1
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Glasenapp MR, Pogson GH. Selection Shapes the Genomic Landscape of Introgressed Ancestry in a Pair of Sympatric Sea Urchin Species. Genome Biol Evol 2024; 16:evae124. [PMID: 38874390 PMCID: PMC11212366 DOI: 10.1093/gbe/evae124] [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: 12/06/2023] [Revised: 05/10/2024] [Accepted: 06/07/2024] [Indexed: 06/15/2024] Open
Abstract
A growing number of recent studies have demonstrated that introgression is common across the tree of life. However, we still have a limited understanding of the fate and fitness consequence of introgressed variation at the whole-genome scale across diverse taxonomic groups. Here, we implemented a phylogenetic hidden Markov model to identify and characterize introgressed genomic regions in a pair of well-diverged, nonsister sea urchin species: Strongylocentrotus pallidus and Strongylocentrotus droebachiensis. Despite the old age of introgression, a sizable fraction of the genome (1% to 5%) exhibited introgressed ancestry, including numerous genes showing signals of historical positive selection that may represent cases of adaptive introgression. One striking result was the overrepresentation of hyalin genes in the identified introgressed regions despite observing considerable overall evidence of selection against introgression. There was a negative correlation between introgression and chromosome gene density, and two chromosomes were observed with considerably reduced introgression. Relative to the nonintrogressed genome-wide background, introgressed regions had significantly reduced nucleotide divergence (dXY) and overlapped fewer protein-coding genes, coding bases, and genes with a history of positive selection. Additionally, genes residing within introgressed regions showed slower rates of evolution (dN, dS, dN/dS) than random samples of genes without introgressed ancestry. Overall, our findings are consistent with widespread selection against introgressed ancestry across the genome and suggest that slowly evolving, low-divergence genomic regions are more likely to move between species and avoid negative selection following hybridization and introgression.
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Affiliation(s)
- Matthew R Glasenapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, USA
| | - Grant H Pogson
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, USA
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2
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Lollar MJ, Kim E, Stern DL, Pool JE. Courtship song differs between African and European populations of Drosophila melanogaster and involves a strong effect locus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594231. [PMID: 38798463 PMCID: PMC11118343 DOI: 10.1101/2024.05.14.594231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The courtship song of Drosophila melanogaster has long served as excellent model system for studies of animal communication and differences in courtship song have been demonstrated among populations and between species. Here, we report that flies of African and European origin, which diverged approximately 13,000 years ago, show significant genetic differentiation in the use of slow versus fast pulse song. Using a combination of quantitative trait mapping and population genetic analysis we detected a single strong QTL underlying this trait and we identified candidate genes that may contribute to the evolution of this trait. Song trait variation between parental strains of our recombinant inbred panel enabled detection of genomic intervals associated with six additional song traits, some of which include known courtship-related genes. These findings improve the prospects for further genetic insights into the evolution of reproductive behavior and the biology underlying courtship song.
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Affiliation(s)
- Matthew J Lollar
- Laboratory of Genetics, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Elizabeth Kim
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147 USA
| | - David L Stern
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147 USA
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin - Madison, Madison, WI, 53705, USA
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3
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Niepoth N, Merritt JR, Uminski M, Lei E, Esquibies VS, Bando IB, Hernandez K, Gebhardt C, Wacker SA, Lutzu S, Poudel A, Soma KK, Rudolph S, Bendesky A. Evolution of a novel adrenal cell type that promotes parental care. Nature 2024; 629:1082-1090. [PMID: 38750354 DOI: 10.1038/s41586-024-07423-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
Cell types with specialized functions fundamentally regulate animal behaviour, and yet the genetic mechanisms that underlie the emergence of novel cell types and their consequences for behaviour are not well understood1. Here we show that the monogamous oldfield mouse (Peromyscus polionotus) has recently evolved a novel cell type in the adrenal gland that expresses the enzyme AKR1C18, which converts progesterone into 20α-hydroxyprogesterone. We then demonstrate that 20α-hydroxyprogesterone is more abundant in oldfield mice, where it induces monogamous-typical parental behaviours, than in the closely related promiscuous deer mice (Peromyscus maniculatus). Using quantitative trait locus mapping in a cross between these species, we ultimately find interspecific genetic variation that drives expression of the nuclear protein GADD45A and the glycoprotein tenascin N, which contribute to the emergence and function of this cell type in oldfield mice. Our results provide an example by which the recent evolution of a new cell type in a gland outside the brain contributes to the evolution of social behaviour.
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Affiliation(s)
- Natalie Niepoth
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Jennifer R Merritt
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Michelle Uminski
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Emily Lei
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Victoria S Esquibies
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Ina B Bando
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Kimberly Hernandez
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Christoph Gebhardt
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Sarah A Wacker
- Department of Chemistry and Biochemistry, Manhattan College, New York, NY, USA
| | - Stefano Lutzu
- Department of Neuroscience, Albert Einstein College of Medicine, New York, NY, USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, New York, NY, USA
| | - Asmita Poudel
- Department of Psychology, University of British Columbia, Vancouver, British Columbia, Canada
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kiran K Soma
- Department of Psychology, University of British Columbia, Vancouver, British Columbia, Canada
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephanie Rudolph
- Department of Neuroscience, Albert Einstein College of Medicine, New York, NY, USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, New York, NY, USA
| | - Andres Bendesky
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA.
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4
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Chen J, Liu C, Li W, Zhang W, Wang Y, Clark AG, Lu J. From sub-Saharan Africa to China: Evolutionary history and adaptation of Drosophila melanogaster revealed by population genomics. SCIENCE ADVANCES 2024; 10:eadh3425. [PMID: 38630810 PMCID: PMC11023512 DOI: 10.1126/sciadv.adh3425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024]
Abstract
Drosophila melanogaster is a widely used model organism for studying environmental adaptation. However, the genetic diversity of populations in Asia is poorly understood, leaving a notable gap in our knowledge of the global evolution and adaptation of this species. We sequenced genomes of 292 D. melanogaster strains from various ecological settings in China and analyzed them along with previously published genome sequences. We have identified six global genetic ancestry groups, despite the presence of widespread genetic admixture. The strains from China represent a unique ancestry group, although detectable differentiation exists among populations within China. We deciphered the global migration and demography of D. melanogaster, and identified widespread signals of adaptation, including genetic changes in response to insecticides. We validated the effects of insecticide resistance variants using population cage trials and deep sequencing. This work highlights the importance of population genomics in understanding the genetic underpinnings of adaptation, an effort that is particularly relevant given the deterioration of ecosystems.
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Affiliation(s)
- Junhao Chen
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Chenlu Liu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Weixuan Li
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wenxia Zhang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yirong Wang
- College of Biology, Hunan University, Changsha 410082, China
| | - Andrew G. Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
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5
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Sianta SA, Moeller DA, Brandvain Y. The extent of introgression between incipient Clarkia species is determined by temporal environmental variation and mating system. Proc Natl Acad Sci U S A 2024; 121:e2316008121. [PMID: 38466849 PMCID: PMC10963018 DOI: 10.1073/pnas.2316008121] [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: 09/18/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024] Open
Abstract
Introgression is pervasive across the tree of life but varies across taxa, geography, and genomic regions. However, the factors modulating this variation and how they may be affected by global change are not well understood. Here, we used 200 genomes and a 15-y site-specific environmental dataset to investigate the effects of environmental variation and mating system divergence on the magnitude of introgression between a recently diverged outcrosser-selfer pair of annual plants in the genus Clarkia. These sister taxa diverged very recently and subsequently came into secondary sympatry where they form replicated contact zones. Consistent with observations of other outcrosser-selfer pairs, we found that introgression was asymmetric between taxa, with substantially more introgression from the selfer to the outcrosser. This asymmetry was caused by a bias in the direction of initial F1 hybrid formation and subsequent backcrossing. We also found extensive variation in the outcrosser's admixture proportion among contact zones, which was predicted nearly entirely by interannual variance in spring precipitation. Greater fluctuations in spring precipitation resulted in higher admixture proportions, likely mediated by the effects of spring precipitation on the expression of traits that determine premating reproductive isolation. Climate-driven hybridization dynamics may be particularly affected by global change, potentially reshaping species boundaries and adaptation to novel environments.
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Affiliation(s)
- Shelley A. Sianta
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN55108
| | - David A. Moeller
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN55108
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN55108
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6
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Feng X, Merilä J, Löytynoja A. Secondary Contact, Introgressive Hybridization, and Genome Stabilization in Sticklebacks. Mol Biol Evol 2024; 41:msae031. [PMID: 38366566 PMCID: PMC10903534 DOI: 10.1093/molbev/msae031] [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: 09/19/2023] [Revised: 12/20/2023] [Accepted: 02/09/2024] [Indexed: 02/18/2024] Open
Abstract
Advances in genomic studies have revealed that hybridization in nature is pervasive and raised questions about the dynamics of different genetic and evolutionary factors following the initial hybridization event. While recent research has proposed that the genomic outcomes of hybridization might be predictable to some extent, many uncertainties remain. With comprehensive whole-genome sequence data, we investigated the genetic introgression between 2 divergent lineages of 9-spined sticklebacks (Pungitius pungitius) in the Baltic Sea. We found that the intensity and direction of selection on the introgressed variation has varied across different genomic elements: while functionally important regions displayed reduced rates of introgression, promoter regions showed enrichment. Despite the general trend of negative selection, we identified specific genomic regions that were enriched for introgressed variants, and within these regions, we detected footprints of selection, indicating adaptive introgression. Geographically, we found the selection against the functional changes to be strongest in the vicinity of the secondary contact zone and weaken as a function of distance from the initial contact. Altogether, the results suggest that the stabilization of introgressed variation in the genomes is a complex, multistage process involving both negative and positive selection. In spite of the predominance of negative selection against introgressed variants, we also found evidence for adaptive introgression variants likely associated with adaptation to Baltic Sea environmental conditions.
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Affiliation(s)
- Xueyun Feng
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Juha Merilä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
- Area of Ecology and Biodiversity, The School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
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7
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Moran BM, Payne CY, Powell DL, Iverson ENK, Donny AE, Banerjee SM, Langdon QK, Gunn TR, Rodriguez-Soto RA, Madero A, Baczenas JJ, Kleczko KM, Liu F, Matney R, Singhal K, Leib RD, Hernandez-Perez O, Corbett-Detig R, Frydman J, Gifford C, Schartl M, Havird JC, Schumer M. A lethal mitonuclear incompatibility in complex I of natural hybrids. Nature 2024; 626:119-127. [PMID: 38200310 PMCID: PMC10830419 DOI: 10.1038/s41586-023-06895-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/23/2023] [Indexed: 01/12/2024]
Abstract
The evolution of reproductive barriers is the first step in the formation of new species and can help us understand the diversification of life on Earth. These reproductive barriers often take the form of hybrid incompatibilities, in which alleles derived from two different species no longer interact properly in hybrids1-3. Theory predicts that hybrid incompatibilities may be more likely to arise at rapidly evolving genes4-6 and that incompatibilities involving multiple genes should be common7,8, but there has been sparse empirical data to evaluate these predictions. Here we describe a mitonuclear incompatibility involving three genes whose protein products are in physical contact within respiratory complex I of naturally hybridizing swordtail fish species. Individuals homozygous for mismatched protein combinations do not complete embryonic development or die as juveniles, whereas those heterozygous for the incompatibility have reduced complex I function and unbalanced representation of parental alleles in the mitochondrial proteome. We find that the effects of different genetic interactions on survival are non-additive, highlighting subtle complexity in the genetic architecture of hybrid incompatibilities. Finally, we document the evolutionary history of the genes involved, showing signals of accelerated evolution and evidence that an incompatibility has been transferred between species via hybridization.
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Affiliation(s)
- Benjamin M Moran
- Department of Biology, Stanford University, Stanford, CA, USA.
- Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', A.C., Calnali, Hidalgo, Mexico.
| | - Cheyenne Y Payne
- Department of Biology, Stanford University, Stanford, CA, USA
- Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', A.C., Calnali, Hidalgo, Mexico
| | - Daniel L Powell
- Department of Biology, Stanford University, Stanford, CA, USA
- Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', A.C., Calnali, Hidalgo, Mexico
| | - Erik N K Iverson
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | | | - Quinn K Langdon
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Theresa R Gunn
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Angel Madero
- Department of Biology, Stanford University, Stanford, CA, USA
| | - John J Baczenas
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Fang Liu
- Stanford University Mass Spectrometry Core, Stanford University, Stanford, CA, USA
| | - Rowan Matney
- Stanford University Mass Spectrometry Core, Stanford University, Stanford, CA, USA
| | - Kratika Singhal
- Stanford University Mass Spectrometry Core, Stanford University, Stanford, CA, USA
| | - Ryan D Leib
- Stanford University Mass Spectrometry Core, Stanford University, Stanford, CA, USA
| | - Osvaldo Hernandez-Perez
- Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', A.C., Calnali, Hidalgo, Mexico
| | - Russell Corbett-Detig
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Casey Gifford
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
- Developmental Biochemistry, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, CA, USA.
- Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', A.C., Calnali, Hidalgo, Mexico.
- Howard Hughes Medical Institute, Stanford, CA, USA.
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8
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Ray DD, Flagel L, Schrider DR. IntroUNET: Identifying introgressed alleles via semantic segmentation. PLoS Genet 2024; 20:e1010657. [PMID: 38377104 PMCID: PMC10906877 DOI: 10.1371/journal.pgen.1010657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/01/2024] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
A growing body of evidence suggests that gene flow between closely related species is a widespread phenomenon. Alleles that introgress from one species into a close relative are typically neutral or deleterious, but sometimes confer a significant fitness advantage. Given the potential relevance to speciation and adaptation, numerous methods have therefore been devised to identify regions of the genome that have experienced introgression. Recently, supervised machine learning approaches have been shown to be highly effective for detecting introgression. One especially promising approach is to treat population genetic inference as an image classification problem, and feed an image representation of a population genetic alignment as input to a deep neural network that distinguishes among evolutionary models (i.e. introgression or no introgression). However, if we wish to investigate the full extent and fitness effects of introgression, merely identifying genomic regions in a population genetic alignment that harbor introgressed loci is insufficient-ideally we would be able to infer precisely which individuals have introgressed material and at which positions in the genome. Here we adapt a deep learning algorithm for semantic segmentation, the task of correctly identifying the type of object to which each individual pixel in an image belongs, to the task of identifying introgressed alleles. Our trained neural network is thus able to infer, for each individual in a two-population alignment, which of those individual's alleles were introgressed from the other population. We use simulated data to show that this approach is highly accurate, and that it can be readily extended to identify alleles that are introgressed from an unsampled "ghost" population, performing comparably to a supervised learning method tailored specifically to that task. Finally, we apply this method to data from Drosophila, showing that it is able to accurately recover introgressed haplotypes from real data. This analysis reveals that introgressed alleles are typically confined to lower frequencies within genic regions, suggestive of purifying selection, but are found at much higher frequencies in a region previously shown to be affected by adaptive introgression. Our method's success in recovering introgressed haplotypes in challenging real-world scenarios underscores the utility of deep learning approaches for making richer evolutionary inferences from genomic data.
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Affiliation(s)
- Dylan D. Ray
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lex Flagel
- Division of Data Science, Gencove Inc., New York, New York, United States of America
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Daniel R. Schrider
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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9
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Ray DD, Flagel L, Schrider DR. IntroUNET: identifying introgressed alleles via semantic segmentation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.07.527435. [PMID: 36865105 PMCID: PMC9979274 DOI: 10.1101/2023.02.07.527435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A growing body of evidence suggests that gene flow between closely related species is a widespread phenomenon. Alleles that introgress from one species into a close relative are typically neutral or deleterious, but sometimes confer a significant fitness advantage. Given the potential relevance to speciation and adaptation, numerous methods have therefore been devised to identify regions of the genome that have experienced introgression. Recently, supervised machine learning approaches have been shown to be highly effective for detecting introgression. One especially promising approach is to treat population genetic inference as an image classification problem, and feed an image representation of a population genetic alignment as input to a deep neural network that distinguishes among evolutionary models (i.e. introgression or no introgression). However, if we wish to investigate the full extent and fitness effects of introgression, merely identifying genomic regions in a population genetic alignment that harbor introgressed loci is insufficient-ideally we would be able to infer precisely which individuals have introgressed material and at which positions in the genome. Here we adapt a deep learning algorithm for semantic segmentation, the task of correctly identifying the type of object to which each individual pixel in an image belongs, to the task of identifying introgressed alleles. Our trained neural network is thus able to infer, for each individual in a two-population alignment, which of those individual's alleles were introgressed from the other population. We use simulated data to show that this approach is highly accurate, and that it can be readily extended to identify alleles that are introgressed from an unsampled "ghost" population, performing comparably to a supervised learning method tailored specifically to that task. Finally, we apply this method to data from Drosophila, showing that it is able to accurately recover introgressed haplotypes from real data. This analysis reveals that introgressed alleles are typically confined to lower frequencies within genic regions, suggestive of purifying selection, but are found at much higher frequencies in a region previously shown to be affected by adaptive introgression. Our method's success in recovering introgressed haplotypes in challenging real-world scenarios underscores the utility of deep learning approaches for making richer evolutionary inferences from genomic data.
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Affiliation(s)
- Dylan D. Ray
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lex Flagel
- Division of Data Science, Gencove Inc., New York, NY 11101, USA
- Department of Plant and Microbial Biology, University of Minnesota, St Paul MN, 55108, USA
| | - Daniel R. Schrider
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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10
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Langdon QK, Groh JS, Aguillon SM, Powell DL, Gunn T, Payne C, Baczenas JJ, Donny A, Dodge TO, Du K, Schartl M, Ríos-Cárdenas O, Gutierrez-Rodríguez C, Morris M, Schumer M. Genome evolution is surprisingly predictable after initial hybridization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572897. [PMID: 38187753 PMCID: PMC10769416 DOI: 10.1101/2023.12.21.572897] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Over the past two decades, evolutionary biologists have come to appreciate that hybridization, or genetic exchange between distinct lineages, is remarkably common - not just in particular lineages but in taxonomic groups across the tree of life. As a result, the genomes of many modern species harbor regions inherited from related species. This observation has raised fundamental questions about the degree to which the genomic outcomes of hybridization are repeatable and the degree to which natural selection drives such repeatability. However, a lack of appropriate systems to answer these questions has limited empirical progress in this area. Here, we leverage independently formed hybrid populations between the swordtail fish Xiphophorus birchmanni and X. cortezi to address this fundamental question. We find that local ancestry in one hybrid population is remarkably predictive of local ancestry in another, demographically independent hybrid population. Applying newly developed methods, we can attribute much of this repeatability to strong selection in the earliest generations after initial hybridization. We complement these analyses with time-series data that demonstrates that ancestry at regions under selection has remained stable over the past ~40 generations of evolution. Finally, we compare our results to the well-studied X. birchmanni×X. malinche hybrid populations and conclude that deeper evolutionary divergence has resulted in stronger selection and higher repeatability in patterns of local ancestry in hybrids between X. birchmanni and X. cortezi.
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Affiliation(s)
- Quinn K. Langdon
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California
| | - Jeffrey S. Groh
- Center for Population Biology and Department of Evolution and Ecology, University of California, Davis
| | - Stepfanie M. Aguillon
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles
| | - Daniel L. Powell
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Theresa Gunn
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Cheyenne Payne
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | | | - Alex Donny
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Tristram O. Dodge
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Kang Du
- Xiphophorus Genetic Stock Center, Texas State University San Marcos
| | - Manfred Schartl
- Xiphophorus Genetic Stock Center, Texas State University San Marcos
- Developmental Biochemistry, Biocenter, University of Würzburg
| | | | | | | | - Molly Schumer
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
- Freeman Hrabowski Fellow, Howard Hughes Medical Institute
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11
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Di Santo LN, Quilodrán CS, Currat M. Temporal Variation in Introgressed Segments' Length Statistics Computed from a Limited Number of Ancient Genomes Sheds Light on Past Admixture Pulses. Mol Biol Evol 2023; 40:msad252. [PMID: 37992125 PMCID: PMC10715198 DOI: 10.1093/molbev/msad252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/16/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023] Open
Abstract
Hybridization is recognized as an important evolutionary force, but identifying and timing admixture events between divergent lineages remain a major aim of evolutionary biology. While this has traditionally been done using inferential tools on contemporary genomes, the latest advances in paleogenomics have provided a growing wealth of temporally distributed genomic data. Here, we used individual-based simulations to generate chromosome-level genomic data for a 2-population system and described temporal neutral introgression patterns under a single- and 2-pulse admixture model. We computed 6 summary statistics aiming to inform the timing and number of admixture pulses between interbreeding entities: lengths of introgressed sequences and their variance within genomes, as well as genome-wide introgression proportions and related measures. The first 2 statistics could confidently be used to infer interlineage hybridization history, peaking at the beginning and shortly after an admixture pulse. Temporal variation in introgression proportions and related statistics provided more limited insights, particularly when considering their application to ancient genomes still scant in number. Lastly, we computed these statistics on Homo sapiens paleogenomes and successfully inferred the hybridization pulse from Neanderthal that occurred approximately 40 to 60 kya. The scarce number of genomes dating from this period prevented more precise inferences, but the accumulation of paleogenomic data opens promising perspectives as our approach only requires a limited number of ancient genomes.
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Affiliation(s)
- Lionel N Di Santo
- Department of Genetics and Evolution, University of Geneva, Geneva CH-1205
| | | | - Mathias Currat
- Department of Genetics and Evolution, University of Geneva, Geneva CH-1205
- Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva CH-1205
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12
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Ayala NM, Genetti M, Corbett-Detig R. Inferring multi-locus selection in admixed populations. PLoS Genet 2023; 19:e1011062. [PMID: 38015992 PMCID: PMC10707604 DOI: 10.1371/journal.pgen.1011062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 12/08/2023] [Accepted: 11/13/2023] [Indexed: 11/30/2023] Open
Abstract
Admixture, the exchange of genetic information between distinct source populations, is thought to be a major source of adaptive genetic variation. Unlike mutation events, which periodically generate single alleles, admixture can introduce many selected alleles simultaneously. As such, the effects of linkage between selected alleles may be especially pronounced in admixed populations. However, existing tools for identifying selected mutations within admixed populations only account for selection at a single site, overlooking phenomena such as linkage among proximal selected alleles. Here, we develop and extensively validate a method for identifying and quantifying the individual effects of multiple linked selected sites on a chromosome in admixed populations. Our approach numerically calculates the expected local ancestry landscape in an admixed population for a given multi-locus selection model, and then maximizes the likelihood of the model. After applying this method to admixed populations of Drosophila melanogaster and Passer italiae, we found that the impacts between linked sites may be an important contributor to natural selection in admixed populations. Furthermore, for the situations we considered, the selection coefficients and number of selected sites are overestimated in analyses that do not consider the effects of linkage among selected sites. Our results imply that linkage among selected sites may be an important evolutionary force in admixed populations. This tool provides a powerful generalized method to investigate these crucial phenomena in diverse populations.
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Affiliation(s)
- Nicolas M. Ayala
- Genomics Institute, University of California, Santa Cruz; Santa Cruz, California, United States of America
- Department of Biomolecular Engineering, University of California, Santa Cruz; Santa Cruz, California, United States of America
| | - Maximilian Genetti
- Genomics Institute, University of California, Santa Cruz; Santa Cruz, California, United States of America
- Department of Biomolecular Engineering, University of California, Santa Cruz; Santa Cruz, California, United States of America
| | - Russell Corbett-Detig
- Genomics Institute, University of California, Santa Cruz; Santa Cruz, California, United States of America
- Department of Biomolecular Engineering, University of California, Santa Cruz; Santa Cruz, California, United States of America
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13
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Preckler-Quisquater S, Kierepka EM, Reding DM, Piaggio AJ, Sacks BN. Can demographic histories explain long-term isolation and recent pulses of asymmetric gene flow between highly divergent grey fox lineages? Mol Ecol 2023; 32:5323-5337. [PMID: 37632719 DOI: 10.1111/mec.17105] [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: 01/12/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/28/2023]
Abstract
Secondary contact zones between deeply divergent, yet interfertile, lineages provide windows into the speciation process. North American grey foxes (Urocyon cinereoargenteus) are divided into western and eastern lineages that diverged approximately 1 million years ago. These ancient lineages currently hybridize in a relatively narrow zone of contact in the southern Great Plains, a pattern more commonly observed in smaller-bodied taxa, which suggests relatively recent contact after a long period of allopatry. Based on local ancestry inference with whole-genome sequencing (n = 43), we identified two distinct Holocene pulses of admixture. The older pulse (500-3500 YBP) reflected unidirectional gene flow from east to west, whereas the more recent pulse (70-200 YBP) of admixture was bi-directional. Augmented with genotyping-by-sequencing data from 216 additional foxes, demographic analyses indicated that the eastern lineage declined precipitously after divergence, remaining small throughout most of the late Pleistocene, and expanding only during the Holocene. Genetic diversity in the eastern lineage was highest in the southeast and lowest near the contact zone, consistent with a westward expansion. Concordantly, distribution modelling indicated that during their isolation, the most suitable habitat occurred far east of today's contact zone or west of the Great Plains. Thus, long-term isolation was likely caused by the small, distant location of the eastern refugium, with recent contact reflecting a large increase in suitable habitat and corresponding demographic expansion from the eastern refugium. Ultimately, long-term isolation in grey foxes may reflect their specialized bio-climatic niche. This system presents an opportunity for future investigation of potential pre- and post-zygotic isolating mechanisms.
