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Amaya Romero JE, Chenal C, Ben Chehida Y, Miles A, Clarkson CS, Pedergnana V, Wertheim B, Fontaine MC. Mitochondrial Variation in Anopheles gambiae and Anopheles coluzzii: Phylogeographic Legacy and Mitonuclear Associations With Metabolic Resistance to Pathogens and Insecticides. Genome Biol Evol 2024; 16:evae172. [PMID: 39226386 PMCID: PMC11370803 DOI: 10.1093/gbe/evae172] [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] [Accepted: 07/22/2024] [Indexed: 09/05/2024] Open
Abstract
Mitochondrial DNA has been a popular marker in phylogeography, phylogeny, and molecular ecology, but its complex evolution is increasingly recognized. Here, we investigated mitochondrial DNA variation in Anopheles gambiae and Anopheles coluzzii, in relation to other species in the Anopheles gambiae complex, by assembling the mitogenomes of 1,219 mosquitoes across Africa. The mitochondrial DNA phylogeny of the Anopheles gambiae complex was consistent with previously reported highly reticulated evolutionary history, revealing important discordances with the species tree. The three most widespread species (An. gambiae, An. coluzzii, and Anopheles arabiensis), known for extensive historical introgression, could not be discriminated based on mitogenomes. Furthermore, a monophyletic clustering of the three saltwater-tolerant species (Anopheles merus, Anopheles melas, and Anopheles bwambae) in the Anopheles gambiae complex also suggested that introgression and possibly selection shaped mitochondrial DNA evolution. Mitochondrial DNA variation in An. gambiae and An. coluzzii across Africa revealed significant partitioning among populations and species. A peculiar mitochondrial DNA lineage found predominantly in An. coluzzii and in the hybrid taxon of the African "far-west" exhibited divergence comparable to the interspecies divergence in the Anopheles gambiae complex, with a geographic distribution matching closely An. coluzzii's geographic range. This phylogeographic relict of the An. coluzzii and An. gambiae split was associated with population and species structure, but not with the rare Wolbachia occurrence. The lineage was significantly associated with single nucleotide polymorphisms in the nuclear genome, particularly in genes associated with pathogen and insecticide resistance. These findings underline potential mitonuclear coevolution history and the role played by mitochondria in shaping metabolic responses to pathogens and insecticides in Anopheles.
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Affiliation(s)
- Jorge E Amaya Romero
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen 9747 AG, Netherlands
- MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Clothilde Chenal
- MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
- Institut des Science de l’Évolution de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Yacine Ben Chehida
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen 9747 AG, Netherlands
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Alistair Miles
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | | | - Bregje Wertheim
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen 9747 AG, Netherlands
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen 9747 AG, Netherlands
- MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
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2
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Papadadonakis S, Kioukis A, Karageorgiou C, Pavlidis P. Evolution of gene regulatory networks by means of selection and random genetic drift. PeerJ 2024; 12:e17918. [PMID: 39221262 PMCID: PMC11365478 DOI: 10.7717/peerj.17918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 07/23/2024] [Indexed: 09/04/2024] Open
Abstract
The evolution of a population by means of genetic drift and natural selection operating on a gene regulatory network (GRN) of an individual has not been scrutinized in depth. Thus, the relative importance of various evolutionary forces and processes on shaping genetic variability in GRNs is understudied. In this study, we implemented a simulation framework, called EvoNET, that simulates forward-in-time the evolution of GRNs in a population. The fitness effect of mutations is not constant, rather fitness of each individual is evaluated on the phenotypic level, by measuring its distance from an optimal phenotype. Each individual goes through a maturation period, where its GRN may reach an equilibrium, thus deciding its phenotype. Afterwards, individuals compete to produce the next generation. We examine properties of the GRN evolution, such as robustness against the deleterious effect of mutations and the role of genetic drift. We are able to confirm previous hypotheses regarding the effect of mutations and we provide new insights on the interplay between random genetic drift and natural selection.
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Affiliation(s)
- Stefanos Papadadonakis
- Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Antonios Kioukis
- School of Medicine, University of Crete, Heraklion, Crete, Greece
| | | | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
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3
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Cars BS, Kessler C, Hoffman EA, Côté SD, Koelsch D, Shafer ABA. Island demographics and trait associations in white-tailed deer. Heredity (Edinb) 2024; 133:1-10. [PMID: 38802598 PMCID: PMC11222433 DOI: 10.1038/s41437-024-00685-2] [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: 08/03/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
When a population is isolated and composed of few individuals, genetic drift is the paramount evolutionary force and results in the loss of genetic diversity. Inbreeding might also occur, resulting in genomic regions that are identical by descent, manifesting as runs of homozygosity (ROHs) and the expression of recessive traits. Likewise, the genes underlying traits of interest can be revealed by comparing fixed SNPs and divergent haplotypes between affected and unaffected individuals. Populations of white-tailed deer (Odocoileus virginianus) on islands of Saint Pierre and Miquelon (SPM, France) have high incidences of leucism and malocclusions, both considered genetic defects; on the Florida Keys islands (USA) deer exhibit smaller body sizes, a polygenic trait. Here we aimed to reconstruct island demography and identify the genes associated with these traits in a pseudo case-control design. The two island populations showed reduced levels of genomic diversity and a build-up of deleterious mutations compared to mainland deer; there was also significant genome-wide divergence in Key deer. Key deer showed higher inbreeding levels, but not longer ROHs, consistent with long-term isolation. We identified multiple trait-related genes in ROHs including LAMTOR2 which has links to pigmentation changes, and NPVF which is linked to craniofacial abnormalities. Our mixed approach of linking ROHs, fixed SNPs and haplotypes matched a high number (~50) of a-priori body size candidate genes in Key deer. This suite of biomarkers and candidate genes should prove useful for population monitoring, noting all three phenotypes show patterns consistent with a complex trait and non-Mendelian inheritance.
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Affiliation(s)
- Brooklyn S Cars
- Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
- Department of Forensics, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
| | - Camille Kessler
- Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
| | - Eric A Hoffman
- Department of Biology, University of Central Florida, 4000, Central Florida Blvd, Orlando, FL, USA
| | - Steeve D Côté
- Département de Biologie and Centre d'Études Nordiques, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Daniel Koelsch
- Fédération des chasseurs de Saint-Pierre et Miquelon, Saint-Pierre et Miquelon, France
- Direction des Territoires de l'Alimentation et de la Mer, service Biodiversité, Saint-Pierre et Miquelon, France
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada.
- Department of Forensics, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada.
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4
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Treindl AD, Stapley J, Croll D, Leuchtmann A. Two-speed genomes of Epichloe fungal pathogens show contrasting signatures of selection between species and across populations. Mol Ecol 2024; 33:e17242. [PMID: 38084851 DOI: 10.1111/mec.17242] [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: 02/08/2023] [Revised: 11/23/2023] [Accepted: 11/30/2023] [Indexed: 12/19/2023]
Abstract
Antagonistic selection between pathogens and their hosts can drive rapid evolutionary change and leave distinct molecular footprints of past and ongoing selection in the genomes of the interacting species. Despite an increasing availability of tools able to identify signatures of selection, the genetic mechanisms underlying coevolutionary interactions and the specific genes involved are still poorly understood, especially in heterogeneous natural environments. We searched the genomes of two species of Epichloe plant pathogen for evidence of recent selection. The Epichloe genus includes highly host-specific species that can sterilize their grass hosts. We performed selection scans using genome-wide SNP data from seven natural populations of two co-occurring Epichloe sibling species specialized on different hosts. We found evidence of recent (and ongoing) selective sweeps across the genome in both species. However, selective sweeps were more abundant in the species with a larger effective population size. Sweep regions often overlapped with highly polymorphic AT-rich regions supporting the role of these genome compartments in adaptive evolution. Although most loci under selection were specific to individual populations, we could also identify several candidate genes targeted by selection in sweep regions shared among populations. The genes encoded small secreted proteins typical of fungal effectors and cell wall-degrading enzymes. By investigating the genomic signatures of selection across multiple populations and species, this study contributes to our understanding of complex adaptive processes in natural plant pathogen systems.
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Affiliation(s)
- Artemis D Treindl
- Plant Ecological Genetics Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Biodiversity and Conservation Biology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Jessica Stapley
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Adrian Leuchtmann
- Plant Ecological Genetics Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
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Feldmeyer B, Bornberg-Bauer E, Dohmen E, Fouks B, Heckenhauer J, Huylmans AK, Jones ARC, Stolle E, Harrison MC. Comparative Evolutionary Genomics in Insects. Methods Mol Biol 2024; 2802:473-514. [PMID: 38819569 DOI: 10.1007/978-1-0716-3838-5_16] [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] [Indexed: 06/01/2024]
Abstract
Genome sequencing quality, in terms of both read length and accuracy, is constantly improving. By combining long-read sequencing technologies with various scaffolding techniques, chromosome-level genome assemblies are now achievable at an affordable price for non-model organisms. Insects represent an exciting taxon for studying the genomic underpinnings of evolutionary innovations, due to ancient origins, immense species-richness, and broad phenotypic diversity. Here we summarize some of the most important methods for carrying out a comparative genomics study on insects. We describe available tools and offer concrete tips on all stages of such an endeavor from DNA extraction through genome sequencing, annotation, and several evolutionary analyses. Along the way we describe important insect-specific aspects, such as DNA extraction difficulties or gene families that are particularly difficult to annotate, and offer solutions. We describe results from several examples of comparative genomics analyses on insects to illustrate the fascinating questions that can now be addressed in this new age of genomics research.
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Affiliation(s)
- Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Molecular Ecology, Frankfurt, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Elias Dohmen
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Bertrand Fouks
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
| | - Ann Kathrin Huylmans
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Alun R C Jones
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Eckart Stolle
- Museum Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | - Mark C Harrison
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
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Fouks B, Harrison MC, Mikhailova AA, Marchal E, English S, Carruthers M, Jennings EC, Chiamaka EL, Frigard RA, Pippel M, Attardo GM, Benoit JB, Bornberg-Bauer E, Tobe SS. Live-bearing cockroach genome reveals convergent evolutionary mechanisms linked to viviparity in insects and beyond. iScience 2023; 26:107832. [PMID: 37829199 PMCID: PMC10565785 DOI: 10.1016/j.isci.2023.107832] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 02/13/2023] [Accepted: 09/01/2023] [Indexed: 10/14/2023] Open
Abstract
Live birth (viviparity) has arisen repeatedly and independently among animals. We sequenced the genome and transcriptome of the viviparous Pacific beetle-mimic cockroach and performed comparative analyses with two other viviparous insect lineages, tsetse flies and aphids, to unravel the basis underlying the transition to viviparity in insects. We identified pathways undergoing adaptive evolution for insects, involved in urogenital remodeling, tracheal system, heart development, and nutrient metabolism. Transcriptomic analysis of cockroach and tsetse flies revealed that uterine remodeling and nutrient production are increased and the immune response is altered during pregnancy, facilitating structural and physiological changes to accommodate and nourish the progeny. These patterns of convergent evolution of viviparity among insects, together with similar adaptive mechanisms identified among vertebrates, highlight that the transition to viviparity requires changes in urogenital remodeling, enhanced tracheal and heart development (corresponding to angiogenesis in vertebrates), altered nutrient metabolism, and shifted immunity in animal systems.
