a hybrid population descendent from the admixture of established populations of feral pigs and an introduction of European wild boar to North America. Accordingly, we genotyped 881 wild pigs with multiple high-density single-nucleotide polymorphism (SNP) arrays. We found 233 markers under putative selection spread over 79 regions across 16 out of 18 autosomes, which contained genes involved in traits affecting feralization. Among these, genes were found to be related to skull formation and neurogenesis, with two genes, TYRP1 and TYR, also encoding for crucial melanogenesis enzymes. The most common haplotypes associated with regions under selection for the Great Smoky Mountains population were also common among other populations throughout the region, indicating a key role of putatively selective variants in the fitness of invasive populations. Interestingly, many of these haplotypes were absent among European wild boar reference genotypes, indicating feralization through genetic adaptation.
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Affiliation(s)
- Niek W G Barmentlo
- Section Ecology & Evolution, Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Patrick G Meirmans
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | | | | | - Blake E McCann
- Theodore Roosevelt National Park, Medora, North Dakota, USA
| | | | - Dominic Wright
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Timothy J Smyser
- USDA APHIS WS National Wildlife Research Center, Fort Collins, Colorado, USA
| | - Mirte Bosse
- Section Ecology & Evolution, Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Wageningen University & Research - Animal Breeding and Genomics, Wageningen, The Netherlands
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7
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Arlé E, Knight TM, Jiménez‐Muñoz M, Biancolini D, Belmaker J, Meyer C. The cumulative niche approach: A framework to assess the performance of ecological niche model projections. Ecol Evol 2024; 14:e11060. [PMID: 38384827 PMCID: PMC10880136 DOI: 10.1002/ece3.11060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 02/04/2024] [Indexed: 02/23/2024] Open
Abstract
Ecological Niche Models (ENMs) are often used to project species distributions within alien ranges and in future climatic scenarios. However, ENMs depend on species-environment equilibrium, which may be absent for actively expanding species. We present a novel framework to estimate whether species have reached environmental equilibrium in their native and alien ranges. The method is based on the estimation of niche breadth with the accumulation of species occurrences. An asymptote will indicate exhaustive knowledge of the realised niches. We demonstrate the CNA framework for 26 species of mammals, amphibians, and birds. Possible outcomes of the framework include: (1) There is enough data to quantify the native and alien realised niches, allowing us to calculate niche expansion between the native and alien ranges, also indicating that ENMs can be reliably projected to new environmental conditions. (2) The data in the native range is not adequate but an asymptote is reached in the alien realised niche, indicating low confidence in our ability to evaluate niche expansion in the alien range but high confidence in model projections to new environmental conditions within the alien range. (3) There is enough data to quantify the native realised niche, but not enough knowledge about the alien realised niche, hindering the reliability of projections beyond sampled conditions. (4) Both the native and alien ranges do not reach an asymptote, and thus few robust conclusions about the species' niche or future projections can be made. Our framework can be used to detect species' environmental equilibrium in both the native and alien ranges, to quantify changes in the realised niche during the invasion processes, and to estimate the likely accuracy of model projections to new environmental conditions.
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Affiliation(s)
- Eduardo Arlé
- German Centre for Integrative Biodiversity Research (iDiv), Halle‐Jena‐LeipzigLeipzigGermany
- School of Zoology, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Tiffany Marie Knight
- German Centre for Integrative Biodiversity Research (iDiv), Halle‐Jena‐LeipzigLeipzigGermany
- Department Community EcologyHelmholtz Centre for Environmental Research‐UFZHalle (Saale)Germany
- Institute of BiologyMartin Luther University Halle‐WittenbergHalle (Saale)Germany
| | - Marina Jiménez‐Muñoz
- Core Facility Statistical Consulting, Helmholz Centre MunichGerman Research Centre for Environmental Health GmbHMunichGermany
| | - Dino Biancolini
- Institute for BioEconomy (CNR‐IBE)National Research Council of ItalyRomeItaly
| | - Jonathan Belmaker
- School of Zoology, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
- The Steinhardt Museum of Natural HistoryTel Aviv UniversityTel AvivIsrael
| | - Carsten Meyer
- German Centre for Integrative Biodiversity Research (iDiv), Halle‐Jena‐LeipzigLeipzigGermany
- Faculty of Biosciences, Pharmacy and PsychologyUniversity of LeipzigLeipzigGermany
- Faculty of Natural Sciences III – Agricultural and Nutritional Sciences, Geosciences and Computer ScienceHalle (Saale)Germany
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8
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Palkovitz RE, Lawler RR. Developing evolutionary anthropology in local ecosystems. Evol Anthropol 2024; 33:e22016. [PMID: 38088455 DOI: 10.1002/evan.22016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/20/2023] [Accepted: 11/29/2023] [Indexed: 12/30/2023]
Abstract
The traditional regional focus of evolutionary anthropology-typically defined as places where hominin fossils, nonhuman primates, and non-western populations reside-forms the basis of much evolutionary anthropological research. Using the highly biodiverse temperate region of Appalachia as an example, we suggest that evolutionary anthropologists have much to gain by stepping outside of this traditional geographic area. Being purposely provocative, we argue that evolutionary anthropologists might also benefit from conducting research in Appalachia and other temperate ecosystems. We briefly discuss multiple areas of study-including studies of seed dispersal, functional redundancy, convergent evolution, human behavioral ecology, and conservation-and how they can be considered within the purview of integrative and evolutionary anthropology. We also highlight broader impacts to higher education that evolutionary anthropologists can help promote by working in local ecosystems.
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Affiliation(s)
- Rachel E Palkovitz
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Richard R Lawler
- Department of Sociology and Anthropology, James Madison University, Harrisonburg, Virginia, USA
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Zunino L, Cubry P, Sarah G, Mournet P, El Bakkali A, Aqbouch L, Sidibé-Bocs S, Costes E, Khadari B. Genomic evidence of genuine wild versus admixed olive populations evolving in the same natural environments in western Mediterranean Basin. PLoS One 2024; 19:e0295043. [PMID: 38232071 DOI: 10.1371/journal.pone.0295043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/14/2023] [Indexed: 01/19/2024] Open
Abstract
Crop-to-wild gene flow is a mechanism process widely documented, both in plants and animals. This can have positive or negative impacts on the evolution of admixed populations in natural environments, yet the phenomenon is still misunderstood in long-lived woody species, contrary to short-lived crops. Wild olive Olea europaea L. occurs in the same eco-geographical range as domesticated olive, i.e. the Mediterranean Basin (MB). Moreover, it is an allogamous and anemophilous species whose seeds are disseminated by birds, i.e. factors that drive gene flow between crops and their wild relatives. Here we investigated the genetic structure of western MB wild olive populations in natural environments assuming a homogenous gene pool with limited impact of cultivated alleles, as previously suggested. We used a target sequencing method based on annotated genes from the Farga reference genome to analyze 27 western MB olive tree populations sampled in natural environments in France, Spain and Morocco. We also target sequenced cultivated olive tree accessions from the Worldwide Olive Germplasm Bank of Marrakech and Porquerolles and from an eastern MB wild olive tree population. We combined PCA, sNMF, pairwise FST and TreeMix and clearly identified genuine wild olive trees throughout their natural distribution range along a north-south gradient including, for the first time, in southern France. However, contrary to our assumption, we highlighted more admixed than genuine wild olive trees. Our results raise questions regarding the admixed population evolution pattern in this environment, which might be facilitated by crop-to-wild gene flow.
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Affiliation(s)
- Lison Zunino
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- DIADE, University of Montpellier, CIRAD, IRD, Montpellier, France
| | - Philippe Cubry
- DIADE, University of Montpellier, CIRAD, IRD, Montpellier, France
| | - Gautier Sarah
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Pierre Mournet
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
| | - Ahmed El Bakkali
- INRA, UR Amélioration des Plantes et Conservation des Ressources Phytogénétiques, Meknes, Morocco
| | - Laila Aqbouch
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Stéphanie Sidibé-Bocs
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
| | - Evelyne Costes
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Bouchaib Khadari
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- Conservatoire Botanique National Méditerranéen (CBNMed), UMR AGAP Institut, Montpellier, France
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10
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Hernández-Alonso G, Ramos-Madrigal J, van Grouw H, Ciucani MM, Cavill EL, Sinding MHS, Gopalakrishnan S, Pacheco G, Gilbert MTP. Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences. Mol Biol Evol 2023; 40:msad243. [PMID: 37950889 PMCID: PMC10667084 DOI: 10.1093/molbev/msad243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/10/2023] [Accepted: 11/03/2023] [Indexed: 11/13/2023] Open
Abstract
The domestic pigeon's exceptional phenotypic diversity was key in developing Darwin's Theory of Evolution and establishing the concept of artificial selection. However, unlike its domestic counterpart, its wild progenitor, the rock dove Columba livia has received considerably less attention. Therefore, questions regarding its domestication, evolution, taxonomy, and conservation status remain unresolved. We generated whole-genome sequencing data from 65 historical rock doves that represent all currently recognized subspecies and span the species' original geographic distribution. Our dataset includes 3 specimens from Darwin's collection, and the type specimens of 5 different taxa. We characterized their population structure, genomic diversity, and gene-flow patterns. Our results show the West African subspecies C. l. gymnocyclus is basal to rock doves and domestic pigeons, and suggests gene-flow between the rock dove's sister species C. rupestris, and the ancestor of rock doves after its split from West African populations. These genomes allowed us to propose a model for the evolution of the rock dove in light of the refugia theory. We propose that rock dove genetic diversity and introgression patterns derive from a history of allopatric cycles and dispersion waves during the Quaternary glacial and interglacial periods. To explore the rock dove domestication history, we combined our new dataset with available genomes from domestic pigeons. Our results point to at least 1 domestication event in the Levant that gave rise to all domestic breeds analysed in this study. Finally, we propose a species-level taxonomic arrangement to reflect the evolutionary history of the West African rock dove populations.