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Affiliation(s)
- Sophie Preckler-Quisquater
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Elizabeth M Kierepka
- North Carolina Museum of Natural Sciences, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, USA
| | - Dawn M Reding
- Department of Biology, Luther College, Decorah, Iowa, USA
| | - Antoinette J Piaggio
- USDA, Wildlife Services, National Wildlife Research Center, Wildlife Genetics Lab, Fort Collins, Colorado, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
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14
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Everitt T, Wallberg A, Christmas MJ, Olsson A, Hoffmann W, Neumann P, Webster MT. The Genomic Basis of Adaptation to High Elevations in Africanized Honey Bees. Genome Biol Evol 2023; 15:evad157. [PMID: 37625795 PMCID: PMC10484329 DOI: 10.1093/gbe/evad157] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
A range of different genetic architectures underpin local adaptation in nature. Honey bees (Apis mellifera) in the Eastern African Mountains harbor high frequencies of two chromosomal inversions that likely govern adaptation to this high-elevation habitat. In the Americas, honey bees are hybrids of European and African ancestries and adaptation to latitudinal variation in climate correlates with the proportion of these ancestries across the genome. It is unknown which, if either, of these forms of genetic variation governs adaptation in honey bees living at high elevations in the Americas. Here, we performed whole-genome sequencing of 29 honey bees from both high- and low-elevation populations in Colombia. Analysis of genetic ancestry indicated that both populations were predominantly of African ancestry, but the East African inversions were not detected. However, individuals in the higher elevation population had significantly higher proportions of European ancestry, likely reflecting local adaptation. Several genomic regions exhibited particularly high differentiation between highland and lowland bees, containing candidate loci for local adaptation. Genes that were highly differentiated between highland and lowland populations were enriched for functions related to reproduction and sperm competition. Furthermore, variation in levels of European ancestry across the genome was correlated between populations of honey bees in the highland population and populations at higher latitudes in South America. The results are consistent with the hypothesis that adaptation to both latitude and elevation in these hybrid honey bees are mediated by variation in ancestry at many loci across the genome.
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Affiliation(s)
- Turid Everitt
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Andreas Wallberg
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Matthew J Christmas
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Olsson
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Wolfgang Hoffmann
- Grupo de Biocalorimetría, Universidad de Pamplona, Pamplona, Colombia
| | - Peter Neumann
- Institute of Bee Health, Vetsuisse Faculty, University of Bern and Agroscope, Bern, Switzerland
| | - Matthew T Webster
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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15
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Nadjsombati MS, Niepoth N, Webeck LM, Kennedy EA, Jones DL, Billipp TE, Baldridge MT, Bendesky A, von Moltke J. Genetic mapping reveals Pou2af2/OCA-T1-dependent tuning of tuft cell differentiation and intestinal type 2 immunity. Sci Immunol 2023; 8:eade5019. [PMID: 37172102 PMCID: PMC10308849 DOI: 10.1126/sciimmunol.ade5019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 04/18/2023] [Indexed: 05/14/2023]
Abstract
Chemosensory epithelial tuft cells contribute to innate immunity at barrier surfaces, but their differentiation from epithelial progenitors is not well understood. Here, we exploited differences between inbred mouse strains to identify an epithelium-intrinsic mechanism that regulates tuft cell differentiation and tunes innate type 2 immunity in the small intestine. Balb/cJ (Balb) mice had fewer intestinal tuft cells than C57BL/6J (B6) mice and failed to respond to the tuft cell ligand succinate. Most of this differential succinate response was determined by the 50- to 67-Mb interval of chromosome 9 (Chr9), such that congenic Balb mice carrying the B6 Chr9 interval had elevated baseline numbers of tuft cells and responded to succinate. The Chr9 locus includes Pou2af2, which encodes the protein OCA-T1, a transcriptional cofactor essential for tuft cell development. Epithelial crypts expressed a previously unannotated short isoform of Pou2af2 predicted to use a distinct transcriptional start site and encode a nonfunctional protein. Low tuft cell numbers and the resulting lack of succinate response in Balb mice were explained by a preferential expression of the short isoform and could be rescued by expression of full-length Pou2af2. Physiologically, Pou2af2 isoform usage tuned innate type 2 immunity in the small intestine. Balb mice maintained responsiveness to helminth pathogens while ignoring commensal Tritrichomonas protists and reducing norovirus burdens.
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Affiliation(s)
- Marija S Nadjsombati
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Natalie Niepoth
- Zuckerman Mind Brain Behavior Institute, Columbia University, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, NY, USA
| | - Lily M Webeck
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Elizabeth A Kennedy
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Danielle L Jones
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Tyler E Billipp
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Megan T Baldridge
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Andres Bendesky
- Zuckerman Mind Brain Behavior Institute, Columbia University, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, NY, USA
| | - Jakob von Moltke
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
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16
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Witt KE, Funk A, Añorve-Garibay V, Fang LL, Huerta-Sánchez E. The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations. Genome Biol Evol 2023; 15:evad066. [PMID: 37103242 PMCID: PMC10194819 DOI: 10.1093/gbe/evad066] [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: 07/08/2022] [Revised: 03/07/2023] [Accepted: 04/17/2023] [Indexed: 04/28/2023] Open
Abstract
Admixture, the genetic merging of parental populations resulting in mixed ancestry, has occurred frequently throughout the course of human history. Numerous admixture events have occurred between human populations across the world, which have shaped genetic ancestry in modern humans. For example, populations in the Americas are often mosaics of different ancestries due to recent admixture events as part of European colonization. Admixed individuals also often have introgressed DNA from Neanderthals and Denisovans that may have come from multiple ancestral populations, which may affect how archaic ancestry is distributed across an admixed genome. In this study, we analyzed admixed populations from the Americas to assess whether the proportion and location of admixed segments due to recent admixture impact an individual's archaic ancestry. We identified a positive correlation between non-African ancestry and archaic alleles, as well as a slight increase of Denisovan alleles in Indigenous American segments relative to European segments in admixed genomes. We also identify several genes as candidates for adaptive introgression, based on archaic alleles present at high frequency in admixed American populations but low frequency in East Asian populations. These results provide insights into how recent admixture events between modern humans redistributed archaic ancestry in admixed genomes.
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Affiliation(s)
- Kelsey E Witt
- Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
| | - Alyssa Funk
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
- Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, Rhode Island
| | - Valeria Añorve-Garibay
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
- Licenciatura en Ciencias Genómicas, Escuela Nacional de Estudios Superiores Unidad Juriquilla, Universidad Nacional Autónoma de México, Querétaro, Mexico
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Lesly Lopez Fang
- Department of Life & Environmental Sciences, University of California, Merced, California, United States of America
| | - Emilia Huerta-Sánchez
- Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
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17
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Hamid I, Korunes KL, Schrider DR, Goldberg A. Localizing Post-Admixture Adaptive Variants with Object Detection on Ancestry-Painted Chromosomes. Mol Biol Evol 2023; 40:msad074. [PMID: 36947126 PMCID: PMC10116606 DOI: 10.1093/molbev/msad074] [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: 09/04/2022] [Revised: 03/14/2023] [Accepted: 03/20/2023] [Indexed: 03/23/2023] Open
Abstract
Gene flow between previously differentiated populations during the founding of an admixed or hybrid population has the potential to introduce adaptive alleles into the new population. If the adaptive allele is common in one source population, but not the other, then as the adaptive allele rises in frequency in the admixed population, genetic ancestry from the source containing the adaptive allele will increase nearby as well. Patterns of genetic ancestry have therefore been used to identify post-admixture positive selection in humans and other animals, including examples in immunity, metabolism, and animal coloration. A common method identifies regions of the genome that have local ancestry "outliers" compared with the distribution across the rest of the genome, considering each locus independently. However, we lack theoretical models for expected distributions of ancestry under various demographic scenarios, resulting in potential false positives and false negatives. Further, ancestry patterns between distant sites are often not independent. As a result, current methods tend to infer wide genomic regions containing many genes as under selection, limiting biological interpretation. Instead, we develop a deep learning object detection method applied to images generated from local ancestry-painted genomes. This approach preserves information from the surrounding genomic context and avoids potential pitfalls of user-defined summary statistics. We find the method is robust to a variety of demographic misspecifications using simulated data. Applied to human genotype data from Cabo Verde, we localize a known adaptive locus to a single narrow region compared with multiple or long windows obtained using two other ancestry-based methods.
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Affiliation(s)
- Iman Hamid
- Department of Evolutionary Anthropology, Duke University, Durham, NC
| | | | - Daniel R Schrider
- Department of Genetics, University of North Carolina, Chapel Hill, NC
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke University, Durham, NC
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18
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Davy T, Ju D, Mathieson I, Skoglund P. Hunter-gatherer admixture facilitated natural selection in Neolithic European farmers. Curr Biol 2023; 33:1365-1371.e3. [PMID: 36963383 PMCID: PMC10153476 DOI: 10.1016/j.cub.2023.02.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/17/2022] [Accepted: 02/15/2023] [Indexed: 03/26/2023]
Abstract
Ancient DNA has revealed multiple episodes of admixture in human prehistory during geographic expansions associated with cultural innovations. One important example is the expansion of Neolithic agricultural groups out of the Near East into Europe and their consequent admixture with Mesolithic hunter-gatherers.1,2,3,4 Ancient genomes from this period provide an opportunity to study the role of admixture in providing new genetic variation for selection to act upon, and also to identify genomic regions that resisted hunter-gatherer introgression and may thus have contributed to agricultural adaptations. We used genome-wide DNA from 677 individuals spanning Mesolithic and Neolithic Europe to infer ancestry deviations in the genomes of admixed individuals and to test for natural selection after admixture by testing for deviations from a genome-wide null distribution. We find that the region around the pigmentation-associated gene SLC24A5 shows the greatest overrepresentation of Neolithic local ancestry in the genome (|Z| = 3.46). In contrast, we find the greatest overrepresentation of Mesolithic ancestry across the major histocompatibility complex (MHC; |Z| = 4.21), a major immunity locus, which also shows allele frequency deviations indicative of selection following admixture (p = 1 × 10-56). This could reflect negative frequency-dependent selection on MHC alleles common in Neolithic populations or that Mesolithic alleles were positively selected for and facilitated adaptation in Neolithic populations to pathogens or other environmental factors. Our study extends previous results that highlight immune function and pigmentation as targets of adaptation in more recent populations to selection processes in the Stone Age.
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Affiliation(s)
- Tom Davy
- Ancient Genomics Laboratory, Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK.
| | - Dan Ju
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd, Philadelphia, PA 19104, USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd, Philadelphia, PA 19104, USA
| | - Pontus Skoglund
- Ancient Genomics Laboratory, Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK.
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19
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The impact of modern admixture on archaic human ancestry in human populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.16.524232. [PMID: 36711776 PMCID: PMC9882123 DOI: 10.1101/2023.01.16.524232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Admixture, the genetic merging of parental populations resulting in mixed ancestry, has occurred frequently throughout the course of human history. Numerous admixture events have occurred between human populations across the world, as well as introgression between humans and archaic humans, Neanderthals and Denisovans. One example are genomes from populations in the Americas, as these are often mosaics of different ancestries due to recent admixture events as part of European colonization. In this study, we analyzed admixed populations from the Americas to assess whether the proportion and location of admixed segments due to recent admixture impact an individual’s archaic ancestry. We identified a positive correlation between non-African ancestry and archaic alleles, as well as a slight enrichment of Denisovan alleles in Indigenous American segments relative to European segments in admixed genomes. We also identify several genes as candidates for adaptive introgression, based on archaic alleles present at high frequency in admixed American populations but low frequency in East Asian populations. These results provide insights into how recent admixture events between modern humans redistributed archaic ancestry in admixed genomes.