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Affiliation(s)
- Bertrand Fouks
- University of Münster, Institute for Evolution and Biodiversity, Molecular Evolution and Bioinformatics, Hüfferstrasse 1, 48149 Münster, Germany
| | - Mark C. Harrison
- University of Münster, Institute for Evolution and Biodiversity, Molecular Evolution and Bioinformatics, Hüfferstrasse 1, 48149 Münster, Germany
| | - Alina A. Mikhailova
- University of Münster, Institute for Evolution and Biodiversity, Molecular Evolution and Bioinformatics, Hüfferstrasse 1, 48149 Münster, Germany
| | - Elisabeth Marchal
- Department of Biology, Molecular Developmental Physiology and Signal Transduction Lab., Division of Animal Physiology and Neurobiology, Naamsestraat 59-Box 2465, B-3000 Leuven, Belgium
| | - Sinead English
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | | | - Emily C. Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Ezemuoka L. Chiamaka
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Ronja A. Frigard
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Geoffrey M. Attardo
- Department of Entomology and Nematology, College of Agriculture and Environmental Sciences, University of California, Davis, Davis, CA, USA
| | - Joshua B. Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Erich Bornberg-Bauer
- University of Münster, Institute for Evolution and Biodiversity, Molecular Evolution and Bioinformatics, Hüfferstrasse 1, 48149 Münster, Germany
- Department of Protein Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Stephen S. Tobe
- Department of Biology, Molecular Developmental Physiology and Signal Transduction Lab., Division of Animal Physiology and Neurobiology, Naamsestraat 59-Box 2465, B-3000 Leuven, Belgium
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
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7
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Deng Z, Zhang X, Wolinska J, Blair D, Hu W, Yin M. Climate has contributed to population diversification of Daphnia galeata across Eurasia. Mol Ecol 2023; 32:5110-5124. [PMID: 37548328 DOI: 10.1111/mec.17094] [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: 05/11/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023]
Abstract
Climate is a fundamental abiotic factor that plays a key role in driving the evolution, distribution and population diversification of species. However, there have been few investigations of genomic signatures of adaptation to local climatic conditions in cladocerans. Here, we have provided the first high-quality chromosome-level genome assembly (~143 Mb, scaffold N50 12.6 Mb) of the waterflea, Daphnia galeata, and investigated genomic variation in 22 populations from Central Europe and Eastern China. Our ecological-niche models suggested that the historic distribution of D. galeata in Eurasia was significantly affected by Quaternary climate fluctuations. We detected pronounced genomic and morphometric divergences between European and Chinese D. galeata populations. Such divergences could be partly explained by genomic signatures of thermal adaptation to distinct climate regimes: a set of candidate single-nucleotide polymorphisms (SNPs) potentially associated with climate were detected. These SNPs were in genes significantly enriched in the Gene ontology terms "determination of adult lifespan" and "translation repressor activity", and especially, mthl5 and SOD1 involved in the IIS pathway, and EIF4EBP2 involved in the target of the rapamycin signalling pathway. Our study indicates that certain alleles might be associated with particular temperature regimes, playing a functional role in shaping the population structure of D. galeata at a large geographical scale. These results highlight the potential role of molecular variation in the response to climate variation, in the context of global climate change.
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Affiliation(s)
- Zhixiong Deng
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Xiuping Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - David Blair
- College of Marine and Environmental Sciences, James Cook University, Townsville, Queensland, Australia
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
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Tóth EG, Cseke K, Benke A, Lados BB, Tomov VT, Zhelev P, Kámpel JD, Borovics A, Köbölkuti ZA. Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data. Heredity (Edinb) 2023:10.1038/s41437-023-00629-2. [PMID: 37316726 PMCID: PMC10382515 DOI: 10.1038/s41437-023-00629-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/16/2023] Open
Abstract
Knowledge on the genetic composition of Quercus petraea in south-eastern Europe is limited despite the species' significant role in the re-colonisation of Europe during the Holocene, and the diverse climate and physical geography of the region. Therefore, it is imperative to conduct research on adaptation in sessile oak to better understand its ecological significance in the region. While large sets of SNPs have been developed for the species, there is a continued need for smaller sets of SNPs that are highly informative about the possible adaptation to this varied landscape. By using double digest restriction site associated DNA sequencing data from our previous study, we mapped RAD-seq loci to the Quercus robur reference genome and identified a set of SNPs putatively related to drought stress-response. A total of 179 individuals from eighteen natural populations at sites covering heterogeneous climatic conditions in the southeastern natural distribution range of Q. petraea were genotyped. The detected highly polymorphic variant sites revealed three genetic clusters with a generally low level of genetic differentiation and balanced diversity among them but showed a north-southeast gradient. Selection tests showed nine outlier SNPs positioned in different functional regions. Genotype-environment association analysis of these markers yielded a total of 53 significant associations, explaining 2.4-16.6% of the total genetic variation. Our work exemplifies that adaptation to drought may be under natural selection in the examined Q. petraea populations.
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Affiliation(s)
- Endre Gy Tóth
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary.
| | - Klára Cseke
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Attila Benke
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Botond B Lados
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Vladimir T Tomov
- Department of Landscape Architecture, Faculty of Ecology and Landscape Architecture, University of Forestry (UF), Kliment Ohridsky 10, Sofia, 1797, Bulgaria
| | - Petar Zhelev
- Department of Dendrology, Faculty of Forestry, University of Forestry (UF), Kliment Ohridsky 10, Sofia, 1797, Bulgaria
| | - József D Kámpel
- Ottó Herman Environmental and Agricultural Technical School, Vocational School and College (Agricultural Vocational Centre of the Kisalföld Region), Ernuszt Kelemen 1, Szombathely, 9700, Hungary
| | - Attila Borovics
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Zoltán A Köbölkuti
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
- Departement of Applied Forest Genetics Research, Bavarian Office for Forest Genetics (AWG), Forstamtsplatz 1, Teisendorf, 83317, Germany
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Rocha RDFB, Garcia AO, Otto PI, da Silva MVB, Martins MF, Machado MA, Panetto JCDC, Guimarães SEF. Runs of homozygosity and signatures of selection for number of oocytes and embryos in the Gir Indicine cattle. Mamm Genome 2023:10.1007/s00335-023-09989-w. [PMID: 37000236 DOI: 10.1007/s00335-023-09989-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/11/2023] [Indexed: 04/01/2023]
Abstract
Runs of homozygosity (ROH) and signatures of selection are the results of selection processes in livestock species that have been shown to affect several traits in cattle. The aim of the current work was to verify the profile of ROH and inbreeding depression in the number of total (TO) and viable oocytes (VO) and the number of embryos (EMBR) in Gir Indicine cattle. In addition, we aim to identify signatures of selection, genes, and enriched regions between Gir subpopulations sorted by breeding value for these traits. The genotype file contained 2093 animals and 420,718 SNP markers. Breeding values used to sort Gir animals were previously obtained. ROH and signature of selection analyses were performed using PLINK software, followed by ROH-based (FROH) and pedigree-based inbreeding (Fped) and a search for genes and their functions. An average of 50 ± 8.59 ROHs were found per animal. ROHs were separated into classes according to size, ranging from 1 to 2 Mb (ROH1-2Mb: 58.17%), representing ancient inbreeding, ROH2-4Mb (22.74%), ROH4-8Mb (11.34%), ROH8-16Mb (5.51%), and ROH>16Mb (2.24%). Combining our results, we conclude that the increase in general FROH and Fped significantly decreases TO and VO; however, in different chromosomes traits can increase or decrease with FROH. In the analysis for signatures of selection, we identified 15 genes from 47 significant genomic regions, indicating differences in populations with high and low breeding value for the three traits.
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Affiliation(s)
| | | | - Pamela Itajara Otto
- Department of Animal Science, Universidade Federal de Santa Maria, Santa Maria, Rio Grande Do Sul, Brazil
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Wei K, Silva-Arias GA, Tellier A. Selective sweeps linked to the colonization of novel habitats and climatic changes in a wild tomato species. THE NEW PHYTOLOGIST 2023; 237:1908-1921. [PMID: 36419182 DOI: 10.1111/nph.18634] [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: 07/12/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
Positive selection is the driving force underpinning local adaptation and leaves footprints of selective sweeps on the underlying major genes. Quantifying the timing of selection and revealing the genetic bases of adaptation in plant species occurring in steep and varying environmental gradients are crucial to predict a species' ability to colonize new niches. We use whole-genome sequence data from six populations across three different habitats of the wild tomato species Solanum chilense to infer the past demographic history and search for genes under strong positive selection. We then correlate current and past climatic projections with the demographic history, allele frequencies, the age of selection events and distribution shifts. Several selective sweeps occur at regulatory networks involved in root-hair development in low altitude and response to photoperiod and vernalization in high-altitude populations. These sweeps appear to occur in a concerted fashion in a given regulatory gene network at particular periods of substantial climatic change. Using a unique combination of genome scans and modelling of past climatic data, we quantify the timing of selection at genes likely underpinning local adaptation to semiarid habitats.
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Affiliation(s)
- Kai Wei
- Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Liesel-Beckmann Strasse 2, 85354, Freising, Germany
| | - Gustavo A Silva-Arias
- Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Liesel-Beckmann Strasse 2, 85354, Freising, Germany
| | - Aurélien Tellier
- Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Liesel-Beckmann Strasse 2, 85354, Freising, Germany
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11
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Fuhrmann N, Prakash C, Kaiser TS. Polygenic adaptation from standing genetic variation allows rapid ecotype formation. eLife 2023; 12:e82824. [PMID: 36852484 PMCID: PMC9977305 DOI: 10.7554/elife.82824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/07/2023] [Indexed: 03/01/2023] Open
Abstract
Adaptive ecotype formation can be the first step to speciation, but the genetic underpinnings of this process are poorly understood. Marine midges of the genus Clunio (Diptera) have recolonized Northern European shore areas after the last glaciation. In response to local tide conditions they have formed different ecotypes with respect to timing of adult emergence, oviposition behavior and larval habitat. Genomic analysis confirms the recent establishment of these ecotypes, reflected in massive haplotype sharing between ecotypes, irrespective of whether there is ongoing gene flow or geographic isolation. QTL mapping and genome screens reveal patterns of polygenic adaptation from standing genetic variation. Ecotype-associated loci prominently include circadian clock genes, as well as genes affecting sensory perception and nervous system development, hinting to a central role of these processes in ecotype formation. Our data show that adaptive ecotype formation can occur rapidly, with ongoing gene flow and largely based on a re-assortment of existing alleles.
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Affiliation(s)
- Nico Fuhrmann
- Max Planck Institute for Evolutionary BiologyPlönGermany
| | - Celine Prakash
- Max Planck Institute for Evolutionary BiologyPlönGermany
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12
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Sekino M, Hashimoto K, Nakamichi R, Yamamoto M, Fujinami Y, Sasaki T. Introgressive hybridization in the west Pacific pen shells (genus Atrina): Restricted interspecies gene flow within the genome. Mol Ecol 2023; 32:2945-2963. [PMID: 36855846 DOI: 10.1111/mec.16908] [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: 07/13/2022] [Revised: 02/03/2023] [Accepted: 02/14/2023] [Indexed: 03/02/2023]
Abstract
A compelling interest in marine biology is to elucidate how species boundaries between sympatric free-spawning marine invertebrates such as bivalve molluscs are maintained in the face of potential hybridization. Hybrid zones provide the natural resources for us to study the underlying genetic mechanisms of reproductive isolation between hybridizing species. Against this backdrop, we examined the occurrence of introgressive hybridization (introgression) between two bivalves distributed in the western Pacific margin, Atrina japonica and Atrina lischkeana, based on single-nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing. Using 1066 ancestry-informative SNP sites, we also investigated the extent of introgression within the genome to search for SNP sites with reduced interspecies gene flow. A series of our individual-level clustering analyses including the principal component analysis, Bayesian model-based clustering, and triangle plotting based on ancestry-heterozygosity relationships for an admixed population sample from the Seto Inland Sea (Japan) consistently suggested the presence of specimens with varying degrees of genomic admixture, thereby implying that the two species are not completely isolated. The Bayesian genomic cline analysis identified 10 SNP sites with reduced introgression, each of which was located within a genic region or an intergenic region physically close to a functional gene. No, or very few, heterozygotes were observed at these sites in the hybrid zone, suggesting that selection acts against heterozygotes. Accordingly, we raised the possibility that the SNP sites are within genomic regions that are incompatible between the two species. Our finding of restricted interspecies gene flow at certain genomic regions gives new insight into the maintenance of species boundaries in hybridizing broadcast-spawning molluscs.
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Affiliation(s)
- Masashi Sekino
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Kazumasa Hashimoto
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Nagasaki, Japan
| | - Reiichiro Nakamichi
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Masayuki Yamamoto
- Fisheries Division, Kagawa Prefectural Government, Takamatsu, Kagawa, Japan
| | - Yuichiro Fujinami
- Goto Field Station, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Nagasaki, Japan
| | - Takenori Sasaki
- The University Museum, The University of Tokyo, Tokyo, Japan
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13
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Antoniou A, Manousaki T, Ramírez F, Cariani A, Cannas R, Kasapidis P, Magoulas A, Albo-Puigserver M, Lloret-Lloret E, Bellido JM, Pennino MG, Follesa MC, Esteban A, Saraux C, Sbrana M, Spedicato MT, Coll M, Tsigenopoulos CS. Sardines at a junction: Seascape genomics reveals ecological and oceanographic drivers of variation in the NW Mediterranean Sea. Mol Ecol 2023; 32:1608-1628. [PMID: 36596297 DOI: 10.1111/mec.16840] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 12/20/2022] [Accepted: 12/30/2022] [Indexed: 01/04/2023]
Abstract
By evaluating genetic variation across the entire genome, one can address existing questions in a novel way while raising new ones. The latter includes how different local environments influence adaptive and neutral genomic variation within and among populations, providing insights into local adaptation of natural populations and their responses to global change. Here, under a seascape genomic approach, ddRAD data of 4609 single nucleotide polymorphisms (SNPs) from 398 sardines (Sardina pilchardus) collected in 11 Mediterranean and one Atlantic site were generated. These were used along with oceanographic and ecological information to detect signals of adaptive divergence with gene flow across environmental gradients. The studied sardines constitute two clusters (FST = 0.07), a pattern attributed to outlier loci, highlighting putative local adaptation. The trend in the number of days with sea surface temperature above 19°C, a critical threshold for successful sardine spawning, was crucial at all levels of population structuring with implications on the species' key biological processes. Outliers link candidate SNPs to the region's environmental heterogeneity. Our findings provide evidence for a dynamic equilibrium in which population structure is maintained by physical and ecological factors under the opposing influences of migration and selection. This dynamic in a natural system warrants continuous monitoring under a seascape genomic approach that might benefit from a temporal and more detailed spatial dimension. Our results may contribute to complementary studies aimed at providing deeper insights into the mechanistic processes underlying population structuring. Those are key to understanding and predicting future changes and responses of this highly exploited species in the face of climate change.