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Affiliation(s)
- Germán Hernández-Alonso
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jazmín Ramos-Madrigal
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hein van Grouw
- Bird Group, Department of Life Sciences, Natural History Museum, Tring, United Kingdom
| | - Marta Maria Ciucani
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Emily Louisa Cavill
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Shyam Gopalakrishnan
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - George Pacheco
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
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11
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Leal-Dutra CA, Yuen LM, Guedes BAM, Contreras-Serrano M, Marques PE, Shik JZ. Evidence that the domesticated fungus Leucoagaricus gongylophorus recycles its cytoplasmic contents as nutritional rewards to feed its leafcutter ant farmers. IMA Fungus 2023; 14:19. [PMID: 37715276 PMCID: PMC10503033 DOI: 10.1186/s43008-023-00126-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 08/22/2023] [Indexed: 09/17/2023] Open
Abstract
Leafcutter ants farm a fungal cultivar (Leucoagaricus gongylophorus) that converts inedible vegetation into food that sustains colonies with up to millions of workers. Analogous to edible fruits of crops domesticated by humans, L. gongylophorus has evolved specialized nutritional rewards-swollen hyphal cells called gongylidia that package metabolites and are consumed by ant farmers. Yet, little is known about how gongylidia form, and thus how fungal physiology and ant provisioning collectively govern farming performance. We explored the process of gongylidium formation using advanced microscopy to image the cultivar at scales of nanometers, and both in vitro experiments and in silico analyses to examine the mechanisms of gongylidia formation when isolated from ant farmers. We first used transmission electron, fluorescence, and confocal microscopy imaging to see inside hyphal cells. This imaging showed that the cultivar uses a process called autophagy to recycle its own cellular material (e.g. cytosol, mitochondria) and then shuttles the resulting metabolites into a vacuole whose continual expansion displaces other organelles and causes the gongylidium cell's bulging bulb-like appearance. We next used scanning electron microscopy and light microscopy to link this intracellular rearrangement to the external branching patterns of gongylidium cells as they clump together into edible bundles called staphyla. We next confirmed that autophagy plays a critical role in gongylidium formation both: (1) in vitro as gongylidium suppression occurred when isolated fungal cultures were grown on media with autophagy inhibitors, and (2) in silico as differential transcript expression (RNA-seq) analyses showed upregulation of multiple autophagy gene isoforms in gongylidia relative to undifferentiated hyphae. While autophagy is a ubiquitous and often highly derived process across the tree of life, our study reveals a new role for autophagy as a mechanism of functional integration between ant farmers and their fungal crop, and potentially as a signifier of higher-level homeostasis between uniquely life-time committed ectosymbionts.
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Affiliation(s)
- Caio Ambrosio Leal-Dutra
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark.
| | - Lok Man Yuen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Department of Biology, ETH Zürich, Universitätsstrasse 16, Zürich, 8092, Switzerland
| | - Bruno Augusto Maciel Guedes
- Departamento de Ciências Básicas da Vida, Universidade Federal de Juiz de Fora, Campus Governador Valadares, Governador Valadares, MG, 35020-360, Brazil
| | - Marta Contreras-Serrano
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Pedro Elias Marques
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Jonathan Zvi Shik
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
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12
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Gonçalves-Dias J, Singh A, Graf C, Stetter MG. Genetic Incompatibilities and Evolutionary Rescue by Wild Relatives Shaped Grain Amaranth Domestication. Mol Biol Evol 2023; 40:msad177. [PMID: 37552934 PMCID: PMC10439364 DOI: 10.1093/molbev/msad177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/20/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023] Open
Abstract
Crop domestication and the subsequent expansion of crops have long been thought of as a linear process from a wild ancestor to a domesticate. However, evidence of gene flow from locally adapted wild relatives that provided adaptive alleles into crops has been identified in multiple species. Yet, little is known about the evolutionary consequences of gene flow during domestication and the interaction of gene flow and genetic load in crop populations. We study the pseudo-cereal grain amaranth that has been domesticated three times in different geographic regions of the Americas. We quantify the amount and distribution of gene flow and genetic load along the genome of the three grain amaranth species and their two wild relatives. Our results show ample gene flow between crop species and between crops and their wild relatives. Gene flow from wild relatives decreased genetic load in the three crop species. This suggests that wild relatives could provide evolutionary rescue by replacing deleterious alleles in crops. We assess experimental hybrids between the three crop species and found genetic incompatibilities between one Central American grain amaranth and the other two crop species. These incompatibilities might have created recent reproductive barriers and maintained species integrity today. Together, our results show that gene flow played an important role in the domestication and expansion of grain amaranth, despite genetic species barriers. The domestication of plants was likely not linear and created a genomic mosaic by multiple contributors with varying fitness effects for today's crops.
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Affiliation(s)
| | - Akanksha Singh
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Corbinian Graf
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Markus G Stetter
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
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13
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Clark FE, Greggor AL, Montgomery SH, Plotnik JM. The endangered brain: actively preserving ex-situ animal behaviour and cognition will benefit in-situ conservation. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230707. [PMID: 37650055 PMCID: PMC10465207 DOI: 10.1098/rsos.230707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023]
Abstract
Endangered species have small, unsustainable population sizes that are geographically or genetically restricted. Ex-situ conservation programmes are therefore faced with the challenge of breeding sufficiently sized, genetically diverse populations earmarked for reintroduction that have the behavioural skills to survive and breed in the wild. Yet, maintaining historically beneficial behaviours may be insufficient, as research continues to suggest that certain cognitive-behavioural skills and flexibility are necessary to cope with human-induced rapid environmental change (HIREC). This paper begins by reviewing interdisciplinary studies on the 'captivity effect' in laboratory, farmed, domesticated and feral vertebrates and finds that captivity imposes rapid yet often reversible changes to the brain, cognition and behaviour. However, research on this effect in ex-situ conservation sites is lacking. This paper reveals an apparent mismatch between ex-situ enrichment aims and the cognitive-behavioural skills possessed by animals currently coping with HIREC. After synthesizing literature across neuroscience, behavioural biology, comparative cognition and field conservation, it seems that ex-situ endangered species deemed for reintroduction may have better chances of coping with HIREC if their natural cognition and behavioural repertoires are actively preserved. Evaluating the effects of environmental challenges rather than captivity per se is recommended, in addition to using targeted cognitive enrichment.
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Affiliation(s)
- Fay E. Clark
- School of Psychological Science, University of Bristol, Bristol, UK
| | | | | | - Joshua M. Plotnik
- Department of Psychology, Hunter College, City University of New York, New York, NY, USA
- Department of Psychology, The Graduate Center, City University of New York, New York, NY, USA
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14
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Dwivedi SL, Chapman MA, Abberton MT, Akpojotor UL, Ortiz R. Exploiting genetic and genomic resources to enhance productivity and abiotic stress adaptation of underutilized pulses. Front Genet 2023; 14:1193780. [PMID: 37396035 PMCID: PMC10311922 DOI: 10.3389/fgene.2023.1193780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/07/2023] [Indexed: 07/04/2023] Open
Abstract
Underutilized pulses and their wild relatives are typically stress tolerant and their seeds are packed with protein, fibers, minerals, vitamins, and phytochemicals. The consumption of such nutritionally dense legumes together with cereal-based food may promote global food and nutritional security. However, such species are deficient in a few or several desirable domestication traits thereby reducing their agronomic value, requiring further genetic enhancement for developing productive, nutritionally dense, and climate resilient cultivars. This review article considers 13 underutilized pulses and focuses on their germplasm holdings, diversity, crop-wild-crop gene flow, genome sequencing, syntenic relationships, the potential for breeding and transgenic manipulation, and the genetics of agronomic and stress tolerance traits. Recent progress has shown the potential for crop improvement and food security, for example, the genetic basis of stem determinacy and fragrance in moth bean and rice bean, multiple abiotic stress tolerant traits in horse gram and tepary bean, bruchid resistance in lima bean, low neurotoxin in grass pea, and photoperiod induced flowering and anthocyanin accumulation in adzuki bean have been investigated. Advances in introgression breeding to develop elite genetic stocks of grass pea with low β-ODAP (neurotoxin compound), resistance to Mungbean yellow mosaic India virus in black gram using rice bean, and abiotic stress adaptation in common bean, using genes from tepary bean have been carried out. This highlights their potential in wider breeding programs to introduce such traits in locally adapted cultivars. The potential of de-domestication or feralization in the evolution of new variants in these crops are also highlighted.