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20
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Runge J, König B, Lindholm AK, Bendesky A. Parent-offspring inference in inbred populations. Mol Ecol Resour 2022; 22:2981-2993. [PMID: 35770342 PMCID: PMC9796703 DOI: 10.1111/1755-0998.13680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 06/03/2022] [Accepted: 06/16/2022] [Indexed: 01/07/2023]
Abstract
Genealogical relationships are fundamental components of genetic studies. However, it is often challenging to infer correct and complete pedigrees even when genome-wide information is available. For example, inbreeding can obscure genetic differences between individuals, making it difficult to even distinguish first-degree relatives such as parent-offspring from full siblings. Similarly, genotyping errors can interfere with the detection of genetic similarity between parents and their offspring. Inbreeding is common in natural, domesticated, and experimental populations and genotyping of these populations often has more errors than in human data sets, so efficient methods for building pedigrees under these conditions are necessary. Here, we present a new method for parent-offspring inference in inbred pedigrees called specific parent-offspring relationship estimation (spore). spore is vastly superior to existing pedigree-inference methods at detecting parent-offspring relationships, in particular when inbreeding is high or in the presence of genotyping errors, or both. spore therefore fills an important void in the arsenal of pedigree inference tools.
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Affiliation(s)
- Jan‐Niklas Runge
- Department of Ecology, Evolution and Environmental Biology, Zuckerman Mind Brain Behavior InstituteColumbia UniversityNew YorkNYUSA,Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZürichSwitzerland
| | - Barbara König
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZürichSwitzerland
| | - Anna K. Lindholm
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZürichSwitzerland
| | - Andres Bendesky
- Department of Ecology, Evolution and Environmental Biology, Zuckerman Mind Brain Behavior InstituteColumbia UniversityNew YorkNYUSA
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21
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A unique Toxoplasma gondii haplotype accompanied the global expansion of cats. Nat Commun 2022; 13:5778. [PMID: 36182919 PMCID: PMC9526699 DOI: 10.1038/s41467-022-33556-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 09/22/2022] [Indexed: 11/08/2022] Open
Abstract
Toxoplasma gondii is a cyst-forming apicomplexan parasite of virtually all warm-blooded species, with all true cats (Felidae) as definitive hosts. It is the etiologic agent of toxoplasmosis, a disease causing substantial public health burden worldwide. Few intercontinental clonal lineages represent the large majority of isolates worldwide. Little is known about the evolutionary forces driving the success of these lineages, the timing and the mechanisms of their global dispersal. In this study, we analyse a set of 156 genomes and we provide estimates of T. gondii mutation rate and generation time. We elucidate how the evolution of T. gondii populations is intimately linked to the major events that have punctuated the recent history of cats. We show that a unique haplotype, whose length represents only 0.16% of the whole T. gondii genome, is common to all intercontinental lineages and hybrid populations derived from these lineages. This haplotype has accompanied wildcats (Felis silvestris) during their emergence from the wild to domestic settlements, their dispersal in the Old World, and their expansion in the last five centuries to the Americas. The selection of this haplotype is most parsimoniously explained by its role in sexual reproduction of T. gondii in domestic cats.
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22
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Vilgalys TP, Fogel AS, Anderson JA, Mututua RS, Warutere JK, Siodi IL, Kim SY, Voyles TN, Robinson JA, Wall JD, Archie EA, Alberts SC, Tung J. Selection against admixture and gene regulatory divergence in a long-term primate field study. Science 2022; 377:635-641. [PMID: 35926022 PMCID: PMC9682493 DOI: 10.1126/science.abm4917] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genetic admixture is central to primate evolution. We combined 50 years of field observations of immigration and group demography with genomic data from ~9 generations of hybrid baboons to investigate the consequences of admixture in the wild. Despite no obvious fitness costs to hybrids, we found signatures of selection against admixture similar to those described for archaic hominins. These patterns were concentrated near genes where ancestry is strongly associated with gene expression. Our analyses also show that introgression is partially predictable across the genome. This study demonstrates the value of integrating genomic and field data for revealing how "genomic signatures of selection" (e.g., reduced introgression in low-recombination regions) manifest in nature; moreover, it underscores the importance of other primates as living models for human evolution.
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Affiliation(s)
- Tauras P. Vilgalys
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA,Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Arielle S. Fogel
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA,University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Jordan A. Anderson
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | | | | | | | - Sang Yoon Kim
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | - Tawni N. Voyles
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | | | - Jeffrey D. Wall
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Elizabeth A. Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Susan C. Alberts
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA,Department of Biology, Duke University, Durham, NC, USA,Duke University Population Research Institute, Duke University, Durham, NC, USA
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA,Department of Biology, Duke University, Durham, NC, USA,Duke University Population Research Institute, Duke University, Durham, NC, USA,Canadian Institute for Advanced Research, Toronto, Canada,Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany,Corresponding author
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23
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Blanco Pastor JL. Alternative modes of introgression-mediated selection shaped crop adaptation to novel climates. Genome Biol Evol 2022; 14:6647590. [PMID: 35859297 PMCID: PMC9348624 DOI: 10.1093/gbe/evac107] [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] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Recent plant genomic studies provide fine-grained details on the evolutionary consequences of adaptive introgression during crop domestication. Modern genomic approaches and analytical methods now make it possible to better separate the introgression signal from the demographic signal thus providing a more comprehensive and complex picture of the role of introgression in local adaptation. Adaptive introgression has been fundamental for crop expansion and has involved complex patterns of gene flow. In addition to providing new and more favorable alleles of large effect, introgression during the early stages of domestication also increased allelic diversity at adaptive loci. Previous studies have largely underestimated the effect of such increased diversity following introgression. Recent genomic studies in wheat, potato, maize, grapevine, and ryegrass show that introgression of multiple genes, of as yet unknown effect, increased the effectiveness of purifying selection, and promoted disruptive or fluctuating selection in early cultivars and landraces. Historical selection processes associated with introgression from crop wild relatives provide an instructive analog for adaptation to current climate change and offer new avenues for crop breeding research that are expected to be instrumental for strengthening food security in the coming years.
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24
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Liang M, Shishkin M, Mikhailova A, Shchur V, Nielsen R. Estimating the timing of multiple admixture events using 3-locus linkage disequilibrium. PLoS Genet 2022; 18:e1010281. [PMID: 35839249 PMCID: PMC9342778 DOI: 10.1371/journal.pgen.1010281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 08/01/2022] [Accepted: 06/02/2022] [Indexed: 11/18/2022] Open
Abstract
Estimating admixture histories is crucial for understanding the genetic diversity we see in present-day populations. Allele frequency or phylogeny-based methods are excellent for inferring the existence of admixture or its proportions. However, to estimate admixture times, spatial information from admixed chromosomes of local ancestry or the decay of admixture linkage disequilibrium (ALD) is used. One popular method, implemented in the programs ALDER and ROLLOFF, uses two-locus ALD to infer the time of a single admixture event, but is only able to estimate the time of the most recent admixture event based on this summary statistic. To address this limitation, we derive analytical expressions for the expected ALD in a three-locus system and provide a new statistical method based on these results that is able to resolve more complicated admixture histories. Using simulations, we evaluate the performance of this method on a range of different admixture histories. As an example, we apply the method to the Colombian and Mexican samples from the 1000 Genomes project. The implementation of our method is available at https://github.com/Genomics-HSE/LaNeta. We establish a theoretical framework to model 3-locus admixture linkage disequilibrium of an admixed population taking into account the effects of genetic drift, migration and recombination. The theory is used to develop a method for estimating the times of multiple admixtures events. We demonstrate the accuracy of the method on simulated data and we apply it to previously published data from Mexican and Colombian populations to explore the complex history of American populations in the post-Colombian period.
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Affiliation(s)
- Mason Liang
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Mikhail Shishkin
- International laboratory of statistical and computational genomics, HSE University, Moscow, Russian Federation
| | - Anastasia Mikhailova
- International laboratory of statistical and computational genomics, HSE University, Moscow, Russian Federation
| | - Vladimir Shchur
- International laboratory of statistical and computational genomics, HSE University, Moscow, Russian Federation
- * E-mail: (VS); (RN)
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (VS); (RN)
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25
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Laidre KL, Supple MA, Born EW, Regehr EV, Wiig Ø, Ugarte F, Aars J, Dietz R, Sonne C, Hegelund P, Isaksen C, Akse GB, Cohen B, Stern HL, Moon T, Vollmers C, Corbett-Detig R, Paetkau D, Shapiro B. Glacial ice supports a distinct and undocumented polar bear subpopulation persisting in late 21st-century sea-ice conditions. Science 2022; 376:1333-1338. [PMID: 35709290 DOI: 10.1126/science.abk2793] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Polar bears are susceptible to climate warming because of their dependence on sea ice, which is declining rapidly. We present the first evidence for a genetically distinct and functionally isolated group of polar bears in Southeast Greenland. These bears occupy sea-ice conditions resembling those projected for the High Arctic in the late 21st century, with an annual ice-free period that is >100 days longer than the estimated fasting threshold for the species. Whereas polar bears in most of the Arctic depend on annual sea ice to catch seals, Southeast Greenland bears have a year-round hunting platform in the form of freshwater glacial mélange. This suggests that marine-terminating glaciers, although of limited availability, may serve as previously unrecognized climate refugia. Conservation of Southeast Greenland polar bears, which meet criteria for recognition as the world's 20th polar bear subpopulation, is necessary to preserve the genetic diversity and evolutionary potential of the species.
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Affiliation(s)
- Kristin L Laidre
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA 98105, USA.,Greenland Institute of Natural Resources, 3900 Nuuk, Greenland
| | - Megan A Supple
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Erik W Born
- Greenland Institute of Natural Resources, 3900 Nuuk, Greenland
| | - Eric V Regehr
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA 98105, USA
| | - Øystein Wiig
- Natural History Museum, University of Oslo, Blindern, NO-0318 Oslo, Norway
| | - Fernando Ugarte
- Greenland Institute of Natural Resources, 3900 Nuuk, Greenland
| | - Jon Aars
- Norwegian Polar Institute, Fram Centre, NO-9296 Tromsø, Norway
| | - Rune Dietz
- Department of Ecoscience and Arctic Research Centre, Aarhus University, DK-4000 Roskilde, Denmark
| | - Christian Sonne
- Department of Ecoscience and Arctic Research Centre, Aarhus University, DK-4000 Roskilde, Denmark
| | - Peter Hegelund
- Greenland Institute of Natural Resources, 3900 Nuuk, Greenland
| | - Carl Isaksen
- Greenland Institute of Natural Resources, 3900 Nuuk, Greenland
| | | | - Benjamin Cohen
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA 98105, USA
| | - Harry L Stern
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA 98105, USA
| | - Twila Moon
- National Snow and Ice Data Center, Cooperative Institute for Research In Environmental Sciences (CIRES), University of Colorado, Boulder, CO 80309, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Russ Corbett-Detig
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Paetkau
- Wildlife Genetics International, Nelson, BC V1L 5P9, Canada
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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26
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Duranton M, Pool JE. Interactions between natural selection and recombination shape the genomic landscape of introgression. Mol Biol Evol 2022; 39:6603329. [PMID: 35666817 PMCID: PMC9317171 DOI: 10.1093/molbev/msac122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Hybridization between lineages that have not reached complete reproductive isolation appears more and more like a common phenomenon. Indeed, speciation genomics studies have now extensively shown that many species' genomes have hybrid ancestry. However, genomic patterns of introgression are often heterogeneous across the genome. In many organisms, a positive correlation between introgression levels and recombination rate has been observed. It is usually explained by the purging of deleterious introgressed material due to incompatibilities. However, the opposite relationship was observed in a North American population of Drosophila melanogaster with admixed European and African ancestry. In order to explore how directional and epistatic selection can impact the relationship between introgression and recombination, we performed forward simulations of whole D. melanogaster genomes reflecting the North American population's history. Our results revealed that the simplest models of positive selection often yield negative correlations between introgression and recombination such as the one observed in D. melanogaster. We also confirmed that incompatibilities tend to produce positive introgression-recombination correlations. And yet, we identify parameter space under each model where the predicted correlation is reversed. These findings deepen our understanding of the evolutionary forces that may shape patterns of ancestry across genomes, and they strengthen the foundation for future studies aimed at estimating genome-wide parameters of selection in admixed populations.