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Affiliation(s)
- Aglaia Antoniou
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece
| | - Tereza Manousaki
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece
| | - Francisco Ramírez
- Institute of Marine Science (ICM-CSIC), Passeig Marítim de la Barceloneta, Barcelona, Spain
| | - Alessia Cariani
- Dept. Biological, Geological & Environmental Sciences (BiGeA), Alma Mater Studiorum - Università di Bologna, Ravenna, Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy
| | - Rita Cannas
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy.,Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Panagiotis Kasapidis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece
| | - Antonios Magoulas
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece
| | - Marta Albo-Puigserver
- Institute of Marine Science (ICM-CSIC), Passeig Marítim de la Barceloneta, Barcelona, Spain.,Centro Oceanográfico de Baleares, Instituto Español de Oceanografía (COB-CNIEO/CSIC), Palma, Spain
| | - Elena Lloret-Lloret
- Institute of Marine Science (ICM-CSIC), Passeig Marítim de la Barceloneta, Barcelona, Spain
| | - Jose Maria Bellido
- Centro Oceanográfico de Murcia, Instituto Español de Oceanografía, (COMU-CNIEO/CSIC), Murcia, Spain
| | - Maria Grazia Pennino
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía (COVI-CNIEO/CSIC), Vigo, Pontevedra, Spain
| | - Maria Cristina Follesa
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy.,Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Antonio Esteban
- Centro Oceanográfico de Murcia, Instituto Español de Oceanografía, (COMU-CNIEO/CSIC), Murcia, Spain
| | - Claire Saraux
- MARBEC, University of Montpellier, CNRS, IFREMER, IRD, Sète, France
| | - Mario Sbrana
- Consorzio per il Centro Interuniversitario di Biologia Marina ed Ecologia Applicata G, Livorno, Italy
| | | | - Marta Coll
- Institute of Marine Science (ICM-CSIC), Passeig Marítim de la Barceloneta, Barcelona, Spain
| | - Costas S Tsigenopoulos
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece
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14
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Lasky JR, Josephs EB, Morris GP. Genotype-environment associations to reveal the molecular basis of environmental adaptation. THE PLANT CELL 2023; 35:125-138. [PMID: 36005926 PMCID: PMC9806588 DOI: 10.1093/plcell/koac267] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/23/2022] [Indexed: 06/14/2023]
Abstract
A fundamental goal in plant biology is to identify and understand the variation underlying plants' adaptation to their environment. Climate change has given new urgency to this goal, as society aims to accelerate adaptation of ecologically important plant species, endangered plant species, and crops to hotter, less predictable climates. In the pre-genomic era, identifying adaptive alleles was painstaking work, leveraging genetics, molecular biology, physiology, and ecology. Now, the rise of genomics and new computational approaches may facilitate this research. Genotype-environment associations (GEAs) use statistical associations between allele frequency and environment of origin to test the hypothesis that allelic variation at a given gene is adapted to local environments. Researchers may scan the genome for GEAs to generate hypotheses on adaptive genetic variants (environmental genome-wide association studies). Despite the rapid adoption of these methods, many important questions remain about the interpretation of GEA findings, which arise from fundamental unanswered questions on the genetic architecture of adaptation and limitations inherent to association-based analyses. We outline strategies to ground GEAs in the underlying hypotheses of genetic architecture and better test GEA-generated hypotheses using genetics and ecophysiology. We provide recommendations for new users who seek to learn about the molecular basis of adaptation. When combined with a rigorous hypothesis testing framework, GEAs may facilitate our understanding of the molecular basis of climate adaptation for plant improvement.
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Affiliation(s)
- Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Emily B Josephs
- Department of Plant Biology; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan 48824, USA
| | - Geoffrey P Morris
- Department of Soil and Crop Sciences; Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado 80526, USA
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15
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Cossette ML, Stewart DT, Haghani A, Zoller JA, Shafer ABA, Horvath S. Epigenetics and island-mainland divergence in an insectivorous small mammal. Mol Ecol 2023; 32:152-166. [PMID: 36226847 DOI: 10.1111/mec.16735] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 12/29/2022]
Abstract
Geographically isolated populations, specifically island-mainland counterparts, tend to exhibit phenotypic variation in many species. The so-called island syndrome occurs when different environmental pressures lead to insular divergence from mainland populations. This phenomenon can be seen in an island population of Nova Scotia masked shrews (Sorex cinereus), which have developed a specialized feeding habit and digestive enzyme compared to their mainland counterparts. Epigenetic modifications, such as DNA methylation (DNAm), can impact phenotypes by altering gene expression without changing the DNA sequence. Here, we used a de novo masked shrew genome assembly and a mammalian methylation array profiling 37 thousand conserved CpGs to investigate morphological and DNA methylation patterns between island and mainland populations. Island shrews were morphologically and epigenetically different than their mainland counterparts, exhibiting a smaller body size. A gene ontology enrichment analyses of differentially methylated CpGs implicated developmental and digestive system related pathways. Based on our shrew epigenetic clock, island shrews might also be aging faster than their mainland counterparts. This study provides novel insight on phenotypic and epigenetic divergence in island-mainland mammal populations and suggests an underlying role of methylation in island-mainland divergence.
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Affiliation(s)
- Marie-Laurence Cossette
- Department of Environmental Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Donald T Stewart
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Joseph A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, California, USA
| | - Aaron B A Shafer
- Department of Environmental Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- Department of Forensic Science, Trent University, Peterborough, Ontario, Canada
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, California, USA
- Altos Labs, San Diego, California, USA
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16
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Detection of Selection Signatures in Anqing Six-End-White Pigs Based on Resequencing Data. Genes (Basel) 2022; 13:genes13122310. [PMID: 36553577 PMCID: PMC9777694 DOI: 10.3390/genes13122310] [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: 11/15/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 12/14/2022] Open
Abstract
As a distinguished Chinese indigenous pig breed that exhibits disease resistance and high meat quality, the Anqing six-end-white (AQ) pig represents a valuable germplasm resource for improving the quality of the pig breeding industry. In this study, 24 AQ pigs that were distantly blood-related and 6 Asian Wild Boar (AWB) were selected for 10× deep-genome resequencing. The signatures of the selection were analyzed to explore the genetic basis of their germplasm characteristics and to identify excellent germplasm-related functional genes based on NGS data. A total of 49,289,052 SNPs and 6,186,123 indels were detected across the genome in 30 pigs. Most of the genetic variations were synonym mutations and existed in the intergenic region. We identified 275 selected regions (top 1%) harboring 85 genes by applying a crossover approach based on genetic differentiation (FST) and polymorphism levels (π ratio). Some genes were found to be positively selected in AQ pigs' breeding. The SMPD4 and DDX18 genes were involved in the immune response to pseudorabies virus (PRV) and porcine reproductive and respiratory syndrome virus (PRRSV). The BCL6 and P2RX6 genes were involved in biological regulation of immune T cells and phagocytes. The SLC7A4 and SPACA4 genes were related to reproductive performance. The MSTN and HIF1A genes were related to fat deposition and muscle development. Moreover, 138 overlapping regions were detected in selected regions and ROH islands of AQ pigs. Additionally, we found that the QTLs with the most overlapping regions were related to back fat thickness, meat color, pH value, fatty acid content, immune cells, parasitic immunity, and bacterial immunity. Based on functional enrichment analysis and QTLs mapping, we conducted further research on the molecular genetic basis of germplasm traits (disease resistance and excellent meat quality). These results are a reliable resource for conserving germplasm resources and exploiting molecular markers of AQ pigs.
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17
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Pepke ML, Kvalnes T, Lundregan S, Boner W, Monaghan P, Saether BE, Jensen H, Ringsby TH. Genetic architecture and heritability of early-life telomere length in a wild passerine. Mol Ecol 2022; 31:6360-6381. [PMID: 34825754 DOI: 10.1111/mec.16288] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 10/01/2021] [Accepted: 11/09/2021] [Indexed: 01/31/2023]
Abstract
Early-life telomere length (TL) is associated with fitness in a range of organisms. Little is known about the genetic basis of variation in TL in wild animal populations, but to understand the evolutionary and ecological significance of TL it is important to quantify the relative importance of genetic and environmental variation in TL. In this study, we measured TL in 2746 house sparrow nestlings sampled across 20 years and used an animal model to show that there is a small heritable component of early-life TL (h2 = 0.04). Variation in TL among individuals was mainly driven by environmental (annual) variance, but also brood and parental effects. Parent-offspring regressions showed a large maternal inheritance component in TL ( h maternal 2 = 0.44), but no paternal inheritance. We did not find evidence for a negative genetic correlation underlying the observed negative phenotypic correlation between TL and structural body size. Thus, TL may evolve independently of body size and the negative phenotypic correlation is likely to be caused by nongenetic environmental effects. We further used genome-wide association analysis to identify genomic regions associated with TL variation. We identified several putative genes underlying TL variation; these have been inferred to be involved in oxidative stress, cellular growth, skeletal development, cell differentiation and tumorigenesis in other species. Together, our results show that TL has a low heritability and is a polygenic trait strongly affected by environmental conditions in a free-living bird.
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Affiliation(s)
- Michael Le Pepke
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Thomas Kvalnes
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Sarah Lundregan
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Winnie Boner
- Institute of Biodiversity, Animal Health and Comparative Medicine (IBAHCM), University of Glasgow, Glasgow, UK
| | - Pat Monaghan
- Institute of Biodiversity, Animal Health and Comparative Medicine (IBAHCM), University of Glasgow, Glasgow, UK
| | - Bernt-Erik Saether
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Henrik Jensen
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Thor Harald Ringsby
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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18
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Lundregan SL, Mäkinen H, Buer A, Holand H, Jensen H, Husby A. Infection by a helminth parasite is associated with changes in DNA methylation in the house sparrow. Ecol Evol 2022; 12:e9539. [PMID: 36447599 PMCID: PMC9702581 DOI: 10.1002/ece3.9539] [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: 05/07/2022] [Revised: 10/24/2022] [Accepted: 11/03/2022] [Indexed: 11/29/2022] Open
Abstract
Parasites can exert strong selective pressures on their hosts and influence the evolution of host immunity. While several studies have examined the genetic basis for parasite resistance, the role of epigenetics in the immune response to parasites is less understood. Yet, epigenetic modifications, such as changes in DNA methylation, may allow species to respond rapidly to parasite prevalence or virulence. To test the role of DNA methylation in relation to parasite infection, we examined genome-wide DNA methylation before and during infection by a parasitic nematode, Syngamus trachea, in a natural population of house sparrows (Passer domesticus) using reduced representation bisulfite sequencing (RRBS). We found that DNA methylation levels were slightly lower in infected house sparrows, and we identified candidate genes relating to the initial immune response, activation of innate and adaptive immunity, and mucus membrane functional integrity that were differentially methylated between infected and control birds. Subsequently, we used methylation-sensitive high-resolution melting (MS-HRM) analyses to verify the relationship between methylation proportion and S. trachea infection status at two candidate genes in a larger sample dataset. We found that methylation level at NR1D1, but not CLDN22, remained related to infection status and that juvenile recruitment probability was positively related to methylation level at NR1D1. This underscores the importance of performing follow-up studies on candidate genes. Our findings demonstrate that plasticity in the immune response to parasites can be epigenetically mediated and highlight the potential for epigenetic studies in natural populations to provide further mechanistic insight into host-parasite interactions.