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Affiliation(s)
| | - Mark A. Chapman
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | | | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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15
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Silva-Ortega M, Muñoz-Pacheco CB, Villaseñor NR. Abundance of Non-Native Birds in the City: Spatial Variation and Relationship with Socioeconomics in a South American City. Animals (Basel) 2023; 13:1737. [PMID: 37889681 PMCID: PMC10252067 DOI: 10.3390/ani13111737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/12/2023] [Accepted: 05/17/2023] [Indexed: 10/29/2023] Open
Abstract
Cities commonly support a high abundance of non-native species that can affect both wildlife and human health; however, their distribution across the urban environment and their relationship with socioeconomics are not well documented. Here, we map the abundance of three non-native birds in a Latin American city-domestic pigeon (Columba livia f. domestica), house sparrow (Passer domesticus), and monk parakeet (Myiopsitta monachus)-and investigate the effect of socioeconomics on their abundance. We found that C. livia f. domestica exhibited a random distribution of abundance across the city but reached its greatest abundance in low-income areas. P. domesticus exhibited an aggregated distribution of abundance, being most abundant in the southern and western areas of the city and in low-income areas. M. monachus exhibited an aggregated distribution of abundance, being most abundant in the northeastern part of the city and reaching its greatest abundance in high-income areas. Low-income areas likely provide high abundance of food, shelter, and nesting sites for both C. livia f. domestica and P. domesticus, whereas high income areas have greater tree cover and larger trees in which M. monachus can build communal nests. Our study finds that the abundance of non-native birds varies across the city and between socioeconomic groups; therefore, targeted management is needed in different city zones to limit negative effects on native species and prevent zoonotic diseases.
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Affiliation(s)
- Macarena Silva-Ortega
- Grupo de Ecología, Naturaleza y Sociedad (GENS), Departamento de Gestión Forestal y su Medio Ambiente, Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Santiago 8820808, Chile (C.B.M.-P.)
| | - Catalina B. Muñoz-Pacheco
- Grupo de Ecología, Naturaleza y Sociedad (GENS), Departamento de Gestión Forestal y su Medio Ambiente, Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Santiago 8820808, Chile (C.B.M.-P.)
- Escuela de Arquitectura del Paisaje, Universidad Central de Chile, Av. Toesca 1783, Santiago 8370292, Chile
| | - Nélida R. Villaseñor
- Grupo de Ecología, Naturaleza y Sociedad (GENS), Departamento de Gestión Forestal y su Medio Ambiente, Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Santiago 8820808, Chile (C.B.M.-P.)
- Departamento de Ciencias Químicas y Biológicas, Universidad Bernardo O’Higgins, Av. Viel 1497, Santiago 8370993, Chile
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16
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Population structure and hybridisation in a population of Hawaiian feral chickens. Heredity (Edinb) 2023; 130:154-162. [PMID: 36725960 PMCID: PMC9981564 DOI: 10.1038/s41437-022-00589-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 02/03/2023] Open
Abstract
Chickens are believed to have inhabited the Hawaiian island of Kauai since the first human migrations around 1200AD, but numbers have peaked since the tropical storms Iniki and Iwa in the 1980s and 1990s that destroyed almost all the chicken coops on the island and released large numbers of domestic chickens into the wild. Previous studies have shown these now feral chickens are an admixed population between Red Junglefowl (RJF) and domestic chickens. Here, using genetic haplotypic data, we estimate the time of the admixture event between the feral population on the island and the RJF to 1981 (1976-1995), coinciding with the timings of storm Iwa and Iniki. Analysis of genetic structure reveals a greater similarity between individuals inhabiting the northern and western part of the island to RJF than individuals from the eastern part of the island. These results point to the possibility of introgression events between feral chickens and the wild chickens in areas surrounding the Koke'e State Park and the Alaka'i plateau, posited as two of the major RJF reservoirs in the island. Furthermore, we have inferred haplotype blocks from pooled data to determine the most plausible source of the feral population. We identify a clear contribution from RJF and layer chickens of the White Leghorn (WL) breed. This work provides independent confirmation of the traditional hypothesis surrounding the origin of the feral populations and draws attention to the possibility of introgression of domestic alleles into the wild reservoir.
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17
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Going Wild in the City-Animal Feralization and Its Impacts on Biodiversity in Urban Environments. Animals (Basel) 2023; 13:ani13040747. [PMID: 36830533 PMCID: PMC9952258 DOI: 10.3390/ani13040747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Domestication describes a range of changes to wild species as they are increasingly brought under human selection and husbandry. Feralization is the process whereby a species leaves the human sphere and undergoes increasing natural selection in a wild context, which may or may not be geographically adjacent to where the originator wild species evolved prior to domestication. Distinguishing between domestic, feral, and wild species can be difficult, since some populations of so-called "wild species" are at least partly descended from domesticated "populations" (e.g., junglefowl, European wild sheep) and because transitions in both directions are gradual rather than abrupt. In urban settings, prior selection for coexistence with humans provides particular benefit for a domestic organism that undergoes feralization. One risk is that such taxa can become invasive not just at the site of release/escape but far away. As humanity becomes increasingly urban and pristine environments rapidly diminish, we believe that feralized populations also hold conservation value.
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Gameiro MBP, Quet M. Feral pharmaceuticalization-Biomedical uses of animal life in light of the global donkey hide trade. BIOSOCIETIES 2023; 18:1-28. [PMID: 36643825 PMCID: PMC9823251 DOI: 10.1057/s41292-022-00288-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2022] [Indexed: 01/09/2023]
Abstract
Medical and pharmaceutical uses of animal life have gone through vast changes in the past centuries. Although the commodification of animals and animal parts is by no means an invention of modernity, its procedures and practices have evolved in multiple ways across time. Most notably, the exploitation of non-human animal life has been increasingly segmented, industrialized, and globalized. The collateral expansion of scientific and market institutions has led to specific modes of rationalization of animal breeding, culture, and trade for pharmaceutical purposes. However, this rationalization process has never been immune to its own matter-and the materiality of non-human commodification processes irrigates seemingly ordered and layered practices. Based upon a study on the international trade of donkey hide, this paper offers a characterization of the current pharmaceutical uses of animal life through a series of epistemic and environmental tensions expressing frictions between the market's absorptive logic and non-human modes of existence. We describe this set of tensions as 'feral pharmaceuticalization' and contend that they offer new perspectives on the analysis of the contemporary pharmaceuticalization process. In addition, such tensions showcase the importance of investigating the expansion of technological markets not only as simultaneous knowledge and milieux (or bodies) making, or as simple science and market hegemonic processes, but also as the construction of new stages of conflict.
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Affiliation(s)
| | - Mathieu Quet
- Ceped, IRD, 45 Rue Des Saints-Pères, 75006 Paris, France
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Pisias MT, Bakala HS, McAlvay AC, Mabry ME, Birchler JA, Yang B, Pires JC. Prospects of Feral Crop De Novo Redomestication. PLANT & CELL PHYSIOLOGY 2022; 63:1641-1653. [PMID: 35639623 DOI: 10.1093/pcp/pcac072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/13/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Modern agriculture depends on a narrow variety of crop species, leaving global food and nutritional security highly vulnerable to the adverse effects of climate change and population expansion. Crop improvement using conventional and molecular breeding approaches leveraging plant genetic diversity using crop wild relatives (CWRs) has been one approach to address these issues. However, the rapid pace of the global change requires additional innovative solutions to adapt agriculture to meet global needs. Neodomestication-the rapid and targeted introduction of domestication traits using introgression or genome editing of CWRs-is being explored as a supplementary approach. These methods show promise; however, they have so far been limited in efficiency and applicability. We propose expanding the scope of neodomestication beyond truly wild CWRs to include feral crops as a source of genetic diversity for novel crop development, in this case 'redomestication'. Feral crops are plants that have escaped cultivation and evolved independently, typically adapting to their local environments. Thus, feral crops potentially contain valuable adaptive features while retaining some domestication traits. Due to their genetic proximity to crop species, feral crops may be easier targets for de novo domestication (i.e. neodomestication via genome editing techniques). In this review, we explore the potential of de novo redomestication as an application for novel crop development by genome editing of feral crops. This approach to efficiently exploit plant genetic diversity would access an underutilized reservoir of genetic diversity that could prove important in support of global food insecurity in the face of the climate change.