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Affiliation(s)
- Maud Duranton
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
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27
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Neo-sex chromosome evolution shapes sex-dependent asymmetrical introgression barrier. Proc Natl Acad Sci U S A 2022; 119:e2119382119. [PMID: 35512091 PMCID: PMC9171612 DOI: 10.1073/pnas.2119382119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
It is increasingly recognized that sex chromosomes are not only the battlegrounds between sexes but also the Great Walls fencing off introgression between diverging lineages. Here we dissect the multifaceted roles of sex chromosomes using experimental evolution, whole-genome resequencing, and theoretical modeling, taking advantage of hybrid populations between a Drosophila sister species pair in the early stage of speciation that have different sex chromosome systems. Our work sheds light onto the complex roles of neo-sex chromosome evolution in creating a sex-dependent asymmetrical introgression barrier at a species boundary, and we show how diverse population genetic forces act in concert to explain observed patterns of introgression across the genome. Sex chromosomes play a special role in the evolution of reproductive barriers between species. Here we describe conflicting roles of nascent sex chromosomes on patterns of introgression in an experimental hybrid swarm. Drosophila nasuta and Drosophila albomicans are recently diverged, fully fertile sister species that have different sex chromosome systems. The fusion between an autosome (Muller CD) with the ancestral X and Y gave rise to neo-sex chromosomes in D. albomicans, while Muller CD remains unfused in D. nasuta. We found that a large block containing overlapping inversions on the neo-sex chromosome stood out as the strongest barrier to introgression. Intriguingly, the neo-sex chromosome introgression barrier is asymmetrical and sex-dependent. Female hybrids showed significant D. albomicans–biased introgression on Muller CD (neo-X excess), while males showed heterosis with excessive (neo-X, D. nasuta Muller CD) genotypes. We used a population genetic model to dissect the interplay of sex chromosome drive, heterospecific pairing incompatibility between the neo-sex chromosomes and unfused Muller CD, neo-Y disadvantage, and neo-X advantage in generating the observed sex chromosome genotypes in females and males. We show that moderate neo-Y disadvantage and D. albomicans specific meiotic drive are required to observe female-specific D. albomicans–biased introgression in this system, together with pairing incompatibility and neo-X advantage. In conclusion, this hybrid swarm between a young species pair sheds light onto the multifaceted roles of neo-sex chromosomes in a sex-dependent asymmetrical introgression barrier at a species boundary.
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28
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Payne C, Bovio R, Powell DL, Gunn TR, Banerjee SM, Grant V, Rosenthal GG, Schumer M. Genomic insights into variation in thermotolerance between hybridizing swordtail fishes. Mol Ecol 2022. [PMID: 35510780 DOI: 10.1111/mec.16489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/22/2022] [Accepted: 04/19/2022] [Indexed: 11/30/2022]
Abstract
Understanding how organisms adapt to changing environments is a core focus of research in evolutionary biology. One common mechanism is adaptive introgression, which has received increasing attention as a potential route to rapid adaptation in populations struggling in the face of ecological change, particularly global climate change. However, hybridization can also result in deleterious genetic interactions that may limit the benefits of adaptive introgression. Here, we used a combination of genome-wide quantitative trait locus mapping and differential gene expression analyses between the swordtail fish species Xiphophorus malinche and X. birchmanni to study the consequences of hybridization on thermotolerance. While these two species are adapted to different thermal environments, we document a complicated architecture of thermotolerance in hybrids. We identify a region of the genome that contributes to reduced thermotolerance in individuals heterozygous for X. malinche and X. birchmanni ancestry, as well as widespread misexpression in hybrids of genes that respond to thermal stress in the parental species, particularly in the circadian clock pathway. We also show that a previously mapped hybrid incompatibility between X. malinche and X. birchmanni contributes to reduced thermotolerance in hybrids. Together, our results highlight the challenges of understanding the impact of hybridization on complex ecological traits and its potential impact on adaptive introgression.
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Affiliation(s)
- Cheyenne Payne
- Department of Biology, Stanford University, Stanford, California, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
| | - Richard Bovio
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Daniel L Powell
- Department of Biology, Stanford University, Stanford, California, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
| | - Theresa R Gunn
- Department of Biology, Stanford University, Stanford, California, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
| | - Shreya M Banerjee
- Department of Biology, Stanford University, Stanford, California, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
| | - Victoria Grant
- Department of Biology, Stanford University, Stanford, California, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
- Department of Biology, Texas A&M University, College Station, Texas, USA
- Department of Biology, University of Padua, Italy
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, California, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
- Department of Biology, University of Padua, Italy
- Hanna H. Gray Fellow, Howard Hughes Medical Institute, Stanford, California, USA
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29
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Kwon YM, Vranken N, Hoge C, Lichak MR, Norovich AL, Francis KX, Camacho-Garcia J, Bista I, Wood J, McCarthy S, Chow W, Tan HH, Howe K, Bandara S, von Lintig J, Rüber L, Durbin R, Svardal H, Bendesky A. Genomic consequences of domestication of the Siamese fighting fish. SCIENCE ADVANCES 2022; 8:eabm4950. [PMID: 35263139 PMCID: PMC8906746 DOI: 10.1126/sciadv.abm4950] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/13/2022] [Indexed: 05/08/2023]
Abstract
Siamese fighting (betta) fish are among the most popular and morphologically diverse pet fish, but the genetic bases of their domestication and phenotypic diversification are largely unknown. We assembled de novo the genome of a wild Betta splendens and whole-genome sequenced 98 individuals across five closely related species. We find evidence of bidirectional hybridization between domesticated ornamental betta and other wild Betta species. We discover dmrt1 as the main sex determination gene in ornamental betta and that it has lower penetrance in wild B. splendens. Furthermore, we find genes with signatures of recent, strong selection that have large effects on color in specific parts of the body or on the shape of individual fins and that most are unlinked. Our results demonstrate how simple genetic architectures paired with anatomical modularity can lead to vast phenotypic diversity generated during animal domestication and launch betta as a powerful new system for evolutionary genetics.
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Affiliation(s)
- Young Mi Kwon
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Nathan Vranken
- Department of Biology, University of Antwerp, 2020 Antwerp, Belgium
- Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Carla Hoge
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Madison R. Lichak
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Amy L. Norovich
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Kerel X. Francis
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | | | - Iliana Bista
- Wellcome Sanger Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | - Shane McCarthy
- Wellcome Sanger Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | - Heok Hui Tan
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
| | | | - Sepalika Bandara
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Johannes von Lintig
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Lukas Rüber
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern 3012, Switzerland
- Naturhistorisches Museum Bern, Bern 3005, Switzerland
| | - Richard Durbin
- Wellcome Sanger Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Hannes Svardal
- Department of Biology, University of Antwerp, 2020 Antwerp, Belgium
- Naturalis Biodiversity Center, 2333 Leiden, Netherlands
| | - Andres Bendesky
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
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30
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MacPherson A, Wang S, Yamaguchi R, Rieseberg L, Otto S. Parental Population Range Expansion Before Secondary Contact Promotes Heterosis. Am Nat 2022; 200:E1-E15. [DOI: 10.1086/719656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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31
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Lange JD, Bastide H, Lack JB, Pool JE. A Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population. Mol Biol Evol 2021; 39:6491261. [PMID: 34971382 PMCID: PMC8826484 DOI: 10.1093/molbev/msab368] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Population genetics seeks to illuminate the forces shaping genetic variation, often based on a single snapshot of genomic variation. However, utilizing multiple sampling times to study changes in allele frequencies can help clarify the relative roles of neutral and non-neutral forces on short time scales. This study compares whole-genome sequence variation of recently collected natural population samples of Drosophila melanogaster against a collection made approximately 35 years prior from the same locality—encompassing roughly 500 generations of evolution. The allele frequency changes between these time points would suggest a relatively small local effective population size on the order of 10,000, significantly smaller than the global effective population size of the species. Some loci display stronger allele frequency changes than would be expected anywhere in the genome under neutrality—most notably the tandem paralogs Cyp6a17 and Cyp6a23, which are impacted by structural variation associated with resistance to pyrethroid insecticides. We find a genome-wide excess of outliers for high genetic differentiation between old and new samples, but a larger number of adaptation targets may have affected SNP-level differentiation versus window differentiation. We also find evidence for strengthening latitudinal allele frequency clines: northern-associated alleles have increased in frequency by an average of nearly 2.5% at SNPs previously identified as clinal outliers, but no such pattern is observed at random SNPs. This project underscores the scientific potential of using multiple sampling time points to investigate how evolution operates in natural populations, by quantifying how genetic variation has changed over ecologically relevant timescales.
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Affiliation(s)
- Jeremy D Lange
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Héloïse Bastide
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Justin B Lack
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706
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32
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Kapun M, Nunez JCB, Bogaerts-Márquez M, Murga-Moreno J, Paris M, Outten J, Coronado-Zamora M, Tern C, Rota-Stabelli O, Guerreiro MPG, Casillas S, Orengo DJ, Puerma E, Kankare M, Ometto L, Loeschcke V, Onder BS, Abbott JK, Schaeffer SW, Rajpurohit S, Behrman EL, Schou MF, Merritt TJS, Lazzaro BP, Glaser-Schmitt A, Argyridou E, Staubach F, Wang Y, Tauber E, Serga SV, Fabian DK, Dyer KA, Wheat CW, Parsch J, Grath S, Veselinovic MS, Stamenkovic-Radak M, Jelic M, Buendía-Ruíz AJ, Gómez-Julián MJ, Espinosa-Jimenez ML, Gallardo-Jiménez FD, Patenkovic A, Eric K, Tanaskovic M, Ullastres A, Guio L, Merenciano M, Guirao-Rico S, Horváth V, Obbard DJ, Pasyukova E, Alatortsev VE, Vieira CP, Vieira J, Torres JR, Kozeretska I, Maistrenko OM, Montchamp-Moreau C, Mukha DV, Machado HE, Lamb K, Paulo T, Yusuf L, Barbadilla A, Petrov D, Schmidt P, Gonzalez J, Flatt T, Bergland AO. Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource. Mol Biol Evol 2021; 38:5782-5805. [PMID: 34469576 PMCID: PMC8662648 DOI: 10.1093/molbev/msab259] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.