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Affiliation(s)
- Sarah L. Lundregan
- Department of Biology, Centre for Biodiversity DynamicsNorwegian University of Science and TechnologyTrondheimNorway
| | - Hannu Mäkinen
- Department of Biology, Centre for Biodiversity DynamicsNorwegian University of Science and TechnologyTrondheimNorway
- Evolutionary Biology, Department of Ecology and GeneticsUppsala UniversityUppsalaSweden
| | - Amberly Buer
- Department of Biology, Centre for Biodiversity DynamicsNorwegian University of Science and TechnologyTrondheimNorway
| | - Håkon Holand
- Department of Biology, Centre for Biodiversity DynamicsNorwegian University of Science and TechnologyTrondheimNorway
| | - Henrik Jensen
- Department of Biology, Centre for Biodiversity DynamicsNorwegian University of Science and TechnologyTrondheimNorway
| | - Arild Husby
- Department of Biology, Centre for Biodiversity DynamicsNorwegian University of Science and TechnologyTrondheimNorway
- Evolutionary Biology, Department of Ecology and GeneticsUppsala UniversityUppsalaSweden
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19
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Arnqvist G, Sayadi A. A possible genomic footprint of polygenic adaptation on population divergence in seed beetles? Ecol Evol 2022; 12:e9440. [PMID: 36311399 PMCID: PMC9608792 DOI: 10.1002/ece3.9440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 09/14/2022] [Accepted: 09/29/2022] [Indexed: 11/25/2022] Open
Abstract
Efforts to unravel the genomic basis of incipient speciation are hampered by a mismatch between our toolkit and our understanding of the ecology and genetics of adaptation. While the former is focused on detecting selective sweeps involving few independently acting or linked speciation genes, the latter states that divergence typically occurs in polygenic traits under stabilizing selection. Here, we ask whether a role of stabilizing selection on polygenic traits in population divergence may be unveiled by using a phenotypically informed integrative approach, based on genome‐wide variation segregating in divergent populations. We compare three divergent populations of seed beetles (Callosobruchus maculatus) where previous work has demonstrated a prominent role for stabilizing selection on, and population divergence in, key life history traits that reflect rate‐dependent metabolic processes. We derive and assess predictions regarding the expected pattern of covariation between genetic variation segregating within populations and genetic differentiation between populations. Population differentiation was considerable (mean FST = 0.23–0.26) and was primarily built by genes showing high selective constraints and an imbalance in inferred selection in different populations (positive Tajima's DNS in one and negative in one), and this set of genes was enriched with genes with a metabolic function. Repeatability of relative population differentiation was low at the level of individual genes but higher at the level of broad functional classes, again spotlighting metabolic genes. Absolute differentiation (dXY) showed a very different general pattern at this scale of divergence, more consistent with an important role for genetic drift. Although our exploration is consistent with stabilizing selection on polygenic metabolic phenotypes as an important engine of genome‐wide relative population divergence and incipient speciation in our study system, we note that it is exceedingly difficult to firmly exclude other scenarios.
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Affiliation(s)
- Göran Arnqvist
- Animal Ecology, Department of Ecology and Genetics, EBCUppsala UniversityUppsalaSweden
| | - Ahmed Sayadi
- Animal Ecology, Department of Ecology and Genetics, EBCUppsala UniversityUppsalaSweden,Rheumatology, Department of Medical SciencesUppsala UniversityUppsalaSweden
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20
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Dorant Y, Laporte M, Rougemont Q, Cayuela H, Rochette R, Bernatchez L. Landscape genomics of the American lobster (Homarus americanus). Mol Ecol 2022; 31:5182-5200. [PMID: 35960266 DOI: 10.1111/mec.16653] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 08/03/2022] [Accepted: 08/08/2022] [Indexed: 01/07/2023]
Abstract
In marine species experiencing intense fishing pressures, knowledge of genetic structure and local adaptation represent a critical information to assist sustainable management. In this study, we performed a landscape genomics analysis in the American lobster to investigate the issues pertaining to the consequences of making use of putative adaptive loci to reliably infer population structure and thus more rigorously delineating biological management units in marine exploited species. Toward this end, we genotyped 14,893 single nucleotide polymorphism (SNPs) in 4190 lobsters sampled across 96 sampling sites distributed along 1000 km in the northwest Atlantic in both Canada and the USA. As typical for most marine species, we observed a weak, albeit highly significant genetic structure. We also found that adaptive genetic variation allows detecting fine-scale population structure not resolved by neutral genetic variation alone. Using the recent genome assembly of the American lobster, we were able to map and annotate several SNPs located in functional genes potentially implicated in adaptive processes such as thermal stress response, salinity tolerance and growth metabolism pathways. Taken together, our study indicates that weak population structure in high gene flow systems can be resolved at various spatial scales, and that putatively adaptive genetic variation can substantially enhance the delineation of biological management units of marine exploited species.
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Affiliation(s)
- Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- IHPE, CNRS, Ifremer, Université de Montpellier, Université de Perpignan Via Domitia, Montpellier, France
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Ministère des Forêts de la Faune et des Parcs du Québec, Québec, Québec, Canada
| | - Quentin Rougemont
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- CEFE, CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
| | - Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- Laboratoire de Biométrie et Biologie Évolutive, CNRS, Université Lyon 1, Villeurbanne, France
| | - Rémy Rochette
- Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
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21
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Hendricks SA, King JL, Duncan CL, Vickers W, Hohenlohe PA, Davis BW. Genomic Assessment of Cancer Susceptibility in the Threatened Catalina Island Fox ( Urocyon littoralis catalinae). Genes (Basel) 2022; 13:1496. [PMID: 36011407 PMCID: PMC9408614 DOI: 10.3390/genes13081496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 12/12/2022] Open
Abstract
Small effective population sizes raise the probability of extinction by increasing the frequency of potentially deleterious alleles and reducing fitness. However, the extent to which cancers play a role in the fitness reduction of genetically depauperate wildlife populations is unknown. Santa Catalina island foxes (Urocyon littoralis catalinae) sampled in 2007-2008 have a high prevalence of ceruminous gland tumors, which was not detected in the population prior to a recent bottleneck caused by a canine distemper epidemic. The disease appears to be associated with inflammation from chronic ear mite (Otodectes) infections and secondary elevated levels of Staphyloccus pseudointermedius bacterial infections. However, no other environmental factors to date have been found to be associated with elevated cancer risk in this population. Here, we used whole genome sequencing of the case and control individuals from two islands to identify candidate loci associated with cancer based on genetic divergence, nucleotide diversity, allele frequency spectrum, and runs of homozygosity. We identified several candidate loci based on genomic signatures and putative gene functions, suggesting that cancer susceptibility in this population may be polygenic. Due to the efforts of a recovery program and weak fitness effects of late-onset disease, the population size has increased, which may allow selection to be more effective in removing these presumably slightly deleterious alleles. Long-term monitoring of the disease alleles, as well as overall genetic diversity, will provide crucial information for the long-term persistence of this threatened population.
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Affiliation(s)
- Sarah A. Hendricks
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Julie L. King
- Catalina Island Conservancy, P.O. Box 2739, Avalon, CA 90704, USA
| | - Calvin L. Duncan
- Catalina Island Conservancy, P.O. Box 2739, Avalon, CA 90704, USA
| | - Winston Vickers
- Institute for Wildlife Studies, Arcata, CA 95521, USA
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Paul A. Hohenlohe
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID 83844, USA
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Brian W. Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Science, Texas A&M University, College Station, TX 77840, USA
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Science, Texas A&M University, College Station, TX 77840, USA
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22
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Momen M, Brounts SH, Binversie EE, Sample SJ, Rosa GJM, Davis BW, Muir P. Selection signature analyses and genome-wide association reveal genomic hotspot regions that reflect differences between breeds of horse with contrasting risk of degenerative suspensory ligament desmitis. G3 (BETHESDA, MD.) 2022; 12:6648349. [PMID: 35866615 PMCID: PMC9526059 DOI: 10.1093/g3journal/jkac179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 06/08/2022] [Indexed: 01/07/2023]
Abstract
Degenerative suspensory ligament desmitis is a progressive idiopathic condition that leads to scarring and rupture of suspensory ligament fibers in multiple limbs in horses. The prevalence of degenerative suspensory ligament desmitis is breed related. Risk is high in the Peruvian Horse, whereas pony and draft breeds have low breed risk. Degenerative suspensory ligament desmitis occurs in families of Peruvian Horses, but its genetic architecture has not been definitively determined. We investigated contrasts between breeds with differing risk of degenerative suspensory ligament desmitis and identified associated risk variants and candidate genes. We analyzed 670k single nucleotide polymorphisms from 10 breeds, each of which was assigned one of the four breed degenerative suspensory ligament desmitis risk categories: control (Belgian, Icelandic Horse, Shetland Pony, and Welsh Pony), low risk (Lusitano, Arabian), medium risk (Standardbred, Thoroughbred, Quarter Horse), and high risk (Peruvian Horse). Single nucleotide polymorphisms were used for genome-wide association and selection signature analysis using breed-assigned risk levels. We found that the Peruvian Horse is a population with low effective population size and our breed contrasts suggest that degenerative suspensory ligament desmitis is a polygenic disease. Variant frequency exhibited signatures of positive selection across degenerative suspensory ligament desmitis breed risk groups on chromosomes 7, 18, and 23. Our results suggest degenerative suspensory ligament desmitis breed risk is associated with disturbances to suspensory ligament homeostasis where matrix responses to mechanical loading are perturbed through disturbances to aging in tendon (PIN1), mechanotransduction (KANK1, KANK2, JUNB, SEMA7A), collagen synthesis (COL4A1, COL5A2, COL5A3, COL6A5), matrix responses to hypoxia (PRDX2), lipid metabolism (LDLR, VLDLR), and BMP signaling (GREM2). Our results do not suggest that suspensory ligament proteoglycan turnover is a primary factor in disease pathogenesis.
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Affiliation(s)
- Mehdi Momen
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sabrina H Brounts
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Emily E Binversie
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Susannah J Sample
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Guilherme J M Rosa
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Peter Muir
- Corresponding author: Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA.
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23
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Rubin CJ, Enbody ED, Dobreva MP, Abzhanov A, Davis BW, Lamichhaney S, Pettersson M, Sendell-Price AT, Sprehn CG, Valle CA, Vasco K, Wallerman O, Grant BR, Grant PR, Andersson L. Rapid adaptive radiation of Darwin's finches depends on ancestral genetic modules. SCIENCE ADVANCES 2022; 8:eabm5982. [PMID: 35857449 PMCID: PMC9269886 DOI: 10.1126/sciadv.abm5982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 05/25/2022] [Indexed: 05/21/2023]
Abstract
Recent adaptive radiations are models for investigating mechanisms contributing to the evolution of biodiversity. An unresolved question is the relative importance of new mutations, ancestral variants, and introgressive hybridization for phenotypic evolution and speciation. Here, we address this issue using Darwin's finches and investigate the genomic architecture underlying their phenotypic diversity. Admixture mapping for beak and body size in the small, medium, and large ground finches revealed 28 loci showing strong genetic differentiation. These loci represent ancestral haplotype blocks with origins predating speciation events during the Darwin's finch radiation. Genes expressed in the developing beak are overrepresented in these genomic regions. Ancestral haplotypes constitute genetic modules for selection and act as key determinants of the unusual phenotypic diversity of Darwin's finches. Such ancestral haplotype blocks can be critical for how species adapt to environmental variability and change.
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Affiliation(s)
- Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Institute of Marine Research, Nordnesgaten 50, 5005 Bergen, Norway
| | - Erik D. Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mariya P. Dobreva
- Department of Life Sciences, Imperial College London, Silwood Park Campus, SL5 7PY Ascot, UK
| | - Arhat Abzhanov
- Department of Life Sciences, Imperial College London, Silwood Park Campus, SL5 7PY Ascot, UK
| | - Brian W. Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | | | - Mats Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ashley T. Sendell-Price
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK
| | - C. Grace Sprehn
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Carlos A. Valle
- Colegio de Ciencias Biológicas y Ambientales, Galápagos Science Center GSC, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Karla Vasco
- Colegio de Ciencias Biológicas y Ambientales, Galápagos Science Center GSC, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - B. Rosemary Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Peter R. Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - 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
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Corresponding author.