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Affiliation(s)
- Michael T Pisias
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
| | - Harmeet Singh Bakala
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
| | - Alex C McAlvay
- Institute of Economic Botany, New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - Makenzie E Mabry
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Tucker Hall, Columbia, MO 65211, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
- Donald Danforth Plant Science Center, 975 N Warson Road, St. Louis, MO 63132, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Tucker Hall, Columbia, MO 65211, USA
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20
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Ma J, Wei H, Yu X, Lv Y, Zhang Y, Qian Q, Shang L, Guo L. Compared analysis with a high-quality genome of weedy rice reveals the evolutionary game of de-domestication. FRONTIERS IN PLANT SCIENCE 2022; 13:1065449. [PMID: 36466225 PMCID: PMC9716140 DOI: 10.3389/fpls.2022.1065449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
The weedy rice (Oryza sativa f. spontanea) harbors large numbers of excellent traits and genetic diversities, which serves as a valuable germplasm resource and has been considered as a typical material for research about de-domestication. However, there are relatively few reference genomes on weedy rice that severely limit exploiting these genetic resources and revealing more details about de-domestication events. In this study, a high-quality genome (~376.4 Mb) of weedy rice A02 was assembled based on Nanopore ultra-long platform with a coverage depth of about 79.3× and 35,423 genes were predicted. Compared to Nipponbare genome, 5,574 structural variations (SVs) were found in A02. Based on super pan-genome graph, population SVs of 238 weedy rice and cultivated rice accessions were identified using public resequencing data. Furthermore, the de-domestication sites of weedy rice and domestication sites of wild rice were analyzed and compared based on SVs and single-nucleotide polymorphisms (SNPs). Interestingly, an average of 2,198 genes about de-domestication could only be found by F ST analysis based on SVs (SV-F ST) while not by F ST analysis based on SNPs (SNP-F ST) in divergent region. Additionally, there was a low overlap between domestication and de-domestication intervals, which demonstrated that two different mechanisms existed in these events. Our finding could facilitate pinpointing of the evolutionary events that had shaped the genomic architecture of wild, cultivated, and weedy rice, and provide a good foundation for cloning of the superior alleles for breeding.
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Affiliation(s)
- Jie Ma
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Hua Wei
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Xiaoman Yu
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Yang Lv
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Yu Zhang
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Qian Qian
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Longbiao Guo
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
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21
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Boltovskoy D, Guiaşu R, Burlakova L, Karatayev A, Schlaepfer MA, Correa N. Misleading estimates of economic impacts of biological invasions: Including the costs but not the benefits. AMBIO 2022; 51:1786-1799. [PMID: 35191001 PMCID: PMC9200917 DOI: 10.1007/s13280-022-01707-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 06/02/2023]
Abstract
The economic costs of non-indigenous species (NIS) are a key factor for the allocation of efforts and resources to eradicate or control baneful invasions. Their assessments are challenging, but most suffer from major flaws. Among the most important are the following: (1) the inclusion of actual damage costs together with various ancillary expenditures which may or may not be indicative of the real economic damage due to NIS; (2) the inclusion of the costs of unnecessary or counterproductive control initiatives; (3) the inclusion of controversial NIS-related costs whose economic impacts are questionable; (4) the assessment of the negative impacts only, ignoring the positive ones that most NIS have on the economy, either directly or through their ecosystem services. Such estimates necessarily arrive at negative and often highly inflated values, do not reflect the net damage and economic losses due to NIS, and can significantly misguide management and resource allocation decisions. We recommend an approach based on holistic costs and benefits that are assessed using likely scenarios and their counter-factual.
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Affiliation(s)
- Demetrio Boltovskoy
- IEGEBA, Instituto de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales - Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón 2, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Radu Guiaşu
- Biology Program, Glendon College, York University, 2275 Bayview Avenue, Toronto, ON M4N 3M6 Canada
| | - Lyubov Burlakova
- Great Lakes Center, SUNY Buffalo State, 1300 Elmwood Ave., Buffalo, NY 14222 USA
| | - Alexander Karatayev
- Great Lakes Center, SUNY Buffalo State, 1300 Elmwood Ave., Buffalo, NY 14222 USA
| | - Martin A. Schlaepfer
- Institute of Environmental Sciences, University of Geneva, Boulevard Carl-Vogt 66, 1205 Geneva, Switzerland
| | - Nancy Correa
- Servicio de Hidrografía Naval y Escuela de Ciencias del Mar, Sede Educativa Universitaria, Facultad de la Armada, UNDEF, Av. Montes de Oca 2124, 1271 Buenos Aires, Argentina
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22
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Beckman AK, Richey BMS, Rosenthal GG. Behavioral responses of wild animals to anthropogenic change: insights from domestication. Behav Ecol Sociobiol 2022. [DOI: 10.1007/s00265-022-03205-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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23
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Abstract
The recent and ever-growing problem of boar (Sus scrofa forms including wild boar, hybrid and feral pig) expansion is a very complex issue in wildlife management. The damages caused to biodiversity and the economies are addressed in different ways by the various countries, but research is needed to shed light on the causal factors of this emergency before defining a useful collaborative management policy. In this review, we screened more than 280 references published between 1975–2022, identifying and dealing with five hot factors (climate change, human induced habitat modifications, predator regulation on the prey, hybridization with domestic forms, and transfaunation) that could account for the boar expansion and its niche invasion. We also discuss some issues arising from this boar emergency, such as epizootic and zoonotic diseases or the depression of biodiversity. Finally, we provide new insights for the research and the development of management policies.
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24
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Smith WJ, Quilodrán CS, Jezierski MT, Sendell-Price AT, Clegg SM. The wild ancestors of domestic animals as a neglected and threatened component of biodiversity. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13867. [PMID: 34811819 DOI: 10.1111/cobi.13867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/27/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
Domestic animals have immense economic, cultural, and practical value and have played pivotal roles in the development of human civilization. Many domesticates have, among their wild relatives, undomesticated forms representative of their ancestors. Resurgent interest in these ancestral forms has highlighted the unclear genetic status of many, and some are threatened with extinction by hybridization with domestic conspecifics. We considered the contemporary status of these ancestral forms relative to their scientific, practical, and ecological importance; the varied impacts of wild-domestic hybridization; and the challenges and potential resolutions involved in conservation efforts. Identifying and conserving ancestral forms, particularly with respect to disentangling patterns of gene flow from domesticates, is complex because of the lack of available genomic and phenotypic baselines. Comparative behavioral, ecological, and genetic studies of ancestral-type, feral, and domestic animals should be prioritized to establish the contemporary status of the former. Such baseline information will be fundamental in ensuring successful conservation efforts.
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Affiliation(s)
- William J Smith
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
| | - Claudio S Quilodrán
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
- Department of Biology and Biochemistry, University of Fribourg, Fribourg, Switzerland
| | - Michał T Jezierski
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
| | - Ashley T Sendell-Price
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Sonya M Clegg
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
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25
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Childebayeva A, Rohrlach AB, Barquera R, Rivollat M, Aron F, Szolek A, Kohlbacher O, Nicklisch N, Alt KW, Gronenborn D, Meller H, Friederich S, Prüfer K, Deguilloux MF, Krause J, Haak W. Population Genetics and Signatures of Selection in Early Neolithic European Farmers. Mol Biol Evol 2022; 39:6586604. [PMID: 35578825 PMCID: PMC9171004 DOI: 10.1093/molbev/msac108] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Human expansion in the course of the Neolithic transition in western Eurasia has been one of the major topics in ancient DNA research in the last 10 years. Multiple studies have shown that the spread of agriculture and animal husbandry from the Near East across Europe was accompanied by large-scale human expansions. Moreover, changes in subsistence and migration associated with the Neolithic transition have been hypothesized to involve genetic adaptation. Here, we present high quality genome-wide data from the Linear Pottery Culture site Derenburg-Meerenstieg II (DER) (N = 32 individuals) in Central Germany. Population genetic analyses show that the DER individuals carried predominantly Anatolian Neolithic-like ancestry and a very limited degree of local hunter-gatherer admixture, similar to other early European farmers. Increasing the Linear Pottery culture cohort size to ∼100 individuals allowed us to perform various frequency- and haplotype-based analyses to investigate signatures of selection associated with changes following the adoption of the Neolithic lifestyle. In addition, we developed a new method called Admixture-informed Maximum-likelihood Estimation for Selection Scans that allowed us test for selection signatures in an admixture-aware fashion. Focusing on the intersection of results from these selection scans, we identified various loci associated with immune function (JAK1, HLA-DQB1) and metabolism (LMF1, LEPR, SORBS1), as well as skin color (SLC24A5, CD82) and folate synthesis (MTHFR, NBPF3). Our findings shed light on the evolutionary pressures, such as infectious disease and changing diet, that were faced by the early farmers of Western Eurasia.