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Affiliation(s)
- Martin Kapun
- Department of Evolutionary Biology and Environmental Studies, University of
Zürich, Switzerland
- Department of Cell & Developmental Biology, Center of Anatomy and Cell
Biology, Medical University of Vienna, Vienna, Austria
| | - Joaquin C B Nunez
- Department of Biology, University of Virginia, Charlottesville,
VA, USA
| | | | - Jesús Murga-Moreno
- Department of Genetics and Microbiology, Universitat Autònoma de
Barcelona, Barcelona, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de
Barcelona, Barcelona, Spain
| | - Margot Paris
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Joseph Outten
- Department of Biology, University of Virginia, Charlottesville,
VA, USA
| | | | - Courtney Tern
- Department of Biology, University of Virginia, Charlottesville,
VA, USA
| | - Omar Rota-Stabelli
- Center Agriculture Food Environment, University of Trento, San Michele all'
Adige, Italy
| | | | - Sònia Casillas
- Department of Genetics and Microbiology, Universitat Autònoma de
Barcelona, Barcelona, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de
Barcelona, Barcelona, Spain
| | - Dorcas J Orengo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia,
Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de
Barcelona, Barcelona, Spain
| | - Eva Puerma
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia,
Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de
Barcelona, Barcelona, Spain
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of
Jyväskylä, Jyväskylä, Finland
| | - Lino Ometto
- Department of Biology and Biotechnology, University of Pavia,
Pavia, Italy
| | | | - Banu S Onder
- Department of Biology, Hacettepe University, Ankara, Turkey
| | | | - Stephen W Schaeffer
- Department of Biology, The Pennsylvania State University,
University Park, PA, USA
| | - Subhash Rajpurohit
- Department of Biology, University of Pennsylvania, Philadelphia,
PA, USA
- Division of Biological and Life Sciences, School of Arts and Sciences,
Ahmedabad University, Ahmedabad, India
| | - Emily L Behrman
- Department of Biology, University of Pennsylvania, Philadelphia,
PA, USA
- Janelia Research Campus, Ashburn, VA, USA
| | - Mads F Schou
- Department of Biology, Aarhus University, Aarhus, Denmark
- Department of Biology, Lund University, Lund, Sweden
| | - Thomas J S Merritt
- Department of Chemistry & Biochemistry, Laurentian
University, Sudbury, ON, Canada
| | - Brian P Lazzaro
- Department of Entomology, Cornell University, Ithaca, NY,
USA
| | - Amanda Glaser-Schmitt
- Division of Evolutionary Biology, Faculty of Biology,
Ludwig-Maximilians-Universität, Munich, Germany
| | - Eliza Argyridou
- Division of Evolutionary Biology, Faculty of Biology,
Ludwig-Maximilians-Universität, Munich, Germany
| | - Fabian Staubach
- Department of Evolution and Ecology, University of Freiburg,
Freiburg, Germany
| | - Yun Wang
- Department of Evolution and Ecology, University of Freiburg,
Freiburg, Germany
| | - Eran Tauber
- Department of Evolutionary and Environmental Biology, Institute of Evolution,
University of Haifa, Haifa, Israel
| | - Svitlana V Serga
- Department of General and Medical Genetics, Taras Shevchenko National
University of Kyiv, Kyiv, Ukraine
- State Institution National Antarctic Scientific Center, Ministry of Education
and Science of Ukraine, Kyiv, Ukraine
| | - Daniel K Fabian
- Department of Genetics, University of Cambridge, Cambridge,
United Kingdom
| | - Kelly A Dyer
- Department of Genetics, University of Georgia, Athens, GA,
USA
| | | | - John Parsch
- Division of Evolutionary Biology, Faculty of Biology,
Ludwig-Maximilians-Universität, Munich, Germany
| | - Sonja Grath
- Division of Evolutionary Biology, Faculty of Biology,
Ludwig-Maximilians-Universität, Munich, Germany
| | | | | | - Mihailo Jelic
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | | | | | | | | | - Aleksandra Patenkovic
- Institute for Biological Research “Siniša Stanković”, National Institute of
Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Katarina Eric
- Institute for Biological Research “Siniša Stanković”, National Institute of
Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Marija Tanaskovic
- Institute for Biological Research “Siniša Stanković”, National Institute of
Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Anna Ullastres
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Lain Guio
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Miriam Merenciano
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Sara Guirao-Rico
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Vivien Horváth
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Darren J Obbard
- Institute of Evolutionary Biology, University of Edinburgh,
Edinburgh, United Kingdom
| | - Elena Pasyukova
- Institute of Molecular Genetics of the National Research Centre “Kurchatov
Institute”, Moscow, Russia
| | - Vladimir E Alatortsev
- Institute of Molecular Genetics of the National Research Centre “Kurchatov
Institute”, Moscow, Russia
| | - Cristina P Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do
Porto, Porto, Portugal
| | - Jorge Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do
Porto, Porto, Portugal
| | | | - Iryna Kozeretska
- Department of General and Medical Genetics, Taras Shevchenko National
University of Kyiv, Kyiv, Ukraine
- State Institution National Antarctic Scientific Center, Ministry of Education
and Science of Ukraine, Kyiv, Ukraine
| | - Oleksandr M Maistrenko
- Department of General and Medical Genetics, Taras Shevchenko National
University of Kyiv, Kyiv, Ukraine
- Structural and Computational Biology Unit, European Molecular Biology
Laboratory, Heidelberg, Germany
| | | | - Dmitry V Mukha
- Vavilov Institute of General Genetics, Russian Academy of
Sciences, Moscow, Russia
| | - Heather E Machado
- Department of Biology, Stanford University, Stanford, CA,
USA
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Keric Lamb
- Department of Biology, University of Virginia, Charlottesville,
VA, USA
| | - Tânia Paulo
- Departamento de Biologia Animal, Instituto Gulbenkian de Ciência,
Oeiras, Portugal
| | - Leeban Yusuf
- Center for Biological Diversity, University of St. Andrews, St
Andrews, United Kingdom
| | - Antonio Barbadilla
- Department of Genetics and Microbiology, Universitat Autònoma de
Barcelona, Barcelona, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de
Barcelona, Barcelona, Spain
| | - Dmitri Petrov
- Department of Biology, Stanford University, Stanford, CA,
USA
| | - Paul Schmidt
- Department of Biology, The Pennsylvania State University,
University Park, PA, USA
| | - Josefa Gonzalez
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Alan O Bergland
- Department of Biology, University of Virginia, Charlottesville,
VA, USA
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33
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Nürnberger B, Baird SJE, Čížková D, Bryjová A, Mudd AB, Blaxter ML, Szymura JM. A dense linkage map for a large repetitive genome: discovery of the sex-determining region in hybridizing fire-bellied toads (Bombina bombina and Bombina variegata). G3 (BETHESDA, MD.) 2021; 11:6353606. [PMID: 34849761 PMCID: PMC8664441 DOI: 10.1093/g3journal/jkab286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/16/2021] [Indexed: 12/20/2022]
Abstract
Genomic analysis of hybrid zones offers unique insights into emerging reproductive isolation and the dynamics of introgression. Because hybrid genomes consist of blocks inherited from one or the other parental taxon, linkage information is essential. In most cases, the spectrum of local ancestry tracts can be efficiently uncovered from dense linkage maps. Here, we report the development of such a map for the hybridizing toads, Bombina bombina and Bombina variegata (Anura: Bombinatoridae). Faced with the challenge of a large (7–10 Gb), repetitive genome, we set out to identify a large number of Mendelian markers in the nonrepetitive portion of the genome that report B. bombina vs B. variegata ancestry with appropriately quantified statistical support. Bait sequences for targeted enrichment were selected from a draft genome assembly, after filtering highly repetitive sequences. We developed a novel approach to infer the most likely diplotype per sample and locus from the raw read mapping data, which is robust to over-merging and obviates arbitrary filtering thresholds. Validation of the resulting map with 4755 markers underscored the large-scale synteny between Bombina and Xenopus tropicalis. By assessing the sex of late-stage F2 tadpoles from histological sections, we identified the sex-determining region in the Bombina genome to 7 cM on LG5, which is homologous to X. tropicalis chromosome 5, and inferred male heterogamety. Interestingly, chromosome 5 has been repeatedly recruited as a sex chromosome in anurans with XY sex determination.
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Affiliation(s)
- Beate Nürnberger
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Stuart J E Baird
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Dagmar Čížková
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Anna Bryjová
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Austin B Mudd
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, 94720 CA, USA
| | - Mark L Blaxter
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Jacek M Szymura
- Department of Comparative Anatomy, Jagiellonian University, 30-387 Kraków, Poland
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34
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Chen ZH, Xu YX, Xie XL, Wang DF, Aguilar-Gómez D, Liu GJ, Li X, Esmailizadeh A, Rezaei V, Kantanen J, Ammosov I, Nosrati M, Periasamy K, Coltman DW, Lenstra JA, Nielsen R, Li MH. Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep. Commun Biol 2021; 4:1307. [PMID: 34795381 PMCID: PMC8602413 DOI: 10.1038/s42003-021-02817-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/27/2021] [Indexed: 02/06/2023] Open
Abstract
The domestication and subsequent development of sheep are crucial events in the history of human civilization and the agricultural revolution. However, the impact of interspecific introgression on the genomic regions under domestication and subsequent selection remains unclear. Here, we analyze the whole genomes of domestic sheep and their wild relative species. We found introgression from wild sheep such as the snow sheep and its American relatives (bighorn and thinhorn sheep) into urial, Asiatic and European mouflons. We observed independent events of adaptive introgression from wild sheep into the Asiatic and European mouflons, as well as shared introgressed regions from both snow sheep and argali into Asiatic mouflon before or during the domestication process. We revealed European mouflons might arise through hybridization events between a now extinct sheep in Europe and feral domesticated sheep around 6000-5000 years BP. We also unveiled later introgressions from wild sheep to their sympatric domestic sheep after domestication. Several of the introgression events contain loci with candidate domestication genes (e.g., PAPPA2, NR6A1, SH3GL3, RFX3 and CAMK4), associated with morphological, immune, reproduction or production traits (wool/meat/milk). We also detected introgression events that introduced genes related to nervous response (NEURL1), neurogenesis (PRUNE2), hearing ability (USH2A), and placental viability (PAG11 and PAG3) into domestic sheep and their ancestral wild species from other wild species.
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Affiliation(s)
- Ze-Hui Chen
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China ,grid.22935.3f0000 0004 0530 8290College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ya-Xi Xu
- grid.22935.3f0000 0004 0530 8290College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xing-Long Xie
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Dong-Feng Wang
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Diana Aguilar-Gómez
- grid.47840.3f0000 0001 2181 7878Center for Computational Biology, University of California at Berkeley, Berkeley, CA 94720 USA
| | | | - Xin Li
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ali Esmailizadeh
- grid.412503.10000 0000 9826 9569Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Vahideh Rezaei
- grid.412503.10000 0000 9826 9569Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Juha Kantanen
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Innokentyi Ammosov
- grid.495192.2Laboratory of Reindeer Husbandry and Traditional Industries, Yakut Scientific Research Institute of Agriculture, The Sakha Republic (Yakutia), Yakutsk, Russia
| | - Maryam Nosrati
- grid.412462.70000 0000 8810 3346Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Kathiravan Periasamy
- grid.420221.70000 0004 0403 8399Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
| | - David W. Coltman
- grid.17089.37Department of Biological Sciences, University of Alberta, Edmonton, AB T6G2E9 Canada
| | - Johannes A. Lenstra
- grid.5477.10000000120346234Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California at Berkeley, Berkeley, CA, 94720, USA. .,Department of Statistics, UC Berkeley, Berkeley, CA, 94707, USA. .,Globe Institute, University of Copenhagen, 1350, København K, Denmark.
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China.
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35
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Janzen T, Miró Pina V. Estimating the time since admixture from phased and unphased molecular data. Mol Ecol Resour 2021; 22:908-926. [PMID: 34599646 PMCID: PMC9291888 DOI: 10.1111/1755-0998.13519] [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: 09/29/2020] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 11/26/2022]
Abstract
After admixture, recombination breaks down genomic blocks of contiguous ancestry. The breakdown of these blocks forms a new “molecular clock” that ticks at a much faster rate than the mutation clock, enabling accurate dating of admixture events in the recent past. However, existing theory on the breakdown of these blocks, or the accumulation of delineations between blocks, so‐called “junctions”, has mostly been limited to using regularly spaced markers on phased data. Here, we present an extension to the theory of junctions using the ancestral recombination graph that describes the expected number of junctions for any distribution of markers along the genome. Furthermore, we provide a new framework to infer the time since admixture using unphased data. We demonstrate both the phased and unphased methods on simulated data and show that our new extensions have improved accuracy with respect to previous methods, especially for smaller population sizes and more ancient admixture times. Lastly, we demonstrate the applicability of our method on three empirical data sets, including labcrosses of yeast (Saccharomyces cerevisae) and two case studies of hybridization in swordtail fish and Populus trees.
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Affiliation(s)
- Thijs Janzen
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands.,Carl von Ossietzky University, Oldenburg, Germany
| | - Verónica Miró Pina
- Instituto de Investigaciones en Matemáticas Aplicadas y Sistemas (IIMAS), Universidad Nacional Autónoma de México (UNAM), México City, México.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
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36
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Calfee E, Gates D, Lorant A, Perkins MT, Coop G, Ross-Ibarra J. Selective sorting of ancestral introgression in maize and teosinte along an elevational cline. PLoS Genet 2021; 17:e1009810. [PMID: 34634032 PMCID: PMC8530355 DOI: 10.1371/journal.pgen.1009810] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/21/2021] [Accepted: 09/07/2021] [Indexed: 12/02/2022] Open
Abstract
While often deleterious, hybridization can also be a key source of genetic variation and pre-adapted haplotypes, enabling rapid evolution and niche expansion. Here we evaluate these opposing selection forces on introgressed ancestry between maize (Zea mays ssp. mays) and its wild teosinte relative, mexicana (Zea mays ssp. mexicana). Introgression from ecologically diverse teosinte may have facilitated maize's global range expansion, in particular to challenging high elevation regions (> 1500 m). We generated low-coverage genome sequencing data for 348 maize and mexicana individuals to evaluate patterns of introgression in 14 sympatric population pairs, spanning the elevational range of mexicana, a teosinte endemic to the mountains of Mexico. While recent hybrids are commonly observed in sympatric populations and mexicana demonstrates fine-scale local adaptation, we find that the majority of mexicana ancestry tracts introgressed into maize over 1000 generations ago. This mexicana ancestry seems to have maintained much of its diversity and likely came from a common ancestral source, rather than contemporary sympatric populations, resulting in relatively low FST between mexicana ancestry tracts sampled from geographically distant maize populations. Introgressed mexicana ancestry in maize is reduced in lower-recombination rate quintiles of the genome and around domestication genes, consistent with pervasive selection against introgression. However, we also find mexicana ancestry increases across the sampled elevational gradient and that high introgression peaks are most commonly shared among high-elevation maize populations, consistent with introgression from mexicana facilitating adaptation to the highland environment. In the other direction, we find patterns consistent with adaptive and clinal introgression of maize ancestry into sympatric mexicana at many loci across the genome, suggesting that maize also contributes to adaptation in mexicana, especially at the lower end of its elevational range. In sympatric maize, in addition to high introgression regions we find many genomic regions where selection for local adaptation maintains steep gradients in introgressed mexicana ancestry across elevation, including at least two inversions: the well-characterized 14 Mb Inv4m on chromosome 4 and a novel 3 Mb inversion Inv9f surrounding the macrohairless1 locus on chromosome 9. Most outlier loci with high mexicana introgression show no signals of sweeps or local sourcing from sympatric populations and so likely represent ancestral introgression sorted by selection, resulting in correlated but distinct outcomes of introgression in different contemporary maize populations.