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24
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Anderson SJ, Côté SD, Richard JH, Shafer ABA. Genomic architecture of phenotypic extremes in a wild cervid. BMC Genomics 2022; 23:126. [PMID: 35151275 PMCID: PMC8841092 DOI: 10.1186/s12864-022-08333-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/24/2022] [Indexed: 12/30/2022] Open
Abstract
Identifying the genes underlying fitness-related traits such as body size and male ornamentation can provide tools for conservation and management and are often subject to various selective pressures. Here we performed high-depth whole genome re-sequencing of pools of individuals representing the phenotypic extremes for antler and body size in white-tailed deer (Odocoileus virginianus). Samples were selected from a tissue repository containing phenotypic data for 4,466 male white-tailed deer from Anticosti Island, Quebec, with four pools representing the extreme phenotypes for antler and body size after controlling for age. Our results revealed a largely homogenous population but detected highly divergent windows between pools for both traits, with the mean allele frequency difference of 14% for and 13% for antler and body SNPs in outlier windows, respectively. Genes in outlier antler windows were enriched for pathways associated with cell death and protein metabolism and some of the most differentiated windows included genes associated with oncogenic pathways and reproduction, processes consistent with antler evolution and growth. Genes associated with body size were more nuanced, suggestive of a highly complex trait. Overall, this study revealed the complex genomic make-up of both antler morphology and body size in free-ranging white-tailed deer and identified target loci for additional analyses.
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25
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Andersen EC, Rockman MV. Natural genetic variation as a tool for discovery in Caenorhabditis nematodes. Genetics 2022; 220:iyab156. [PMID: 35134197 PMCID: PMC8733454 DOI: 10.1093/genetics/iyab156] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 09/11/2021] [Indexed: 11/12/2022] Open
Abstract
Over the last 20 years, studies of Caenorhabditis elegans natural diversity have demonstrated the power of quantitative genetic approaches to reveal the evolutionary, ecological, and genetic factors that shape traits. These studies complement the use of the laboratory-adapted strain N2 and enable additional discoveries not possible using only one genetic background. In this chapter, we describe how to perform quantitative genetic studies in Caenorhabditis, with an emphasis on C. elegans. These approaches use correlations between genotype and phenotype across populations of genetically diverse individuals to discover the genetic causes of phenotypic variation. We present methods that use linkage, near-isogenic lines, association, and bulk-segregant mapping, and we describe the advantages and disadvantages of each approach. The power of C. elegans quantitative genetic mapping is best shown in the ability to connect phenotypic differences to specific genes and variants. We will present methods to narrow genomic regions to candidate genes and then tests to identify the gene or variant involved in a quantitative trait. The same features that make C. elegans a preeminent experimental model animal contribute to its exceptional value as a tool to understand natural phenotypic variation.
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Affiliation(s)
- Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Matthew V Rockman
- Department of Biology and Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
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26
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De La Torre AR, Sekhwal MK, Neale DB. Selective Sweeps and Polygenic Adaptation Drive Local Adaptation along Moisture and Temperature Gradients in Natural Populations of Coast Redwood and Giant Sequoia. Genes (Basel) 2021; 12:1826. [PMID: 34828432 PMCID: PMC8621000 DOI: 10.3390/genes12111826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/18/2021] [Accepted: 11/18/2021] [Indexed: 12/26/2022] Open
Abstract
Dissecting the genomic basis of local adaptation is a major goal in evolutionary biology and conservation science. Rapid changes in the climate pose significant challenges to the survival of natural populations, and the genomic basis of long-generation plant species is still poorly understood. Here, we investigated genome-wide climate adaptation in giant sequoia and coast redwood, two iconic and ecologically important tree species. We used a combination of univariate and multivariate genotype-environment association methods and a selective sweep analysis using non-overlapping sliding windows. We identified genomic regions of potential adaptive importance, showing strong associations to moisture variables and mean annual temperature. Our results found a complex architecture of climate adaptation in the species, with genomic regions showing signatures of selective sweeps, polygenic adaptation, or a combination of both, suggesting recent or ongoing climate adaptation along moisture and temperature gradients in giant sequoia and coast redwood. The results of this study provide a first step toward identifying genomic regions of adaptive significance in the species and will provide information to guide management and conservation strategies that seek to maximize adaptive potential in the face of climate change.
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Affiliation(s)
- Amanda R. De La Torre
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, Flagstaff, AZ 86011, USA;
| | - Manoj K. Sekhwal
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, Flagstaff, AZ 86011, USA;
| | - David B. Neale
- Department of Plant Sciences, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA
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27
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Johri P, Charlesworth B, Howell EK, Lynch M, Jensen JD. Revisiting the notion of deleterious sweeps. Genetics 2021; 219:iyab094. [PMID: 34125884 PMCID: PMC9101445 DOI: 10.1093/genetics/iyab094] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/08/2021] [Indexed: 11/14/2022] Open
Abstract
It has previously been shown that, conditional on its fixation, the time to fixation of a semi-dominant deleterious autosomal mutation in a randomly mating population is the same as that of an advantageous mutation. This result implies that deleterious mutations could generate selective sweep-like effects. Although their fixation probabilities greatly differ, the much larger input of deleterious relative to beneficial mutations suggests that this phenomenon could be important. We here examine how the fixation of mildly deleterious mutations affects levels and patterns of polymorphism at linked sites-both in the presence and absence of interference amongst deleterious mutations-and how this class of sites may contribute to divergence between-populations and species. We find that, while deleterious fixations are unlikely to represent a significant proportion of outliers in polymorphism-based genomic scans within populations, minor shifts in the frequencies of deleterious mutations can influence the proportions of private variants and the value of FST after a recent population split. As sites subject to deleterious mutations are necessarily found in functional genomic regions, interpretations in terms of recurrent positive selection may require reconsideration.
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Affiliation(s)
- Parul Johri
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Emma K Howell
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Michael Lynch
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
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28
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Vu NTT, Zenger KR, Silva CNS, Guppy JL, Jerry DR. Population Structure, Genetic Connectivity, and Signatures of Local Adaptation of the Giant Black Tiger Shrimp (Penaeus monodon) throughout the Indo-Pacific Region. Genome Biol Evol 2021; 13:evab214. [PMID: 34529049 PMCID: PMC8495139 DOI: 10.1093/gbe/evab214] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2021] [Indexed: 12/04/2022] Open
Abstract
The giant black tiger shrimp (Penaeus monodon) is native to the Indo-Pacific and is the second most farmed penaeid shrimp species globally. Understanding genetic structure, connectivity, and local adaptation among Indo-Pacific black tiger shrimp populations is important for informing sustainable fisheries management and aquaculture breeding programs. Population genetic and outlier detection analyses were undertaken using 10,593 genome-wide single nucleotide polymorphisms (SNPs) from 16 geographically disparate Indo-Pacific P. monodon populations. Levels of genetic diversity were highest for Southeast Asian populations and were lowest for Western Indian Ocean (WIO) populations. Both neutral (n = 9,930) and outlier (n = 663) loci datasets revealed a pattern of strong genetic structure of P. monodon corresponding with broad geographical regions and clear genetic breaks among samples within regions. Neutral loci revealed seven genetic clusters and the separation of Fiji and WIO clusters from all other clusters, whereas outlier loci revealed six genetic clusters and high genetic differentiation among populations. The neutral loci dataset estimated five migration events that indicated migration to Southeast Asia from the WIO, with partial connectivity to populations in both oceans. We also identified 26 putatively adaptive SNPs that exhibited significant Pearson correlation (P < 0.05) between minor allele frequency and maximum or minimum sea surface temperature. Matched transcriptome contig annotations suggest putatively adaptive SNPs involvement in cellular and metabolic processes, pigmentation, immune response, and currently unknown functions. This study provides novel genome-level insights that have direct implications for P. monodon aquaculture and fishery management practices.
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Affiliation(s)
- Nga T T Vu
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Kyall R Zenger
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Catarina N S Silva
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Jarrod L Guppy
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Dean R Jerry
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Tropical Futures Institute, James Cook University, Singapore
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29
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Tietgen L, Hagen IJ, Kleven O, Bernardi CD, Kvalnes T, Norén K, Hasselgren M, Wallén JF, Angerbjörn A, Landa A, Eide NE, Flagstad Ø, Jensen H. Fur colour in the Arctic fox: genetic architecture and consequences for fitness. Proc Biol Sci 2021; 288:20211452. [PMID: 34583587 PMCID: PMC8479361 DOI: 10.1098/rspb.2021.1452] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Genome-wide association studies provide good opportunities for studying the genetic basis of adaptive traits in wild populations. Yet, previous studies often failed to identify major effect genes. In this study, we used high-density single nucleotide polymorphism and individual fitness data from a wild non-model species. Using a whole-genome approach, we identified the MC1R gene as the sole causal gene underlying Arctic fox Vulpes lagopus fur colour. Further, we showed the adaptive importance of fur colour genotypes through measures of fitness that link ecological and evolutionary processes. We found a tendency for blue foxes that are heterozygous at the fur colour locus to have higher fitness than homozygous white foxes. The effect of genotype on fitness was independent of winter duration but varied with prey availability, with the strongest effect in years of increasing rodent populations. MC1R is located in a genomic region with high gene density, and we discuss the potential for indirect selection through linkage and pleiotropy. Our study shows that whole-genome analyses can be successfully applied to wild species and identify major effect genes underlying adaptive traits. Furthermore, we show how this approach can be used to identify knowledge gaps in our understanding of interactions between ecology and evolution.
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Affiliation(s)
- Lukas Tietgen
- Centre for Biodiversity Dynamics (CBD), Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway.,Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway
| | - Ingerid J Hagen
- Centre for Biodiversity Dynamics (CBD), Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway.,Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway
| | - Oddmund Kleven
- Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway
| | - Cecilia Di Bernardi
- Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway.,Department of Biology and Biotechnologies 'Charles Darwin', University of Rome La Sapienza, Viale dell' Università 32, Rome 00185, Italy
| | - Thomas Kvalnes
- Centre for Biodiversity Dynamics (CBD), Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway
| | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Malin Hasselgren
- Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Johan Fredrik Wallén
- Department of Zoology, Stockholm University, Stockholm 10691, Sweden.,Swedish Museum of Natural History, Stockholm 10405, Sweden
| | - Anders Angerbjörn
- Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Arild Landa
- Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway
| | - Nina E Eide
- Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway
| | - Øystein Flagstad
- Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway
| | - Henrik Jensen
- Centre for Biodiversity Dynamics (CBD), Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway
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30
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Johnsson M, Henriksen R, Wright D. The neural crest cell hypothesis: no unified explanation for domestication. Genetics 2021; 219:iyab097. [PMID: 34849908 PMCID: PMC8633120 DOI: 10.1093/genetics/iyab097] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/11/2021] [Indexed: 12/03/2022] Open
Affiliation(s)
- Martin Johnsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Rie Henriksen
- IFM Biology, Linköping University, Linköping 58183, Sweden
| | - Dominic Wright
- IFM Biology, Linköping University, Linköping 58183, Sweden
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31
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Rodrigues MF, Vibranovski MD, Cogni R. Clinal and seasonal changes are correlated in Drosophila melanogaster natural populations. Evolution 2021; 75:2042-2054. [PMID: 34184262 DOI: 10.1111/evo.14300] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 12/22/2022]
Abstract
Spatial and seasonal variations in the environment are ubiquitous. Environmental heterogeneity can affect natural populations and lead to covariation between environment and allele frequencies. Drosophila melanogaster is known to harbor polymorphisms that change both with latitude and seasons. Identifying the role of selection in driving these changes is not trivial, because nonadaptive processes can cause similar patterns. Given the environment changes in similar ways across seasons and along the latitudinal gradient, one promising approach may be to look for parallelism between clinal and seasonal changes. Here, we test whether there is a genome-wide correlation between clinal and seasonal changes, and whether the pattern is consistent with selection. Allele frequency estimates were obtained from pooled samples from seven different locations along the east coast of the United States, and across seasons within Pennsylvania. We show that there is a genome-wide correlation between clinal and seasonal variations, which cannot be explained by linked selection alone. This pattern is stronger in genomic regions with higher functional content, consistent with natural selection. We derive a way to biologically interpret these correlations and show that around 3.7% of the common, autosomal variants could be under parallel seasonal and spatial selection. Our results highlight the contribution of natural selection in driving fluctuations in allele frequencies in natural fly populations and point to a shared genomic basis to climate adaptation that happens over space and time in D. melanogaster.