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Affiliation(s)
- Ainash Childebayeva
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Adam Benjamin Rohrlach
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, The University of Adelaide, Adelaide, Australia
| | - Rodrigo Barquera
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Maïté Rivollat
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Université de Bordeaux, CNRS, PACEA-UMR 5199, 33615 Pessac, France
| | - Franziska Aron
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany
| | - András Szolek
- Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Tübingen, Germany.,Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Tübingen, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.,Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Nicole Nicklisch
- Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria.,State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany
| | - Kurt W Alt
- Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria.,State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany
| | - Detlef Gronenborn
- Römisch-Germanisches Zentralmuseum, Leibniz Research Institute for Archaeology, Ernst-Ludwig-Platz 2, 55116 Mainz, Germany
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany
| | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany
| | - Kay Prüfer
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | | | - Johannes Krause
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Wolfgang Haak
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
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26
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Purugganan MD. What is domestication? Trends Ecol Evol 2022; 37:663-671. [PMID: 35534288 DOI: 10.1016/j.tree.2022.04.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/12/2022] [Accepted: 04/11/2022] [Indexed: 01/06/2023]
Abstract
The nature of domestication is often misunderstood. Most definitions of the process are anthropocentric and center on human intentionality, which minimizes the role of unconscious selection and also excludes non-human domesticators. An overarching, biologically grounded definition of domestication is discussed, which emphasizes its core nature as a coevolutionary process that arises from a specialized mutualism, in which one species controls the fitness of another in order to gain resources and/or services. This inclusive definition encompasses both human-associated domestication of crop plants and livestock as well as other non-human domesticators, such as insects. It also calls into question the idea that humans are themselves domesticated, given that evolution of human traits did not arise through the control of fitness by another species.
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Affiliation(s)
- Michael D Purugganan
- Center for Genomics and Systems Biology, New York University, New York, NY 10011, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates; Institute for the Study of the Ancient World, New York University, New York, NY 10028, USA.
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27
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Molecular Evidence Reveals the Sympatric Distribution of Cervus nippon yakushimae and Cervus nippon taiouanus on Jeju Island, South Korea. Animals (Basel) 2022; 12:ani12080998. [PMID: 35454244 PMCID: PMC9029077 DOI: 10.3390/ani12080998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/09/2022] [Accepted: 04/10/2022] [Indexed: 11/17/2022] Open
Abstract
Non-native species threaten native ecosystems and species, particularly on islands where rates of endemism and vulnerability to threats are high. Understanding species invasion will aid in providing insights into ecological and evolutionary processes. To identify the non-native sika deer (Cervus nippon) population in Jeju, South Korea, and their phylogenetic affinities, we collected tissue samples from roadkill and the World Natural Heritage Headquarters in Jeju. Mitochondrial DNA cytochrome B (CytB) gene sequences were analyzed to determine two distinct CytB haplotypes. Phylogenetic analysis using maximum likelihood tree revealed two haplotypes of CytB clustered into two different groups representing two subspecies: C. n. yakushimae, native to Japan, and C. n. taiouanus, native to Taiwan. The tentative divergence time between the two subspecies was estimated at 1.81 million years. Our study confirmed that the two subspecies of sika deer are sympatric in the natural ecosystem of Jeju Island. This study provides valuable information to help government and conservation agencies understand alien species and determine control policies for conserving native biodiversity in South Korea.
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28
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Islam SS, Xue X, Caballero-Solares A, Bradbury IR, Rise ML, Fleming IA. Distinct early life stage gene expression effects of hybridization among European and North American farmed and wild Atlantic salmon populations. Mol Ecol 2022; 31:2712-2729. [PMID: 35243721 DOI: 10.1111/mec.16418] [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: 09/20/2021] [Revised: 01/29/2022] [Accepted: 02/21/2022] [Indexed: 11/27/2022]
Abstract
Due to multi-generation domestication selection, farmed and wild Atlantic salmon diverge genetically, which raises concerns about potential genetic interactions among escaped farmed and wild populations and disruption of local adaptation through introgression. When farmed strains of distant geographic origin are used, it is unknown whether the genetic consequences posed by escaped farmed fish will be greater than if more locally derived strains are used. Quantifying gene transcript expression differences among divergent farmed, wild and F1 hybrids under controlled conditions is one of the ways to explore the consequences of hybridization. We compared the transcriptomes of fry at the end of yolk sac absorption of a European (EO) farmed ("StofnFiskur", Norwegian strain), a North American (NA) farmed (Saint John River, NB strain), a Newfoundland (NF) wild population with EO ancestry, and related F1 hybrids using 44K microarrays. Our findings indicate that the wild population showed greater transcriptome differences from the EO farmed strain than that of the NA farmed strain. We also found the largest differences in global gene expression between the two farmed strains. We detected the fewest differentially expressed transcripts between F1 hybrids and domesticated/wild maternal strains. We also found that the differentially expressed genes between cross types over-represented GO terms associated with metabolism, development, growth, immune response, and redox homeostasis processes. These findings suggest that the interbreeding of escaped EO/NA farmed and NF wild population would alter gene transcription, and the consequences of hybridization would be greater from escaped EO farmed than NA farmed salmon, resulting in potential effects on the wild populations.
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Affiliation(s)
- Shahinur S Islam
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Xi Xue
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Albert Caballero-Solares
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Ian R Bradbury
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada.,Salmonids Section, Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 East White Hills Road, St. John's, NL, A1C 5X, Canada
| | - Matthew L Rise
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Ian A Fleming
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
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29
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Panzeri D, Guidi Nissim W, Labra M, Grassi F. Revisiting the Domestication Process of African Vigna Species (Fabaceae): Background, Perspectives and Challenges. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040532. [PMID: 35214865 PMCID: PMC8879845 DOI: 10.3390/plants11040532] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/12/2022] [Accepted: 02/13/2022] [Indexed: 05/14/2023]
Abstract
Legumes are one of the most economically important and biodiverse families in plants recognised as the basis to develop functional foods. Among these, the Vigna genus stands out as a good representative because of its relatively recent African origin as well as its outstanding potential. Africa is a great biodiversity centre in which a great number of species are spread, but only three of them, Vigna unguiculata, Vigna subterranea and Vigna vexillata, were successfully domesticated. This review aims at analysing and valorising these species by considering the perspective of human activity and what effects it exerts. For each species, we revised the origin history and gave a focus on where, when and how many times domestication occurred. We provided a brief summary of bioactive compounds naturally occurring in these species that are fundamental for human wellbeing. The great number of wild lineages is a key point to improve landraces since the domestication process caused a loss of gene diversity. Their genomes hide a precious gene pool yet mostly unexplored, and genes lost during human activity can be recovered from the wild lineages and reintroduced in cultivated forms through modern technologies. Finally, we describe how all this information is game-changing to the design of future crops by domesticating de novo.
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Affiliation(s)
- Davide Panzeri
- Department of Biotechnology and Bioscience, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (W.G.N.); (M.L.)
- Correspondence: (D.P.); (F.G.)
| | - Werther Guidi Nissim
- Department of Biotechnology and Bioscience, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (W.G.N.); (M.L.)
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Viale delle Idee 30, 50019 Sesto Fiorentino, Italy
| | - Massimo Labra
- Department of Biotechnology and Bioscience, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (W.G.N.); (M.L.)
| | - Fabrizio Grassi
- Department of Biotechnology and Bioscience, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (W.G.N.); (M.L.)
- Correspondence: (D.P.); (F.G.)
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30
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The Social Lives of Free-Ranging Cats. Animals (Basel) 2022; 12:ani12010126. [PMID: 35011232 PMCID: PMC8749887 DOI: 10.3390/ani12010126] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/13/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022] Open
Abstract
Despite the diversity of social situations in which cats live, the degree to which free-ranging cats (FRCs) are social is still debated. The aim of this review is to explore the literature on the social behavior of FRCs. A search of two major databases revealed that observations of intraspecies and interspecies social interactions have been conducted. The intraspecific social dynamics of FRCs differ based on group of cats surveyed. Some groups display strong social bonds and preferential affiliations, while other groups are more loosely associated and display little to no social interaction. Factors impacting FRC conspecific interactions include cat body size, cat social rank, cat individuality, cat age, relationship to conspecific (kin/familiar), cat sex, level of human caretaking, presence of food, the health of the individual, or sexual status of conspecifics. Interspecies interactions also occur with humans and wildlife. The human’s sex and the weather conditions on the day of interaction have been shown to impact FRC social behavior. Interactions with wildlife were strongly linked to the timing of cat feeding events. These findings support the idea that FRCs are “social generalists” who display flexibility in their social behavior. The social lives of FRCs exist, are complex, and deserve further study.