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Affiliation(s)
- Erin Calfee
- Center for Population Biology, University of California, Davis, California, United States of America
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | - Daniel Gates
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | - Anne Lorant
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - M. Taylor Perkins
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | - Graham Coop
- Center for Population Biology, University of California, Davis, California, United States of America
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | - Jeffrey Ross-Ibarra
- Center for Population Biology, University of California, Davis, California, United States of America
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
- Genome Center, University of California, Davis, California, United States of America
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37
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Moran BM, Payne C, Langdon Q, Powell DL, Brandvain Y, Schumer M. The genomic consequences of hybridization. eLife 2021; 10:e69016. [PMID: 34346866 PMCID: PMC8337078 DOI: 10.7554/elife.69016] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/09/2021] [Indexed: 12/29/2022] Open
Abstract
In the past decade, advances in genome sequencing have allowed researchers to uncover the history of hybridization in diverse groups of species, including our own. Although the field has made impressive progress in documenting the extent of natural hybridization, both historical and recent, there are still many unanswered questions about its genetic and evolutionary consequences. Recent work has suggested that the outcomes of hybridization in the genome may be in part predictable, but many open questions about the nature of selection on hybrids and the biological variables that shape such selection have hampered progress in this area. We synthesize what is known about the mechanisms that drive changes in ancestry in the genome after hybridization, highlight major unresolved questions, and discuss their implications for the predictability of genome evolution after hybridization.
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Affiliation(s)
- Benjamin M Moran
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Cheyenne Payne
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Quinn Langdon
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Daniel L Powell
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Yaniv Brandvain
- Department of Ecology, Evolution & Behavior and Plant and Microbial Biology, University of MinnesotaMinneapolisUnited States
| | - Molly Schumer
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
- Hanna H. Gray Fellow, Howard Hughes Medical InstituteStanfordUnited States
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38
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Frayer ME, Payseur BA. Demographic history shapes genomic ancestry in hybrid zones. Ecol Evol 2021; 11:10290-10302. [PMID: 34367575 PMCID: PMC8328415 DOI: 10.1002/ece3.7833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 12/26/2022] Open
Abstract
Demographic factors such as migration rate and population size can impede or facilitate speciation. In hybrid zones, reproductive boundaries between species are tested and demography mediates the opportunity for admixture between lineages that are partially isolated. Genomic ancestry is a powerful tool for revealing the history of admixed populations, but models and methods based on local ancestry are rarely applied to structured hybrid zones. To understand the effects of demography on ancestry in hybrids zones, we performed individual-based simulations under a stepping-stone model, treating migration rate, deme size, and hybrid zone age as parameters. We find that the number of ancestry junctions (the transition points between genomic regions with different ancestries) and heterogenicity (the genomic proportion heterozygous for ancestry) are often closely connected to demographic history. Reducing deme size reduces junction number and heterogenicity. Elevating migration rate increases heterogenicity, but migration affects junction number in more complex ways. We highlight the junction frequency spectrum as a novel and informative summary of ancestry that responds to demographic history. A substantial proportion of junctions are expected to fix when migration is limited or deme size is small, changing the shape of the spectrum. Our findings suggest that genomic patterns of ancestry could be used to infer demographic history in hybrid zones.
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Affiliation(s)
- Megan E. Frayer
- Laboratory of GeneticsUniversity of Wisconsin MadisonMadisonWIUSA
| | - Bret A. Payseur
- Laboratory of GeneticsUniversity of Wisconsin MadisonMadisonWIUSA
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39
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Janzen T, Diaz F. Individual‐based simulations of genome evolution with ancestry: The
GenomeAdmixR
R package. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Thijs Janzen
- Groningen Institute for Evolutionary Life Sciences University of Groningen Groningen The Netherlands
- Carl von Ossietzky University Oldenburg Germany
| | - Fernando Diaz
- Department of Entomology University of Arizona Tucson AZ USA
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40
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Lovell JT, Bentley NB, Bhattarai G, Jenkins JW, Sreedasyam A, Alarcon Y, Bock C, Boston LB, Carlson J, Cervantes K, Clermont K, Duke S, Krom N, Kubenka K, Mamidi S, Mattison CP, Monteros MJ, Pisani C, Plott C, Rajasekar S, Rhein HS, Rohla C, Song M, Hilaire RS, Shu S, Wells L, Webber J, Heerema RJ, Klein PE, Conner P, Wang X, Grauke LJ, Grimwood J, Schmutz J, Randall JJ. Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding. Nat Commun 2021; 12:4125. [PMID: 34226565 PMCID: PMC8257795 DOI: 10.1038/s41467-021-24328-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023] Open
Abstract
Genome-enabled biotechnologies have the potential to accelerate breeding efforts in long-lived perennial crop species. Despite the transformative potential of molecular tools in pecan and other outcrossing tree species, highly heterozygous genomes, significant presence-absence gene content variation, and histories of interspecific hybridization have constrained breeding efforts. To overcome these challenges, here, we present diploid genome assemblies and annotations of four outbred pecan genotypes, including a PacBio HiFi chromosome-scale assembly of both haplotypes of the 'Pawnee' cultivar. Comparative analysis and pan-genome integration reveal substantial and likely adaptive interspecific genomic introgressions, including an over-retained haplotype introgressed from bitternut hickory into pecan breeding pedigrees. Further, by leveraging our pan-genome presence-absence and functional annotation database among genomes and within the two outbred haplotypes of the 'Lakota' genome, we identify candidate genes for pest and pathogen resistance. Combined, these analyses and resources highlight significant progress towards functional and quantitative genomics in highly diverse and outbred crops.
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Affiliation(s)
- John T. Lovell
- grid.417691.c0000 0004 0408 3720Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Nolan B. Bentley
- grid.264756.40000 0004 4687 2082Department of Horticultural Science, Texas A&M University, College Station, TX USA
| | - Gaurab Bhattarai
- grid.213876.90000 0004 1936 738XInstitute of Plant Breeding, Genetics & Genomics, University of Georgia, Athens, GA USA
| | - Jerry W. Jenkins
- grid.417691.c0000 0004 0408 3720Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Avinash Sreedasyam
- grid.417691.c0000 0004 0408 3720Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Yanina Alarcon
- grid.419447.b0000 0004 0370 5663Noble Research Institute, Ardmore, OK USA
| | - Clive Bock
- USDA Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA USA
| | - Lori Beth Boston
- grid.417691.c0000 0004 0408 3720Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Joseph Carlson
- grid.451309.a0000 0004 0449 479XDOE Joint Genome Institute, Berkeley, CA USA
| | - Kimberly Cervantes
- grid.24805.3b0000 0001 0687 2182Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM USA
| | - Kristen Clermont
- grid.507314.4USDA-ARS Food Processing and Sensory Quality Research, New Orleans, LA USA
| | - Sara Duke
- USDA-ARS Plains Area Administrative Office, College Station, TX USA
| | - Nick Krom
- grid.419447.b0000 0004 0370 5663Noble Research Institute, Ardmore, OK USA
| | - Keith Kubenka
- USDA Pecan Breeding and Genetics, College Station, TX USA
| | - Sujan Mamidi
- grid.417691.c0000 0004 0408 3720Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | | | - Maria J. Monteros
- grid.419447.b0000 0004 0370 5663Noble Research Institute, Ardmore, OK USA
| | - Cristina Pisani
- USDA Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA USA
| | - Christopher Plott
- grid.417691.c0000 0004 0408 3720Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Shanmugam Rajasekar
- grid.134563.60000 0001 2168 186XArizona Genomics Institute, University of Arizona, Tucson, AZ USA
| | - Hormat Shadgou Rhein
- grid.24805.3b0000 0001 0687 2182Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM USA
| | - Charles Rohla
- grid.419447.b0000 0004 0370 5663Noble Research Institute, Ardmore, OK USA
| | - Mingzhou Song
- grid.24805.3b0000 0001 0687 2182Department of Computer Science, New Mexico State University, Las Cruces, NM USA
| | - Rolston St. Hilaire
- grid.24805.3b0000 0001 0687 2182Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM USA
| | - Shengqiang Shu
- grid.451309.a0000 0004 0449 479XDOE Joint Genome Institute, Berkeley, CA USA
| | - Lenny Wells
- grid.213876.90000 0004 1936 738XDepartment of Horticulture, University of Georgia-Tifton Campus, Tifton, GA USA
| | - Jenell Webber
- grid.417691.c0000 0004 0408 3720Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Richard J. Heerema
- grid.24805.3b0000 0001 0687 2182Department of Computer Science, New Mexico State University, Las Cruces, NM USA
| | - Patricia E. Klein
- grid.264756.40000 0004 4687 2082Department of Horticultural Science, Texas A&M University, College Station, TX USA
| | - Patrick Conner
- grid.213876.90000 0004 1936 738XDepartment of Horticulture, University of Georgia-Tifton Campus, Tifton, GA USA
| | - Xinwang Wang
- USDA Pecan Breeding and Genetics, College Station, TX USA
| | - L. J. Grauke
- USDA Pecan Breeding and Genetics, College Station, TX USA
| | - Jane Grimwood
- grid.417691.c0000 0004 0408 3720Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Jeremy Schmutz
- grid.417691.c0000 0004 0408 3720Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL USA ,grid.451309.a0000 0004 0449 479XDOE Joint Genome Institute, Berkeley, CA USA
| | - Jennifer J. Randall
- grid.24805.3b0000 0001 0687 2182Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM USA
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Abstract
Recent studies suggest that admixture with archaic hominins played an important role in facilitating biological adaptations to new environments. For example, interbreeding with Denisovans facilitated the adaptation to high-altitude environments on the Tibetan Plateau. Specifically, the EPAS1 gene, a transcription factor that regulates the response to hypoxia, exhibits strong signatures of both positive selection and introgression from Denisovans in Tibetan individuals. Interestingly, despite being geographically closer to the Denisova Cave, East Asian populations do not harbor as much Denisovan ancestry as populations from Melanesia. Recently, two studies have suggested two independent waves of Denisovan admixture into East Asians, one of which is shared with South Asians and Oceanians. Here, we leverage data from EPAS1 in 78 Tibetan individuals to interrogate which of these two introgression events introduced the EPAS1 beneficial sequence into the ancestral population of Tibetans, and we use the distribution of introgressed segment lengths at this locus to infer the timing of the introgression and selection event. We find that the introgression event unique to East Asians most likely introduced the beneficial haplotype into the ancestral population of Tibetans around 48,700 (16,000-59,500) y ago, and selection started around 9,000 (2,500-42,000) y ago. Our estimates suggest that one of the most convincing examples of adaptive introgression is in fact selection acting on standing archaic variation.