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Affiliation(s)
- Murillo F Rodrigues
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil.,Current Address: Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, 97403
| | - Maria D Vibranovski
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil
| | - Rodrigo Cogni
- Department of Ecology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil
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32
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Bourgeois YXC, Warren BH. An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes. Mol Ecol 2021; 30:6036-6071. [PMID: 34009688 DOI: 10.1111/mec.15989] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/26/2021] [Accepted: 05/11/2021] [Indexed: 01/01/2023]
Abstract
Characterizing the population history of a species and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy. The constant improvement of high-throughput sequencing techniques has facilitated the production of whole genome data in a wide range of species. Population genomics now provides tools to better integrate selection into a historical framework, and take into account selection when reconstructing demographic history. However, this improvement has come with a profusion of analytical tools that can confuse and discourage users. Such confusion limits the amount of information effectively retrieved from complex genomic data sets, and impairs the diffusion of the most recent analytical tools into fields such as conservation biology. It may also lead to redundancy among methods. To address these isssues, we propose an overview of more than 100 state-of-the-art methods that can deal with whole genome data. We summarize the strategies they use to infer demographic history and selection, and discuss some of their limitations. A website listing these methods is available at www.methodspopgen.com.
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Affiliation(s)
| | - Ben H Warren
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, CP 51, Paris, France
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33
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Herrera-Álvarez S, Karlsson E, Ryder OA, Lindblad-Toh K, Crawford AJ. How to Make a Rodent Giant: Genomic Basis and Tradeoffs of Gigantism in the Capybara, the World's Largest Rodent. Mol Biol Evol 2021; 38:1715-1730. [PMID: 33169792 PMCID: PMC8097284 DOI: 10.1093/molbev/msaa285] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Gigantism results when one lineage within a clade evolves extremely large body size relative to its small-bodied ancestors, a common phenomenon in animals. Theory predicts that the evolution of giants should be constrained by two tradeoffs. First, because body size is negatively correlated with population size, purifying selection is expected to be less efficient in species of large body size, leading to increased mutational load. Second, gigantism is achieved through generating a higher number of cells along with higher rates of cell proliferation, thus increasing the likelihood of cancer. To explore the genetic basis of gigantism in rodents and uncover genomic signatures of gigantism-related tradeoffs, we assembled a draft genome of the capybara (Hydrochoerus hydrochaeris), the world's largest living rodent. We found that the genome-wide ratio of nonsynonymous to synonymous mutations (ω) is elevated in the capybara relative to other rodents, likely caused by a generation-time effect and consistent with a nearly neutral model of molecular evolution. A genome-wide scan for adaptive protein evolution in the capybara highlighted several genes controlling postnatal bone growth regulation and musculoskeletal development, which are relevant to anatomical and developmental modifications for an increase in overall body size. Capybara-specific gene-family expansions included a putative novel anticancer adaptation that involves T-cell-mediated tumor suppression, offering a potential resolution to the increased cancer risk in this lineage. Our comparative genomic results uncovered the signature of an intragenomic conflict where the evolution of gigantism in the capybara involved selection on genes and pathways that are directly linked to cancer.
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Affiliation(s)
| | - Elinor Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, Escondido, CA, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
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Nosková A, Bhati M, Kadri NK, Crysnanto D, Neuenschwander S, Hofer A, Pausch H. Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs. BMC Genomics 2021; 22:290. [PMID: 33882824 PMCID: PMC8061004 DOI: 10.1186/s12864-021-07610-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/13/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The key-ancestor approach has been frequently applied to prioritize individuals for whole-genome sequencing based on their marginal genetic contribution to current populations. Using this approach, we selected 70 key ancestors from two lines of the Swiss Large White breed that have been selected divergently for fertility and fattening traits and sequenced their genomes with short paired-end reads. RESULTS Using pedigree records, we estimated the effective population size of the dam and sire line to 72 and 44, respectively. In order to assess sequence variation in both lines, we sequenced the genomes of 70 boars at an average coverage of 16.69-fold. The boars explained 87.95 and 95.35% of the genetic diversity of the breeding populations of the dam and sire line, respectively. Reference-guided variant discovery using the GATK revealed 26,862,369 polymorphic sites. Principal component, admixture and fixation index (FST) analyses indicated considerable genetic differentiation between the lines. Genomic inbreeding quantified using runs of homozygosity was higher in the sire than dam line (0.28 vs 0.26). Using two complementary approaches, we detected 51 signatures of selection. However, only six signatures of selection overlapped between both lines. We used the sequenced haplotypes of the 70 key ancestors as a reference panel to call 22,618,811 genotypes in 175 pigs that had been sequenced at very low coverage (1.11-fold) using the GLIMPSE software. The genotype concordance, non-reference sensitivity and non-reference discrepancy between thus inferred and Illumina PorcineSNP60 BeadChip-called genotypes was 97.60, 98.73 and 3.24%, respectively. The low-pass sequencing-derived genomic relationship coefficients were highly correlated (r > 0.99) with those obtained from microarray genotyping. CONCLUSIONS We assessed genetic diversity within and between two lines of the Swiss Large White pig breed. Our analyses revealed considerable differentiation, even though the split into two populations occurred only few generations ago. The sequenced haplotypes of the key ancestor animals enabled us to implement genotyping by low-pass sequencing which offers an intriguing cost-effective approach to increase the variant density over current array-based genotyping by more than 350-fold.
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Affiliation(s)
- Adéla Nosková
- Animal Genomics, ETH Zürich, Eschikon 27, 8315, Lindau, Switzerland.
| | - Meenu Bhati
- Animal Genomics, ETH Zürich, Eschikon 27, 8315, Lindau, Switzerland
| | | | - Danang Crysnanto
- Animal Genomics, ETH Zürich, Eschikon 27, 8315, Lindau, Switzerland
| | | | | | - Hubert Pausch
- Animal Genomics, ETH Zürich, Eschikon 27, 8315, Lindau, Switzerland
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Olazcuaga L, Loiseau A, Parrinello H, Paris M, Fraimout A, Guedot C, Diepenbrock LM, Kenis M, Zhang J, Chen X, Borowiec N, Facon B, Vogt H, Price DK, Vogel H, Prud'homme B, Estoup A, Gautier M. A Whole-Genome Scan for Association with Invasion Success in the Fruit Fly Drosophila suzukii Using Contrasts of Allele Frequencies Corrected for Population Structure. Mol Biol Evol 2021; 37:2369-2385. [PMID: 32302396 PMCID: PMC7403613 DOI: 10.1093/molbev/msaa098] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Evidence is accumulating that evolutionary changes are not only common during biological invasions but may also contribute directly to invasion success. The genomic basis of such changes is still largely unexplored. Yet, understanding the genomic response to invasion may help to predict the conditions under which invasiveness can be enhanced or suppressed. Here, we characterized the genome response of the spotted wing drosophila Drosophila suzukii during the worldwide invasion of this pest insect species, by conducting a genome-wide association study to identify genes involved in adaptive processes during invasion. Genomic data from 22 population samples were analyzed to detect genetic variants associated with the status (invasive versus native) of the sampled populations based on a newly developed statistic, we called C2, that contrasts allele frequencies corrected for population structure. We evaluated this new statistical framework using simulated data sets and implemented it in an upgraded version of the program BayPass. We identified a relatively small set of single-nucleotide polymorphisms that show a highly significant association with the invasive status of D. suzukii populations. In particular, two genes, RhoGEF64C and cpo, contained single-nucleotide polymorphisms significantly associated with the invasive status in the two separate main invasion routes of D. suzukii. Our methodological approaches can be applied to any other invasive species, and more generally to any evolutionary model for species characterized by nonequilibrium demographic conditions for which binary covariables of interest can be defined at the population level.
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Affiliation(s)
- Laure Olazcuaga
- INRAE, UMR CBGP (INRAE-IRD-Cirad - Montpellier SupAgro), Montferrier-sur-Lez, France
| | - Anne Loiseau
- INRAE, UMR CBGP (INRAE-IRD-Cirad - Montpellier SupAgro), Montferrier-sur-Lez, France
| | - Hugues Parrinello
- MGX, Biocampus Montpellier, CNRS, INSERM, Universite de Montpellier, Montpellier, France
| | | | - Antoine Fraimout
- INRAE, UMR CBGP (INRAE-IRD-Cirad - Montpellier SupAgro), Montferrier-sur-Lez, France
| | | | | | | | - Jinping Zhang
- MoA-CABI Joint Laboratory for Bio-Safety, Chinese Academy of Agricultural Sciences, BeiXiaGuan, Haidian Qu, China
| | - Xiao Chen
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan Province, China
| | - Nicolas Borowiec
- UMR INRAE-CNRS-Université Côte d'Azur Sophia Agrobiotech Institute, Sophia Antipolis, France
| | - Benoit Facon
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, INRAE, Saint-Pierre, La Réunion, France
| | - Heidrun Vogt
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Dossenheim, Germany
| | - Donald K Price
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | - Arnaud Estoup
- INRAE, UMR CBGP (INRAE-IRD-Cirad - Montpellier SupAgro), Montferrier-sur-Lez, France
| | - Mathieu Gautier
- INRAE, UMR CBGP (INRAE-IRD-Cirad - Montpellier SupAgro), Montferrier-sur-Lez, France
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36
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Bootsma ML, Miller L, Sass GG, Euclide PT, Larson WA. The ghosts of propagation past: haplotype information clarifies the relative influence of stocking history and phylogeographic processes on contemporary population structure of walleye ( Sander vitreus). Evol Appl 2021; 14:1124-1144. [PMID: 33897825 PMCID: PMC8061267 DOI: 10.1111/eva.13186] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 12/05/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
Stocking of fish is an important tool for maintaining fisheries but can also significantly alter population genetic structure and erode the portfolio of within-species diversity that is important for promoting resilience and adaptability. Walleye (Sander vitreus) are a highly valued sportfish in the midwestern United States, a region characterized by postglacial recolonization from multiple lineages and an extensive history of stocking. We leveraged genomic data and recently developed analytical approaches to explore the population structure of walleye from two midwestern states, Minnesota and Wisconsin. We genotyped 954 walleye from 23 populations at ~20,000 loci using genotyping by sequencing and tested for patterns of population structure with single-SNP and microhaplotype data. Populations from Minnesota and Wisconsin were highly differentiated from each other, with additional substructure found in each state. Population structure did not consistently adhere to drainage boundaries, as cases of high intra-drainage and low inter-drainage differentiation were observed. Low genetic structure was observed between populations from the upper Wisconsin and upper Chippewa river watersheds, which are found as few as 50 km apart and were likely homogenized through historical stocking. Nevertheless, we were able to differentiate these populations using microhaplotype-based co-ancestry analysis, providing increased resolution over previous microsatellite studies and our other single SNP-based analyses. Although our results illustrate that walleye population structure has been influenced by past stocking practices, native ancestry still exists in most populations and walleye populations may be able to purge non-native alleles and haplotypes in the absence of stocking. Our study is one of the first to use genomic tools to investigate the influence of stocking on population structure in a nonsalmonid fish and outlines a workflow leveraging recently developed analytical methods to improve resolution of complex population structure that will be highly applicable in many species and systems.
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Affiliation(s)
- Matthew L. Bootsma
- Wisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
| | - Loren Miller
- Minnesota Department of Natural ResourcesUniversity of MinnesotaSt. PaulMNUSA
| | - Greg G. Sass
- Office of Applied ScienceWisconsin Department of Natural ResourcesEscanaba Lake Research StationBoulder JunctionWIUSA
| | - Peter T. Euclide
- Wisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
| | - Wesley A. Larson
- U.S. Geological SurveyWisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
- Present address:
Ted Stevens Marine Research InstituteAlaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationJuneauAKUSA
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37
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Graf L, Shin Y, Yang JH, Choi JW, Hwang IK, Nelson W, Bhattacharya D, Viard F, Yoon HS. A genome-wide investigation of the effect of farming and human-mediated introduction on the ubiquitous seaweed Undaria pinnatifida. Nat Ecol Evol 2021; 5:360-368. [PMID: 33495590 PMCID: PMC7929912 DOI: 10.1038/s41559-020-01378-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023]
Abstract
Human activity is an important driver of ecological and evolutionary change on our planet. In particular, domestication and biological introductions have important and long-lasting effects on species' genomic architecture and diversity. However, genome-wide analysis of independent domestication and introduction events within a single species has not previously been performed. The Pacific kelp Undaria pinnatifida provides such an opportunity because it has been cultivated in its native range in Northeast Asia but also introduced to four other continents in the past 50 years. Here we present the results of a genome-wide analysis of natural, cultivated and introduced populations of U. pinnatifida to elucidate human-driven evolutionary change. We demonstrate that these three categories of origin can be distinguished at the genome level, reflecting the combined influence of neutral (demography and migration) and non-neutral (selection) processes.
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Affiliation(s)
- Louis Graf
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Younhee Shin
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Ji Won Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Il Ki Hwang
- Aquaculture Management Division, National Institute of Fisheries Science, Busan, South Korea
| | - Wendy Nelson
- National Institute of Water & Atmospheric Research, Wellington, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Frédérique Viard
- Sorbonne Université, CNRS, AD2M, Station Biologique de Roscoff, Roscoff, France
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea.