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31
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Niego A, Benítez-Burraco A. Are feralization and domestication truly mirror processes? ETHOL ECOL EVOL 2021. [DOI: 10.1080/03949370.2021.1975314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Amy Niego
- PhD Program, Faculty of Philology, University of Seville, C/Palos de la Frontera s/n, 41004 Sevilla, Spain
| | - Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, C/Palos de la Frontera s/n, 41004 Sevilla, Spain (E-mail: )
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32
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Petrelli S, Buglione M, Maselli V, Troiano C, Larson G, Frantz L, Manin A, Ricca E, Baccigalupi L, Wright D, Pietri C, Fulgione D. Population genomic, olfactory, dietary, and gut microbiota analyses demonstrate the unique evolutionary trajectory of feral pigs. Mol Ecol 2021; 31:220-237. [PMID: 34676935 DOI: 10.1111/mec.16238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 08/31/2021] [Accepted: 10/12/2021] [Indexed: 10/20/2022]
Abstract
Domestication is an intriguing evolutionary process. Many domestic populations are subjected to strong human-mediated selection, and when some individuals return to the wild, they are again subjected to selective forces associated with new environments. Generally, these feral populations evolve into something different from their wild predecessors and their members typically possess a combination of both wild and human selected traits. Feralisation can manifest in different forms on a spectrum from a wild to a domestic phenotype. This depends on how the rewilded domesticated populations can readapt to natural environments based on how much potential and flexibility the ancestral genome retains after its domestication signature. Whether feralisation leads to the evolution of new traits that do not exist in the wild or to convergence with wild forms, however, remains unclear. To address this question, we performed population genomic, olfactory, dietary, and gut microbiota analyses on different populations of Sus scrofa (wild boar, hybrid, feral and several domestic pig breeds). Porcine single nucleotide polymorphisms (SNPs) analysis shows that the feral population represents a cluster distinctly separate from all others. Its members display signatures of past artificial selection, as demonstrated by values of FST in specific regions of the genome and bottleneck signature, such as the number and length of runs of homozygosity. Generalised FST values, reacquired olfactory abilities, diet, and gut microbiota variation show current responses to natural selection. Our results suggest that feral pigs are an independent evolutionary unit which can persist so long as levels of human intervention remain unchanged.
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Affiliation(s)
- Simona Petrelli
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Maria Buglione
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Valeria Maselli
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Claudia Troiano
- Department of Humanities, University of Naples Federico II, Naples, Italy
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Laurent Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Aurelie Manin
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Ezio Ricca
- Department of Biology, University of Naples Federico II, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Napoli, Italy
| | - Loredana Baccigalupi
- Task Force on Microbiome Studies, University of Naples Federico II, Napoli, Italy.,Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Dominic Wright
- IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Christian Pietri
- Fédération Départementale des Chasseurs de Haute-Corse (FDCHC), Résidence Nouvelle-Corniche, St Joseph, Bastia, France
| | - Domenico Fulgione
- Department of Biology, University of Naples Federico II, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Napoli, Italy
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33
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Racicot KJ, Popic C, Cunha F, Wright D, Henriksen R, Iwaniuk AN. The cerebellar anatomy of red junglefowl and white leghorn chickens: insights into the effects of domestication on the cerebellum. ROYAL SOCIETY OPEN SCIENCE 2021; 8:211002. [PMID: 34659779 PMCID: PMC8511745 DOI: 10.1098/rsos.211002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/17/2021] [Indexed: 05/07/2023]
Abstract
Domestication is the process by which wild organisms become adapted for human use. Many phenotypic changes are associated with animal domestication, including decreases in brain and brain region sizes. In contrast with this general pattern, the chicken has a larger cerebellum compared with the wild red junglefowl, but what neuroanatomical changes are responsible for this difference have yet to be investigated. Here, we quantified cell layer volumes, neuron numbers and neuron sizes in the cerebella of chickens and junglefowl. Chickens have larger, more folded cerebella with more and larger granule cells than junglefowl, but neuron numbers and cerebellar folding were proportional to cerebellum size. However, chickens do have relatively larger granule cell layer volumes and relatively larger granule cells than junglefowl. Thus, the chicken cerebellum can be considered a scaled-up version of the junglefowl cerebellum, but with enlarged granule cells. The combination of scaling neuron number and disproportionate enlargement of cell bodies partially supports a recent theory that domestication does not affect neuronal density within brain regions. Whether the neuroanatomical changes we observed are typical of domestication or not requires similar quantitative analyses in other domesticated species and across multiple brain regions.
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Affiliation(s)
- Kelsey J. Racicot
- Department of Neuroscience, University of Lethbridge, Lethbridge, Alberta, Canada T1K3M4
| | - Christina Popic
- Department of Neuroscience, University of Lethbridge, Lethbridge, Alberta, Canada T1K3M4
| | - Felipe Cunha
- Department of Neuroscience, University of Lethbridge, Lethbridge, Alberta, Canada T1K3M4
| | - Dominic Wright
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping 58183, Sweden
| | - Rie Henriksen
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping 58183, Sweden
| | - Andrew N. Iwaniuk
- Department of Neuroscience, University of Lethbridge, Lethbridge, Alberta, Canada T1K3M4
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34
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Li C, Liu M, Sun F, Zhao X, He M, Li T, Lu P, Xu Y. Genetic Divergence and Population Structure in Weedy and Cultivated Broomcorn Millets ( Panicum miliaceum L.) Revealed by Specific-Locus Amplified Fragment Sequencing (SLAF-Seq). FRONTIERS IN PLANT SCIENCE 2021; 12:688444. [PMID: 34249058 PMCID: PMC8264369 DOI: 10.3389/fpls.2021.688444] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/31/2021] [Indexed: 06/07/2023]
Abstract
Broomcorn millet (Panicum miliaceum L.) is one of the earliest domesticated crops in the world. Weedy broomcorn millet [Panicum ruderale (Kitag.) Chang or Panicum miliaceum subsp. ruderale (Kitag.) Tzvel] is thought to be the descendant of the wild ancestor or the feral type of this cereal. The genealogical relationships and genetic divergence among these taxa have not been clarified. In this study, the genetic diversity and population structure of weedy and cultivated broomcorn millets were investigated by using the high-throughput sequencing technology, i.e., the specific-locus amplified fragment sequencing (SLAF-seq). Our analyses consistently revealed both the wild and the feral genotypes in the weedy broomcorn millets. The single nucleotide polymorphisms (SNPs) at the genomic level provided useful evidence to distinguish the wild and the endoferal/exoferal types of weedy broomcorn millets. The genetic divergence revealed between the cultivated broomcorn millet from eastern Eurasia and those from central-western Eurasia was probably derived from either the genetic introgression from weedy broomcorn millets along the spread routes or the founder effect, while the limited gene flow of broomcorn millets from eastern and central-western Eurasia was probably due to the different uses of broomcorn millets and eating habits of the local people.
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Affiliation(s)
- Chunxiang Li
- School of Life Sciences, Jilin University, Changchun, China
- Key Laboratory for Evolution of Past Life and Environment in Northeast Asia, Ministry of Education, Jilin University, Changchun, China
| | - Minxuan Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Fengjie Sun
- School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA, United States
| | - Xinyu Zhao
- School of Life Sciences, Jilin University, Changchun, China
| | - Mingyue He
- School of Life Sciences, Jilin University, Changchun, China
| | - Tianshu Li
- School of Life Sciences, Jilin University, Changchun, China
| | - Ping Lu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yue Xu
- School of Life Sciences, Jilin University, Changchun, China
- Key Laboratory for Evolution of Past Life and Environment in Northeast Asia, Ministry of Education, Jilin University, Changchun, China
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35
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Mabry ME, Turner-Hissong SD, Gallagher EY, McAlvay AC, An H, Edger PP, Moore JD, Pink DAC, Teakle GR, Stevens CJ, Barker G, Labate J, Fuller DQ, Allaby RG, Beissinger T, Decker JE, Gore MA, Pires JC. The Evolutionary History of Wild, Domesticated, and Feral Brassica Oleracea (Brassicaceae). Mol Biol Evol 2021; 38:4419-4434. [PMID: 34157722 PMCID: PMC8476135 DOI: 10.1093/molbev/msab183] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for conservation and crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the evolutionary history of this species remains understudied. With such different vegetables produced from a single species, B. oleracea is a model organism for understanding the power of artificial selection. Persistent challenges in the study of B. oleracea include conflicting hypotheses regarding domestication and the identity of the closest living wild relative. Using newly generated RNA-seq data for a diversity panel of 224 accessions, which represents 14 different B. oleracea crop types and nine potential wild progenitor species, we integrate phylogenetic and population genetic techniques with ecological niche modeling, archaeological, and literary evidence to examine relationships among cultivars and wild relatives to clarify the origin of this horticulturally important species. Our analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region. Additionally, we identify several feral lineages, suggesting that cultivated plants of this species can revert to a wild-like state with relative ease. By expanding our understanding of the evolutionary history in B. oleracea, these results contribute to a growing body of knowledge on crop domestication that will facilitate continued breeding efforts including adaptation to changing environmental conditions.