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Leroy T, Rougemont Q. Introduction to Population Genomics Methods. Methods Mol Biol 2021; 2222:287-324. [PMID: 33301100 DOI: 10.1007/978-1-0716-0997-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-throughput sequencing technologies have provided an unprecedented opportunity to study the different evolutionary forces that have shaped present-day patterns of genetic diversity, with important implications for many directions in plant biology research. To manage such massive quantities of sequencing data, biologists, however, need new additional skills in informatics and statistics. In this chapter, our objective is to introduce population genomics methods to beginners following a learning-by-doing strategy in order to help the reader to analyze the sequencing data by themselves. Conducted analyses cover several main areas of evolutionary biology, such as an initial description of the evolutionary history of a given species or the identification of genes targeted by natural or artificial selection. In addition to the practical advices, we performed re-analyses of two cases studies with different kind of data: a domesticated cereal (African rice) and a non-domesticated tree species (sessile oak). All the code needed to replicate this work is publicly available on github ( https://github.com/ThibaultLeroyFr/Intro2PopGenomics/ ).
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Affiliation(s)
- Thibault Leroy
- Montpellier Institute of Evolutionary Sciences (ISEM), Université de Montpellier, Montpellier, France. .,Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.
| | - Quentin Rougemont
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, QC, Canada
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39
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Rodríguez-Valera Y, Rocha D, Naves M, Renand G, Pérez-Pineda E, Ramayo-Caldas Y, Ramos-Onsins SE. The Identification of Runs of Homozygosity Gives a Focus on the Genetic Diversity and Adaptation of the "Charolais de Cuba" Cattle. Animals (Basel) 2020; 10:ani10122233. [PMID: 33261195 PMCID: PMC7760288 DOI: 10.3390/ani10122233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/23/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The Charolais de Cuba cattle is a tropical adapted breed founded in Cuba around 120 years ago from Charolais French specimens. Nowadays, it is still a closed breed and remains as a small population. In this work, we analyzed the inbreeding and diversity patterns, as well as the population size, of this recent adapted breed via a run of homozygosity (ROH) analysis. We found that the genomic inbreeding levels are higher in the Charolais de Cuba breed compared to French and British Charolais populations. Nevertheless, we detected that the effective population size experienced a very similar decline during the last century in the three Charolais populations studied. Finally, a number of regions with exceptional patterns of long homozygosity were identified in this breed, and these could be related to processes of adaptation to tropical conditions. Abstract Inbreeding and effective population size (Ne) are fundamental indicators for the management and conservation of genetic diversity in populations. Genomic inbreeding gives accurate estimates of inbreeding, and the Ne determines the rate of the loss of genetic variation. The objective of this work was to study the distribution of runs of homozygosity (ROHs) in order to estimate genomic inbreeding (FROH) and an effective population size using 38,789 Single Nucleotide Polymorphisms (SNPs) from the Illumina Bovine 50K BeadChip in 86 samples from populations of Charolais de Cuba (n = 40) cattle and to compare this information with French (n = 20) and British Charolais (n = 26) populations. In the Cuban, French, and British Charolais populations, the average estimated genomic inbreeding values using the FROH statistics were 5.7%, 3.4%, and 4%, respectively. The dispersion measured by variation coefficient was high at 43.9%, 37.0%, and 54.2%, respectively. The effective population size experienced a very similar decline during the last century in Charolais de Cuba (from 139 to 23 individuals), in French Charolais (from 142 to 12), and in British Charolais (from 145 to 14) for the ~20 last generations. However, the high variability found in the ROH indicators and FROH reveals an opportunity for maintaining the genetic diversity of this breed with an adequate mating strategy, which can be favored with the use of molecular markers. Moreover, the detected ROH were compared to previous results obtained on the detection of signatures of selection in the same breed. Some of the observed signatures were confirmed by the ROHs, emphasizing the process of adaptation to tropical climate experienced by the Charolais de Cuba population.
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Affiliation(s)
- Yoel Rodríguez-Valera
- Faculty of Agricultural Sciences, University of Granma, Bayamo 95100, Cuba; (Y.R.-V.); (E.P.-P.)
| | - Dominique Rocha
- GABI, INRAE, AgroParisTech, University Paris-Saclay, F-78350 Jouy-en-Josas, France; (D.R.); (G.R.)
| | - Michel Naves
- INRAE, URZ, 97170 Petit Bourg, Guadeloupe, France;
| | - Gilles Renand
- GABI, INRAE, AgroParisTech, University Paris-Saclay, F-78350 Jouy-en-Josas, France; (D.R.); (G.R.)
| | - Eliecer Pérez-Pineda
- Faculty of Agricultural Sciences, University of Granma, Bayamo 95100, Cuba; (Y.R.-V.); (E.P.-P.)
| | - Yuliaxis Ramayo-Caldas
- GABI, INRAE, AgroParisTech, University Paris-Saclay, F-78350 Jouy-en-Josas, France; (D.R.); (G.R.)
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
- Correspondence: (Y.R.-C.); (S.E.R.-O.)
| | - Sebastian E. Ramos-Onsins
- Plant and Animal Genomics, Centre of Research in Agricultural Genomics (CRAG) Consortium CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Spain
- Correspondence: (Y.R.-C.); (S.E.R.-O.)
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40
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Lu B, Jin H, Fu J. Molecular convergent and parallel evolution among four high-elevation anuran species from the Tibetan region. BMC Genomics 2020; 21:839. [PMID: 33246413 PMCID: PMC7694343 DOI: 10.1186/s12864-020-07269-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/23/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To date, evidence for the relative prevalence or rarity of molecular convergent and parallel evolution is conflicting, and understanding of how these processes contribute to adaptation is limited. We compared four high-elevation anuran species (Bufo tibetanus, Nanorana parkeri, Rana kukunoris and Scutiger boulengeri) from the Tibetan region, and examined convergent and parallel amino acid substitutions between them and how they may have contributed to high-elevation adaptation. RESULTS Genomic data of the four high-elevation species and eight of their low-elevation close relatives were gathered. A total of 1098 orthologs shared by all species were identified. We first conducted pairwise comparisons using Zhang and Kumar's test. Then, the Rconv index was calculated and convergence/divergence correlation plotting was conducted. Furthermore, genes under positive selection and with elevated evolutionary rate were examined. We detected a large number of amino acid sites with convergent or parallel substitutions. Several pairs of high-elevation species, in particular, R. kukunoris vs N. parkeri and B. tibetanus vs S. boulengeri, had excessive amounts of convergent substitutions compared to neutral expectation. Nevertheless, these sites were mostly concentrated in a small number of genes (3-32), and no genome-wide convergence was detected. Furthermore, the majority of these convergent genes were neither under detectable positive selection nor had elevated evolutionary rates, although functional prediction analysis suggested some of the convergent genes could potentially contribute to high-elevation adaptation. CONCLUSIONS There is a substantial amount of convergent evolution at the amino-acid level among high-elevation amphibians, although these sites are concentrated in a few genes, not widespread across the genomes. This may attribute to the fact that all the target species are from the same environment. The relative prevalence of convergent substitutions among high-elevation amphibians provides an excellent opportunity for further study of molecular convergent evolution.
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Affiliation(s)
- Bin Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Hong Jin
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Jinzhong Fu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China. .,Department of Integrative Biology, University of Guelph, Guelph, Canada.
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41
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Brousseau L, Fine PVA, Dreyer E, Vendramin GG, Scotti I. Genomic and phenotypic divergence unveil microgeographic adaptation in the Amazonian hyperdominant tree Eperua falcata Aubl. (Fabaceae). Mol Ecol 2020; 30:1136-1154. [PMID: 32786115 DOI: 10.1111/mec.15595] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 06/19/2020] [Accepted: 07/31/2020] [Indexed: 01/04/2023]
Abstract
Plant populations can undergo very localized adaptation, allowing widely distributed populations to adapt to divergent habitats in spite of recurrent gene flow. Neotropical trees-whose large and undisturbed populations often span a variety of environmental conditions and local habitats-are particularly good models to study this process. Here, we explore patterns of adaptive divergence from large (i.e., regional) to small (i.e., microgeographic) spatial scales in the hyperdominant Amazonian tree Eperua falcata Aubl. (Fabaceae) under a replicated design involving two microhabitats (~300 m apart) in two study sites (~300 km apart). A three-year reciprocal transplant illustrates that, beyond strong maternal effects and phenotypic plasticity, genetically driven divergence in seedling growth and leaf traits was detected both between seedlings originating from different regions, and between seedlings from different microhabitats. In parallel, a complementary genome scan for selection was carried out through whole-genome sequencing of tree population pools. A set of 290 divergence outlier SNPs was detected at the regional scale (between study sites), while 185 SNPs located in the vicinity of 106 protein-coding genes were detected as replicated outliers between microhabitats within regions. Outlier-surrounding genomic regions are involved in a variety of physiological processes, including plant responses to stress (e.g., oxidative stress, hypoxia and metal toxicity) and biotic interactions. Together with evidence of microgeographic divergence in functional traits, the discovery of genomic candidates for microgeographic adaptive divergence represents a promising advance in our understanding of local adaptation, which probably operates across multiple spatial scales and underpins divergence and diversification in Neotropical trees.
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Affiliation(s)
- Louise Brousseau
- UMR EcoFoG, AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles, Kourou Cedex, France.,AMAP, Univ. Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
| | - Paul V A Fine
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Erwin Dreyer
- Université de Lorraine, AgroParisTech, INRAE, Silva, Nancy, France
| | - Giovanni G Vendramin
- Institute of Biosciences and BioResources (IBBR-CNR), National Research Council, Division of Florence, Sesto Fiorentino, Italy
| | - Ivan Scotti
- UR629 Ecologie des Forêts Méditerranéennes (URFM), INRAE, Avignon, France
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Horscroft C, Ennis S, Pengelly RJ, Sluckin TJ, Collins A. Sequencing era methods for identifying signatures of selection in the genome. Brief Bioinform 2020; 20:1997-2008. [PMID: 30053138 DOI: 10.1093/bib/bby064] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/16/2018] [Indexed: 12/12/2022] Open
Abstract
Insights into genetic loci which are under selection and their functional roles contribute to increased understanding of the patterns of phenotypic variation we observe today. The availability of whole-genome sequence data, for humans and other species, provides opportunities to investigate adaptation and evolution at unprecedented resolution. Many analytical methods have been developed to interrogate these large data sets and characterize signatures of selection in the genome. We review here recently developed methods and consider the impact of increased computing power and data availability on the detection of selection signatures. Consideration of demography, recombination and other confounding factors is important, and use of a range of methods in combination is a powerful route to resolving different forms of selection in genome sequence data. Overall, a substantial improvement in methods for application to whole-genome sequencing is evident, although further work is required to develop robust and computationally efficient approaches which may increase reproducibility across studies.
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Affiliation(s)
- Clare Horscroft
- Genetic Epidemiology and Bioinformatics, Faculty of Medicine, University of Southampton, Duthie Building (808), Tremona Road, Southampton, UK.,Institute for Life Sciences, University of Southampton, Life Sciences Building (85), Highfield, Southampton, UK
| | - Sarah Ennis
- Genetic Epidemiology and Bioinformatics, Faculty of Medicine, University of Southampton, Duthie Building (808), Tremona Road, Southampton, UK.,Institute for Life Sciences, University of Southampton, Life Sciences Building (85), Highfield, Southampton, UK
| | - Reuben J Pengelly
- Genetic Epidemiology and Bioinformatics, Faculty of Medicine, University of Southampton, Duthie Building (808), Tremona Road, Southampton, UK.,Institute for Life Sciences, University of Southampton, Life Sciences Building (85), Highfield, Southampton, UK
| | - Timothy J Sluckin
- Institute for Life Sciences, University of Southampton, Life Sciences Building (85), Highfield, Southampton, UK.,Mathematical Sciences, University of Southampton, Highfield, Southampton, UK
| | - Andrew Collins
- Genetic Epidemiology and Bioinformatics, Faculty of Medicine, University of Southampton, Duthie Building (808), Tremona Road, Southampton, UK.,Institute for Life Sciences, University of Southampton, Life Sciences Building (85), Highfield, Southampton, UK
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Garcia-Elfring A, Barrett RDH, Millien V. Genomic Signatures of Selection along a Climatic Gradient in the Northern Range Margin of the White-Footed Mouse (Peromyscus leucopus). J Hered 2020; 110:684-695. [PMID: 31300816 DOI: 10.1093/jhered/esz045] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 07/10/2019] [Indexed: 02/07/2023] Open
Abstract
Identifying genetic variation involved in thermal adaptation is likely to yield insights into how species adapt to different climates. Physiological and behavioral responses associated with overwintering (e.g., torpor) are thought to serve important functions in climate adaptation. In this study, we use 2 isolated Peromyscus leucopus lineages on the northern margin of the species range to identify single nucleotide polymorphisms (SNPs) showing a strong environmental association and test for evidence of parallel evolution. We found signatures of clinal selection in each lineage, but evidence of parallelism was limited, with only 2 SNPs showing parallel allele frequencies across transects. These parallel SNPs map to a gene involved in protection against iron-dependent oxidative stress (Fxn) and to a gene with unknown function but containing a forkhead-associated domain (Fhad1). Furthermore, within transects, we find significant clinal patterns in genes enriched for functions associated with glycogen homeostasis, synaptic function, intracellular Ca2+ balance, H3 histone modification, as well as the G2/M transition of cell division. Our results are consistent with recent literature on the cellular and molecular basis of climate adaptation in small mammals and provide candidate genomic regions for further study.