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Affiliation(s)
- Makenzie E Mabry
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, U.S.A
| | | | - Evan Y Gallagher
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, U.S.A
| | - Alex C McAlvay
- Institute of Economic Botany, The New York Botanical Garden, Bronx, NY, U.S.A
| | - Hong An
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, U.S.A
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, MI, USA
| | | | - David A C Pink
- Agriculture and Environment Department, Harper Adams University, UK
| | | | - Chris J Stevens
- School of Archaeology and Museology, Peking University, Beijing, China.,Institute of Archaeology, University College London, London, UK
| | - Guy Barker
- School of Life Science, University of Warwick, UK
| | - Joanne Labate
- USDA, ARS Plant Genetic Resources Unit, Cornell AgriTech, Geneva, NY, USA
| | - Dorian Q Fuller
- Institute of Archaeology, University College London, London, UK.,School of Cultural Heritage, Northwest University, Xi'an, Shaanxi, China.,Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | | | - Timothy Beissinger
- Division of Plant Breeding Methodology, Department of Crop Sciences, University of Goettingen, Goettingen, Germany
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - J Chris Pires
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, U.S.A
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36
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Zhou C, Feng Y, Li G, Wang M, Jian J, Wang Y, Zhang W, Song Z, Li L, Lu B, Yang J. The New Is Old: Novel Germination Strategy Evolved From Standing Genetic Variation in Weedy Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:699464. [PMID: 34234803 PMCID: PMC8256273 DOI: 10.3389/fpls.2021.699464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/28/2021] [Indexed: 06/01/2023]
Abstract
Feralization of crop plants has aroused an increasing interest in recent years, not only for the reduced yield and quality of crop production caused by feral plants but also for the rapid evolution of novel traits that facilitate the evolution and persistence of weedy forms. Weedy rice (Oryza sativa f. spontanea) is a conspecific weed of cultivated rice, with separate and independent origins. The weedy rice distributed in eastern and northeastern China did not diverge from their cultivated ancestors by reverting to the pre-domestication trait of seed dormancy during feralization. Instead, they developed a temperature-sensing mechanism to control the timing of seed germination. Subsequent divergence in the minimum critical temperature for germination has been detected between northeastern and eastern populations. An integrative analysis was conducted using combinations of phenotypic, genomic and transcriptomic data to investigate the genetic mechanism underlying local adaptation and feralization. A dozen genes were identified, which showed extreme allele frequency differences between eastern and northeastern populations, and high correlations between allele-specific gene expression and feral phenotypes. Trancing the origin of potential adaptive alleles based on genomic sequences revealed the presence of most selected alleles in wild and cultivated rice genomes, indicating that weedy rice drew upon pre-existing, "conditionally neutral" alleles to respond to the feral selection regimes. The cryptic phenotype was exposed by activating formerly silent alleles to facilitate the transition from cultivation to wild existence, promoting the evolution and persistence of weedy forms.
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Affiliation(s)
- Chengchuan Zhou
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Yang Feng
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Gengyun Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Mengli Wang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Jinjing Jian
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Yuguo Wang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Wenju Zhang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Zhiping Song
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Linfeng Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Baorong Lu
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Ji Yang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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37
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Ren S, Lyu G, Irwin DM, Liu X, Feng C, Luo R, Zhang J, Sun Y, Shang S, Zhang S, Wang Z. Pooled Sequencing Analysis of Geese ( Anser cygnoides) Reveals Genomic Variations Associated With Feather Color. Front Genet 2021; 12:650013. [PMID: 34220935 PMCID: PMC8249929 DOI: 10.3389/fgene.2021.650013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/28/2021] [Indexed: 02/03/2023] Open
Abstract
During the domestication of the goose a change in its feather color took place, however, the molecular mechanisms responsible for this change are not completely understood. Here, we performed whole-genome resequencing on three pooled samples of geese (feral and domestic geese), with two distinct feather colors, to identify genes that might regulate feather color. We identified around 8 million SNPs within each of the three pools and validated allele frequencies for a subset of these SNPs using PCR and Sanger sequencing. Several genomic regions with signatures of differential selection were found when we compared the gray and white feather color populations using the FST and Hp approaches. When we combined previous functional studies with our genomic analyses we identified 26 genes (KITLG, MITF, TYRO3, KIT, AP3B1, SMARCA2, ROR2, CSNK1G3, CCDC112, VAMP7, SLC16A2, LOC106047519, RLIM, KIAA2022, ST8SIA4, LOC106044163, TRPM6, TICAM2, LOC106038556, LOC106038575, LOC106038574, LOC106038594, LOC106038573, LOC106038604, LOC106047489, and LOC106047492) that potentially regulate feather color in geese. These results substantially expand the catalog of potential feather color regulators in geese and provide a basis for further studies on domestication and avian feather coloration.
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Affiliation(s)
- Shuang Ren
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.,College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Guangqi Lyu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Xin Liu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chunyu Feng
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Runhong Luo
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Junpeng Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yongfeng Sun
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Songyang Shang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhe Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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38
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Scossa F, Fernie AR. When a Crop Goes Back to the Wild: Feralization. TRENDS IN PLANT SCIENCE 2021; 26:543-545. [PMID: 33674174 DOI: 10.1016/j.tplants.2021.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/01/2020] [Accepted: 02/01/2021] [Indexed: 05/27/2023]
Abstract
Feral plants have been known since the inception of modern agriculture, but the genetic changes during what seemed to be a simple reversion of a domesticated form are poorly understood. Recent studies, revealing the changes occurring in weedy rice, show an unexpected degree of differentiation in these feral escapes.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), 00178 Rome, Italy.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
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39
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Wu D, Lao S, Fan L. De-Domestication: An Extension of Crop Evolution. TRENDS IN PLANT SCIENCE 2021; 26:560-574. [PMID: 33648850 DOI: 10.1016/j.tplants.2021.02.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/24/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
De-domestication or feralization is an interesting phenomenon in crops and livestock. Previously, evidence for crop de-domestication was based mainly on studies using phenotypic and genotypic data from limited molecular markers or gene segments. Recent genomic studies in rice, barley, and wheat provide comprehensive landscapes of de-domestication on a whole-genome scale. Here, we summarize crop de-domestication processes, ecological roles of de-domesticates, mechanisms underlying crop de-domestication syndromes, and conditions potentially favoring de-domestication events. We further explain how recent de-domestication studies have expanded our understanding of the complexity of crop evolution, and highlight the genetic novelties of de-domesticates beneficial for modern crop breeding.
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Affiliation(s)
- Dongya Wu
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sangting Lao
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Longjiang Fan
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute of Zhejiang University, Yonyou Industrial Park, Sanya 572025, China.
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40
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Alavez V, Cuervo-Robayo ÁP, Martínez-Meyer E, Wegier A. Eco-Geography of Feral Cotton: A Missing Piece in the Puzzle of Gene Flow Dynamics Among Members of Gossypium hirsutum Primary Gene Pool. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.653271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mexico is the center of origin and genetic diversity of upland cotton (Gossypium hirsutum L.), the most important source of natural fiber in the world. Currently, wild and domesticated populations (including genetically modified [GM] varieties) occur in this country and gene flow among them has shaped the species’ genetic diversity and structure, setting a complex and challenging scenario for its conservation. Moreover, recent gene flow from GM cultivars to wild Mexican cotton populations has been reported since 2011. In situ conservation of G. hirsutum requires knowledge about the extent of its geographic distribution, both wild and domesticated, as well as the possible routes and mechanisms that contribute to gene flow between the members of the species wild-to-domesticated continuum (i.e., the primary gene pool). However, little is known about the distribution of feral populations that could facilitate gene flow by acting as bridges. In this study, we analyzed the potential distribution of feral cotton based on an ecological niche modeling approach and discussed its implications in the light of the distribution of wild and domesticated cotton. Then, we examined the processes that could be leading to the escape of seeds from the cultivated fields. Our results indicate that the climatic suitability of feral plants in the environmental and geographic space is broad and overlaps with areas of wild cotton habitat and crop fields, suggesting a region that could bridge cultivated cotton and its wild relatives by allowing gene flow between them. This study provides information for management efforts focused on the conservation of wild populations, native landraces, and non-GM domesticated cotton at its center of origin and genetic diversity.
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41
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Domestication and feralization influence the distribution and phenotypes of escaped ornamental fish. Biol Invasions 2021. [DOI: 10.1007/s10530-020-02415-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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42
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Ballard JWO, Gardner C, Ellem L, Yadav S, Kemp RI. Eye contact and sociability data suggests that Australian dingoes were never domesticated. Curr Zool 2021; 68:423-432. [PMID: 36090142 PMCID: PMC9450177 DOI: 10.1093/cz/zoab024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 03/04/2021] [Indexed: 11/14/2022] Open
Abstract
Dogs were the first animal to become domesticated by humans, and they represent a classic model system for unraveling the processes of domestication. We compare Australian dingo eye contact and socialization with Basenji and German Shepherd dog (GSD) breeds. Australian dingoes arrived in Australia 5,000–8,000 BP, and there is debate whether they were domesticated before their arrival. The Basenji represents a primitive breed that diverged from the remaining breeds early in the domestication process, while GSDs are a breed dog selected from existing domestic dogs in the late 1800s. We conducted a 4-phase study with unfamiliar and familiar investigators either sitting passively or actively calling each canid. We found 75% of dingoes made eye contact in each phase. In contrast, 86% of Basenjis and 96% of GSDs made eye contact. Dingoes also exhibited shorter eye-gaze duration than breed dogs and did not respond to their name being called actively. Sociability, quantified as a canid coming within 1 m of the experimenter, was lowest for dingoes and highest for GSDs. For sociability duration, dingoes spent less time within 1 m of the experimenter than either breed dog. When compared with previous studies, these data show that the dingo is behaviorally intermediate between wild wolves and Basenji dogs and suggest that it was not domesticated before it arrived in Australia. However, it remains possible that the accumulation of mutations since colonization has obscured historical behaviors, and dingoes now exist in a feralized retamed cycle. Additional morphological and genetic data are required to resolve this conundrum.
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Affiliation(s)
- J William O Ballard
- Department of Ecology, Environment, and Evolution, Latrobe University, Melbourne, VIC 3086, Australia
- Department of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Chloe Gardner
- School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| | | | - Sonu Yadav
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Richard I Kemp
- School of Psychology, UNSW Sydney, Sydney, NSW 2052, Australia
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43
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Feralization: Confronting the Complexity of Domestication and Evolution. Trends Genet 2021; 37:302-305. [PMID: 33546926 DOI: 10.1016/j.tig.2021.01.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/21/2022]
Abstract
Feral populations, those which successfully persist outside of cultivation or husbandry, provide unique opportunities to study the genomic impacts of domestication and local adaptation. We argue that by leveraging genomic resources designed for domestic counterparts, powerful phylogenetic and population genomic data collection and analyses can be designed to disentangle complex demographic processes.
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44
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Hinshaw C, Evans KC, Rosa C, López-Uribe MM. The Role of Pathogen Dynamics and Immune Gene Expression in the Survival of Feral Honey Bees. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.594263] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Studies of the ecoimmunology of feral organisms can provide valuable insight into how host–pathogen dynamics change as organisms transition from human-managed conditions back into the wild. Honey bees (Apis mellifera Linnaeus) offer an ideal system to investigate these questions as colonies of these social insects often escape management and establish in the wild. While managed honey bee colonies have low probability of survival in the absence of disease treatments, feral colonies commonly survive in the wild, where pathogen pressures are expected to be higher due to the absence of disease treatments. Here, we investigate the role of pathogen infections [Deformed wing virus (DWV), Black queen cell virus (BQCV), and Nosema ceranae] and immune gene expression (defensin-1, hymenoptaecin, pgrp-lc, pgrp-s2, argonaute-2, vago) in the survival of feral and managed honey bee colonies. We surveyed a total of 25 pairs of feral and managed colonies over a 2-year period (2017–2018), recorded overwintering survival, and measured pathogen levels and immune gene expression using quantitative polymerase chain reaction (qPCR). Our results showed that feral colonies had higher levels of DWV but it was variable over time compared to managed colonies. Higher pathogen levels were associated with increased immune gene expression, with feral colonies showing higher expression in five out of the six examined immune genes for at least one sampling period. Further analysis revealed that differential expression of the genes hymenoptaecin and vago increased the odds of overwintering survival in managed and feral colonies. Our results revealed that feral colonies express immune genes at higher levels in response to high pathogen burdens, providing evidence for the role of feralization in altering pathogen landscapes and host immune responses.
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45
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Neaux D, Sansalone G, Lecompte F, Haruda A, Schafberg R, Cucchi T. Examining the effect of feralization on craniomandibular morphology in pigs, Sus scrofa (Artiodactyla: Suidae). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa156] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Abstract
Feralization is the process by which domestic animals return to the wild and produce self-sustaining populations. It is often considered as a model in understanding the permanence of morphological changes associated with domestication; however, it is still unclear how much the release of anthropogenic selective pressures affects domestic traits. Here, we assessed the influence of feralization on the domestic morphological traits acquired through selective breeding using craniomandibular differences in shape and size between populations of feral pigs, wild boar and domestic pigs, using landmark-based geometric morphometrics. Our results suggest that numerous cranial and mandibular traits associated with domestication still exist in feral specimens, corroborating that domestication-induced changes in the shape of morphological elements are broadly maintained in feral populations. This is not the case for size variations, however, as the cranium is significantly smaller in feral pigs than in domesticated breeds, which could be due to the selective pressures associated with founding events. Our exploratory study, therefore, underlines the complexity of feral population history, the intricate influence of variations in genetic diversity, and novel selection pressures in the morphology of these groups. Future studies will need to expand the sample to take into account the diversity of morphotypes.
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Affiliation(s)
- Dimitri Neaux
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements, UMR 7209, Muséum national d’Histoire naturelle CNRS, CP, Paris, France
- Laboratoire Paléontologie Evolution Paléoécosystèmes Paléoprimatologie, UMR 7262, Université de Poitiers CNRS, Poitiers, France
| | - Gabriele Sansalone
- Function, Evolution & Anatomy Research Laboratory, School of Environmental and Rural Science, University of New England, NSW, Armidale, Australia
- Department of Sciences, Roma Tre University, Rome, Italy
- Center for Evolutionary Ecology, Rome, Italy
| | - François Lecompte
- Plateforme Chirurgie et Imagerie pour la Recherche et l’Enseignement, INRAE, Nouzilly, France
| | - Ashleigh Haruda
- Central Natural Science Collections, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Renate Schafberg
- Central Natural Science Collections, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Thomas Cucchi
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements, UMR 7209, Muséum national d’Histoire naturelle CNRS, CP, Paris, France
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46
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The genetic regulation of size variation in the transcriptome of the cerebrum in the chicken and its role in domestication and brain size evolution. BMC Genomics 2020; 21:518. [PMID: 32727510 PMCID: PMC7392834 DOI: 10.1186/s12864-020-06908-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/13/2020] [Indexed: 12/03/2022] Open
Abstract
Background Large difference in cerebrum size exist between avian species and populations of the same species and is believed to reflect differences in processing power, i.e. in the speed and efficiency of processing information in this brain region. During domestication chickens developed a larger cerebrum compared to their wild progenitor, the Red jungle fowl. The underlying mechanisms that control cerebrum size and the extent to which genetic regulation is similar across brain regions is not well understood. In this study, we combine measurement of cerebrum size with genome-wide genetical genomics analysis to identify the genetic architecture of the cerebrum, as well as compare the regulation of gene expression in this brain region with gene expression in other regions of the brain (the hypothalamus) and somatic tissue (liver). Results We identify one candidate gene that putatively regulates cerebrum size (MTF2) as well as a large number of eQTL that regulate the transcriptome in cerebrum tissue, with the majority of these eQTL being trans-acting. The overall regulation of gene expression variation in the cerebrum was markedly different to the hypothalamus, with relatively few eQTL in common. In comparison, the cerebrum tissue shared more eQTL with a distant tissue (liver) than with a neighboring tissue (hypothalamus). Conclusion The candidate gene for cerebrum size (MTF2) has previously been linked to brain development making it a good candidate for further investigation as a regulator of inter-population variation in cerebrum size. The lack of shared eQTL between the two brain regions implies that genetic regulation of gene expression appears to be relatively independent between the two brain regions and suggest that coevolution between these two brain regions might be more functionally driven than developmental. These findings have relevance for current brain size evolution theories.
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