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Affiliation(s)
- Alan Garcia-Elfring
- Redpath Museum, McGill University, Montreal, QC, Canada.,Department of Biology, McGill University, Montreal, QC, Canada
| | - Rowan D H Barrett
- Redpath Museum, McGill University, Montreal, QC, Canada.,Department of Biology, McGill University, Montreal, QC, Canada
| | - Virginie Millien
- Redpath Museum, McGill University, Montreal, QC, Canada.,Department of Biology, McGill University, Montreal, QC, Canada
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Cayuela H, Rougemont Q, Laporte M, Mérot C, Normandeau E, Dorant Y, Tørresen OK, Hoff SNK, Jentoft S, Sirois P, Castonguay M, Jansen T, Praebel K, Clément M, Bernatchez L. Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish. Mol Ecol 2020; 29:2379-2398. [DOI: 10.1111/mec.15499] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 05/19/2020] [Accepted: 05/26/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Quentin Rougemont
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Siv Nam Khang Hoff
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo Oslo Norway
| | - Pascal Sirois
- Département des sciences fondamentales Université du Québec à Chicoutimi Chicoutimi QC Canada
| | - Martin Castonguay
- Fisheries and Oceans Canada Institut Maurice‐Lamontagne Mont‐Joli QC Canada
| | - Teunis Jansen
- GINR‐Greenland Institute of Natural Resources Nuuk Greenland
- DTU Aqua‐National Institute of Aquatic Resources Technical University of Denmark Charlottenlund Castle, Charlottenlund Denmark
| | - Kim Praebel
- Norwegian College of Fishery Science Faculty of Biosciences, Fisheries and Economics UiT The Arctic University of Norway Tromsø Norway
| | - Marie Clément
- Center for Fisheries Ecosystems Research Fisheries and Marine Institute of Memorial University of Newfoundland St. John's NL Canada
- Labrador Institute of Memorial University of Newfoundland Happy Valley‐Goose Bay NL Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Quebec City QC Canada
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45
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Sellinger TPP, Abu Awad D, Moest M, Tellier A. Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data. PLoS Genet 2020; 16:e1008698. [PMID: 32251472 PMCID: PMC7173940 DOI: 10.1371/journal.pgen.1008698] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 04/21/2020] [Accepted: 02/24/2020] [Indexed: 02/04/2023] Open
Abstract
Several methods based on the Sequential Markovian coalescence (SMC) have been developed that make use of genome sequence data to uncover population demographic history, which is of interest in its own right and is a key requirement to generate a null model for selection tests. While these methods can be applied to all possible kind of species, the underlying assumptions are sexual reproduction in each generation and non-overlapping generations. However, in many plants, invertebrates, fungi and other taxa, those assumptions are often violated due to different ecological and life history traits, such as self-fertilization or long term dormant structures (seed or egg-banking). We develop a novel SMC-based method to infer 1) the rates/parameters of dormancy and of self-fertilization, and 2) the populations' past demographic history. Using simulated data sets, we demonstrate the accuracy of our method for a wide range of demographic scenarios and for sequence lengths from one to 30 Mb using four sampled genomes. Finally, we apply our method to a Swedish and a German population of Arabidopsis thaliana demonstrating a selfing rate of ca. 0.87 and the absence of any detectable seed-bank. In contrast, we show that the water flea Daphnia pulex exhibits a long lived egg-bank of three to 18 generations. In conclusion, we here present a novel method to infer accurate demographies and life-history traits for species with selfing and/or seed/egg-banks. Finally, we provide recommendations for the use of SMC-based methods for non-model organisms, highlighting the importance of the per site and the effective ratios of recombination over mutation.
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Affiliation(s)
| | - Diala Abu Awad
- Department of Population Genetics, Technische Universitaet Muenchen, Freising, Germany
| | - Markus Moest
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Aurélien Tellier
- Department of Population Genetics, Technische Universitaet Muenchen, Freising, Germany
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46
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Analyzing drivers of speciation in the Southern Ocean using the sea spider species complex Colossendeis megalonyx as a test case. Polar Biol 2020. [DOI: 10.1007/s00300-020-02636-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
AbstractColossendeis megalonyx Hoek, 1881 has the broadest distribution of all sea spiders in the Southern Ocean. Previous studies have detected several evolutionarily young lineages within this taxon and interpreted them as a result of allopatric speciation in a few shelf refuges during glacial maxima. However, alternative scenarios such as ecological speciation in sympatry have rarely been considered or tested. Here, we generated the most extensive genomic and morphometric data set on the C. megalonyx species complex to (i) comprehensively describe species diversity, (ii) explore intraspecific connectivity between populations located around Antarctica, and (iii) systematically test for positive selection indicative of adaptive speciation. We successfully applied a target hybrid enrichment approach and recovered all 1607 genes targeted. Phylogenomic analysis was consistent with previous findings and, moreover, increased the resolution of branching within lineages. We found specimens of phylogenetically well-separated lineages occurring in sympatry to be genetically distinct from each other and gene flow between geographically separated populations of the same lineages to be restricted. Evidence for positive selection was found for four genes associated with structural and neuronal functions. Hence, there is an indication for positive selection in the C. megalonyx species complex, yet its specific contribution to the speciation process remains to be explored further. Finally, morphometric analyses revealed multiple significant differences between lineages, but a clear separation proved difficult. Our study highlights the relevance of positive selection as a potential driver for speciation in the Southern Ocean.
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47
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Sun YQ, Zhao W, Xu CQ, Xu Y, El-Kassaby YA, De La Torre AR, Mao JF. Genetic Variation Related to High Elevation Adaptation Revealed by Common Garden Experiments in Pinus yunnanensis. Front Genet 2020; 10:1405. [PMID: 32117429 PMCID: PMC7027398 DOI: 10.3389/fgene.2019.01405] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/23/2019] [Indexed: 12/30/2022] Open
Abstract
Local adaptation, adaptation to specialized niches and environmental clines have been extensively reported for forest trees. Investigation of the adaptive genetic variation is crucial for forest resource management and breeding, especially in the context of global climate change. Here, we utilized a Pinus yunnanensis common garden experiments established at high and low elevation sites to assess the differences in growth and survival among populations and between the two common garden sites. The studied traits showed significant variation between the two test sites and among populations, suggesting adaptive divergence. To detect genetic variation related to environment, we captured 103,608 high quality SNPs based on RNA sequencing, and used them to assess the genetic diversity and population structure. We identified 321 outlier SNPs from 131 genes showing significant divergence in allelic frequency between survival populations of two sites. Functional categories associated with adaptation to high elevation were found to be related to flavonoid biosynthesis, response to UV, DNA repair, response to reactive oxygen species, and membrane lipid metabolic process. Further investigation of the outlier genes showed overrepresentation of the flavonoid biosynthesis pathway, suggesting that this pathway may play a key role in P. yunnanensis adaptation to high elevation environments. The outlier genes identified, and their variants, provide a basic reference for advanced investigations.
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Affiliation(s)
- Yan-Qiang Sun
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Wei Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Chao-Qun Xu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yulan Xu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Southwest Forestry University, Kunming, China
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC, Canada
| | | | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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48
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Apata M, Pfeifer SP. Recent population genomic insights into the genetic basis of arsenic tolerance in humans: the difficulties of identifying positively selected loci in strongly bottlenecked populations. Heredity (Edinb) 2020; 124:253-262. [PMID: 31776483 PMCID: PMC6972707 DOI: 10.1038/s41437-019-0285-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/22/2019] [Accepted: 11/13/2019] [Indexed: 02/06/2023] Open
Abstract
Recent advances in genomics have enabled researchers to shed light on the evolutionary processes driving human adaptation, by revealing the genetic architectures underlying traits ranging from lactase persistence, to skin pigmentation, to hypoxic response, to arsenic tolerance. Complicating the identification of targets of positive selection in modern human populations is their complex demographic history, characterized by population bottlenecks and expansions, population structure, migration, and admixture. In particular, founder effects and recent strong population size reductions, such as those experienced by the indigenous peoples of the Americas, have severe impacts on genetic variation that can lead to the accumulation of large allele frequency differences between populations due to genetic drift rather than natural selection. While distinguishing the effects of demographic history from selection remains challenging, neglecting neutral processes can lead to the incorrect identification of candidate loci. We here review the recent population genomic insights into the genetic basis of arsenic tolerance in Andean populations, and utilize this example to highlight both the difficulties pertaining to the identification of local adaptations in strongly bottlenecked populations, as well as the importance of controlling for demographic history in selection scans.
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Affiliation(s)
- Mario Apata
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85821, USA
| | - Susanne P Pfeifer
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85821, USA.
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49
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Bekkevold D, Höjesjö J, Nielsen EE, Aldvén D, Als TD, Sodeland M, Kent MP, Lien S, Hansen MM. Northern European Salmo trutta (L.) populations are genetically divergent across geographical regions and environmental gradients. Evol Appl 2020; 13:400-416. [PMID: 31993085 PMCID: PMC6976966 DOI: 10.1111/eva.12877] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/06/2019] [Accepted: 09/22/2019] [Indexed: 12/19/2022] Open
Abstract
The salmonid fish Brown trout is iconic as a model for the application of conservation genetics to understand and manage local interspecific variation. However, there is still scant information about relationships between local and large-scale population structure, and to what extent geographical and environmental variables are associated with barriers to gene flow. We used information from 3,782 mapped SNPs developed for the present study and conducted outlier tests and gene-environment association (GEA) analyses in order to examine drivers of population structure. Analyses comprised >2,600 fish from 72 riverine populations spanning a central part of the species' distribution in northern Europe. We report hitherto unidentified genetic breaks in population structure, indicating strong barriers to gene flow. GEA loci were widely spread across genomic regions and showed correlations with climatic, abiotic and geographical parameters. In some cases, individual loci showed consistent GEA across the geographical regions Britain, Europe and Scandinavia. In other cases, correlations were observed only within a sub-set of regions, suggesting that locus-specific variation was associated with local processes. A paired-population sampling design allowed us to evaluate sampling effects on detection of outlier loci and GEA. Two widely applied methods for outlier detection (pcadapt and bayescan) showed low overlap in loci identified as statistical outliers across sub-sets of data. Two GEA analytical approaches (LFMM and RDA) showed good correspondence concerning loci associated with specific variables, but LFMM identified five times more statistically significant associations than RDA. Our results emphasize the importance of carefully considering the statistical methods applied for the hypotheses being tested in outlier analysis. Sampling design may have lower impact on results if the objective is to identify GEA loci and their population distribution. Our study provides new insights into trout populations, and results have direct management implications in serving as a tool for identification of conservation units.
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Affiliation(s)
- Dorte Bekkevold
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Johan Höjesjö
- Department of Biological & Environmental SciencesUniversity of GothenburgGothenburgSweden
| | - Einar Eg Nielsen
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | | | | | - Marte Sodeland
- Department of Natural SciencesUniversity of AgderKristiansandNorway
| | | | - Sigbjørn Lien
- Faculty of BiosciencesNorwegian University of Life SciencesÅsNorway
| | - Michael Møller Hansen
- Department of Bioscience – Genetics, Ecology and EvolutionAarhus UniversityAarhusDenmark
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50
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Popovic I, Riginos C. Comparative genomics reveals divergent thermal selection in warm‐ and cold‐tolerant marine mussels. Mol Ecol 2020; 29:519-535. [DOI: 10.1111/mec.15339] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Iva Popovic
- School of Biological Sciences University of Queensland St Lucia Qld Australia
| | - Cynthia Riginos
- School of Biological Sciences University of Queensland St Lucia Qld Australia
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