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42
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Svedberg J, Shchur V, Reinman S, Nielsen R, Corbett-Detig R. Inferring Adaptive Introgression Using Hidden Markov Models. Mol Biol Evol 2021; 38:2152-2165. [PMID: 33502512 PMCID: PMC8097282 DOI: 10.1093/molbev/msab014] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Adaptive introgression-the flow of adaptive genetic variation between species or populations-has attracted significant interest in recent years and it has been implicated in a number of cases of adaptation, from pesticide resistance and immunity, to local adaptation. Despite this, methods for identification of adaptive introgression from population genomic data are lacking. Here, we present Ancestry_HMM-S, a hidden Markov model-based method for identifying genes undergoing adaptive introgression and quantifying the strength of selection acting on them. Through extensive validation, we show that this method performs well on moderately sized data sets for realistic population and selection parameters. We apply Ancestry_HMM-S to a data set of an admixed Drosophila melanogaster population from South Africa and we identify 17 loci which show signatures of adaptive introgression, four of which have previously been shown to confer resistance to insecticides. Ancestry_HMM-S provides a powerful method for inferring adaptive introgression in data sets that are typically collected when studying admixed populations. This method will enable powerful insights into the genetic consequences of admixture across diverse populations. Ancestry_HMM-S can be downloaded from https://github.com/jesvedberg/Ancestry_HMM-S/.
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Affiliation(s)
- Jesper Svedberg
- Department of Biomolecular Engineering, Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Vladimir Shchur
- National Research University Higher School of Economics, Moscow, Russian Federation
| | - Solomon Reinman
- Department of Biomolecular Engineering, Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Rasmus Nielsen
- National Research University Higher School of Economics, Moscow, Russian Federation
- Department of Integrative Biology and Department of Statistics, UC Berkeley, Berkeley, CA, USA
- Center for GeoGenetics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
- National Research University Higher School of Economics, Moscow, Russian Federation
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43
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Grassa CJ, Weiblen GD, Wenger JP, Dabney C, Poplawski SG, Timothy Motley S, Michael TP, Schwartz CJ. A new Cannabis genome assembly associates elevated cannabidiol (CBD) with hemp introgressed into marijuana. THE NEW PHYTOLOGIST 2021; 230:1665-1679. [PMID: 33521943 PMCID: PMC8248131 DOI: 10.1111/nph.17243] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/18/2021] [Indexed: 05/20/2023]
Abstract
Demand for cannabidiol (CBD), the predominant cannabinoid in hemp (Cannabis sativa), has favored cultivars producing unprecedented quantities of CBD. We investigated the ancestry of a new cultivar and cannabinoid synthase genes in relation to cannabinoid inheritance. A nanopore-based assembly anchored to a high-resolution linkage map provided a chromosome-resolved genome for CBDRx, a potent CBD-type cultivar. We measured cannabinoid synthase expression by cDNA sequencing and conducted a population genetic analysis of diverse Cannabis accessions. Quantitative trait locus mapping of cannabinoids in a hemp × marijuana segregating population was also performed. Cannabinoid synthase paralogs are arranged in tandem arrays embedded in long terminal repeat retrotransposons on chromosome 7. Although CBDRx is predominantly of marijuana ancestry, the genome has cannabidiolic acid synthase (CBDAS) introgressed from hemp and lacks a complete sequence for tetrahydrocannabinolic acid synthase (THCAS). Three additional genomes, including one with complete THCAS, confirmed this genomic structure. Only cannabidiolic acid synthase (CBDAS) was expressed in CBD-type Cannabis, while both CBDAS and THCAS were expressed in a cultivar with an intermediate tetrahydrocannabinol (THC) : CBD ratio. Although variation among cannabinoid synthase loci might affect the THC : CBD ratio, variability among cultivars in overall cannabinoid content (potency) was also associated with other chromosomes.
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Affiliation(s)
| | - George D. Weiblen
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMN55108USA
| | - Jonathan P. Wenger
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMN55108USA
| | - Clemon Dabney
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMN55108USA
| | | | - S. Timothy Motley
- Department of InformaticsJ. Craig Venter InstituteLa JollaCA92037USA
| | - Todd P. Michael
- Department of InformaticsJ. Craig Venter InstituteLa JollaCA92037USA
- Present address:
Molecular and Cellular Biology LaboratorySalk Institute for Biological StudiesLa JollaCA92037USA
| | - C. J. Schwartz
- Sunrise Genetics Inc.Fort CollinsCO80525USA
- Present address:
Industrial Hemp Genetics LLCMadisonWI53705USA
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44
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Oppenheimer J, Rosen BD, Heaton MP, Vander Ley BL, Shafer WR, Schuetze FT, Stroud B, Kuehn LA, McClure JC, Barfield JP, Blackburn HD, Kalbfleisch TS, Bickhart DM, Davenport KM, Kuhn KL, Green RE, Shapiro B, Smith TPL. A Reference Genome Assembly of American Bison, Bison bison bison. J Hered 2021; 112:174-183. [PMID: 33595645 PMCID: PMC8006816 DOI: 10.1093/jhered/esab003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 01/13/2021] [Indexed: 11/14/2022] Open
Abstract
Bison are an icon of the American West and an ecologically, commercially, and culturally important species. Despite numbering in the hundreds of thousands today, conservation concerns remain for the species, including the impact on genetic diversity of a severe bottleneck around the turn of the 20th century and genetic introgression from domestic cattle. Genetic diversity and admixture are best evaluated at genome-wide scale, for which a high-quality reference is necessary. Here, we use trio binning of long reads from a bison-Simmental cattle (Bos taurus taurus) male F1 hybrid to sequence and assemble the genome of the American plains bison (Bison bison bison). The male haplotype genome is chromosome-scale, with a total length of 2.65 Gb across 775 scaffolds (839 contigs) and a scaffold N50 of 87.8 Mb. Our bison genome is ~13× more contiguous overall and ~3400× more contiguous at the contig level than the current bison reference genome. The bison genome sequence presented here (ARS-UCSC_bison1.0) will enable new research into the evolutionary history of this iconic megafauna species and provide a new tool for the management of bison populations in federal and commercial herds.
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Affiliation(s)
- Jonas Oppenheimer
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Benjamin D Rosen
- USDA, ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, USA
| | - Michael P Heaton
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Brian L Vander Ley
- Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | | | - Brad Stroud
- Stroud Veterinary Embryo Services, Weatherford, TE, USA
| | - Larry A Kuehn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | | | - Jennifer P Barfield
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | | | | | | | - Kimberly M Davenport
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, ID, USA
| | - Kristen L Kuhn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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45
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Powell DL, Payne C, Banerjee SM, Keegan M, Bashkirova E, Cui R, Andolfatto P, Rosenthal GG, Schumer M. The Genetic Architecture of Variation in the Sexually Selected Sword Ornament and Its Evolution in Hybrid Populations. Curr Biol 2021; 31:923-935.e11. [PMID: 33513352 DOI: 10.1016/j.cub.2020.12.049] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/27/2020] [Accepted: 12/25/2020] [Indexed: 10/22/2022]
Abstract
Biologists since Darwin have been fascinated by the evolution of sexually selected ornaments, particularly those that reduce viability. Uncovering the genetic architecture of these traits is key to understanding how they evolve and are maintained. Here, we investigate the genetic architecture and evolutionary loss of a sexually selected ornament, the "sword" fin extension that characterizes many species of swordtail fish (Xiphophorus). Using sworded and swordless sister species of Xiphophorus, we generated a mapping population and show that the sword ornament is polygenic-with ancestry across the genome explaining substantial variation in the trait. After accounting for the impacts of genome-wide ancestry, we identify one major-effect quantitative trait locus (QTL) that explains ~5% of the overall variation in the trait. Using a series of approaches, we narrow this large QTL interval to several likely candidate genes, including genes involved in fin regeneration and growth. Furthermore, we find evidence of selection on ancestry at one of these candidates in four natural hybrid populations, consistent with selection against the sword in these populations.
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Affiliation(s)
- Daniel L Powell
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843, USA.
| | - Cheyenne Payne
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México
| | - Shreya M Banerjee
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México
| | - Mackenzie Keegan
- Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Elizaveta Bashkirova
- Department of Biochemistry and Molecular Biophysics, Columbia University, 701 West 168th Street, New York, NY 10032, USA; Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University Irving Medical Center, 622 West 168th Street, New York, NY 10032, USA
| | - Rongfeng Cui
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843, USA; Max Planck Institute for the Biology of Aging, Postfach 41 06 23, 50931 Cologne, Germany; School of Ecology, Sun Yat-sen University, 135 Xingang West Road, Binjiang Road, Haizhu District, Guangdong Province, China
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, NY 10027, USA
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843, USA
| | - Molly Schumer
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Howard Hughes Medical Institute, 327 Campus Drive, Stanford, CA 94305, USA.
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46
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Abstract
Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of genetic tools that allow to uncover mechanistic links between genotype and phenotype. Moreover, given its worldwide distribution in diverse habitats and its moderate genome-size, Drosophila has proven very powerful for population genetics inference and was one of the first eukaryotes whose genome was fully sequenced. In this book chapter, we provide a brief historical overview of research in Drosophila and then focus on recent advances during the genomic era. After describing different types and sources of genomic data, we discuss mechanisms of neutral evolution including the demographic history of Drosophila and the effects of recombination and biased gene conversion. Then, we review recent advances in detecting genome-wide signals of selection, such as soft and hard selective sweeps. We further provide a brief introduction to background selection, selection of noncoding DNA and codon usage and focus on the role of structural variants, such as transposable elements and chromosomal inversions, during the adaptive process. Finally, we discuss how genomic data helps to dissect neutral and adaptive evolutionary mechanisms that shape genetic and phenotypic variation in natural populations along environmental gradients. In summary, this book chapter serves as a starting point to Drosophila population genomics and provides an introduction to the system and an overview to data sources, important population genetic concepts and recent advances in the field.
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47
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Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. Nature 2021; 590:438-444. [PMID: 33505029 PMCID: PMC7886653 DOI: 10.1038/s41586-020-03127-1] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 12/16/2020] [Indexed: 01/30/2023]
Abstract
Long-term climate change and periodic environmental extremes threaten food and fuel security1 and global crop productivity2-4. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience5, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation6-knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate-gene-biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene-trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.
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48
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Local ancestry inference provides insight into Tilapia breeding programmes. Sci Rep 2020; 10:18613. [PMID: 33122794 PMCID: PMC7596482 DOI: 10.1038/s41598-020-75744-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/12/2020] [Indexed: 11/30/2022] Open
Abstract
Tilapia is one of the most commercially valuable species in aquaculture with over 5 million tonnes of Nile tilapia, Oreochromis niloticus, produced worldwide every year. It has become increasingly important to keep track of the inheritance of the selected traits under continuous improvement (e.g. growth rate, size at maturity or genetic gender), as selective breeding has also resulted in genes that can hitchhike as part of the process. The goal of this study was to generate a Local Ancestry Interence workflow that harnessed existing tilapia genotyping-by-sequencing studies, such as Double Digest RAD-seq derived Single-Nucleotide Polymorphism markers. We developed a workflow and implemented a suite of tools to resolve the local ancestry of each chromosomal locus based on reference panels of tilapia species of known origin. We used tilapia species, wild populations and breeding programmes to validate our methods. The precision of the pipeline was evaluated on the basis of its ability to identify the genetic makeup of samples of known ancestry. The easy and inexpensive application of local ancestry inference in breeding programmes will facilitate the monitoring of the genetic profile of individuals of interest, the tracking of the movement of genes from parents to offspring and the detection of hybrids and their origin.
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49
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Shchur V, Svedberg J, Medina P, Corbett-Detig R, Nielsen R. On the Distribution of Tract Lengths During Adaptive Introgression. G3 (BETHESDA, MD.) 2020; 10:3663-3673. [PMID: 32763953 PMCID: PMC7534438 DOI: 10.1534/g3.120.401616] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 07/29/2020] [Indexed: 11/26/2022]
Abstract
Admixture is increasingly being recognized as an important factor in evolutionary genetics. The distribution of genomic admixture tracts, and the resulting effects on admixture linkage disequilibrium, can be used to date the timing of admixture between species or populations. However, the theory used for such prediction assumes selective neutrality despite the fact that many famous examples of admixture involve natural selection acting for or against admixture. In this paper, we investigate the effects of positive selection on the distribution of tract lengths. We develop a theoretical framework that relies on approximating the trajectory of the selected allele using a logistic function. By numerically calculating the expected allele trajectory, we also show that the approach can be extended to cases where the logistic approximation is poor due to the effects of genetic drift. Using simulations, we show that the model is highly accurate under most scenarios. We use the model to show that positive selection on average will tend to increase the admixture tract length. However, perhaps counter-intuitively, conditional on the allele frequency at the time of sampling, positive selection will actually produce shorter expected tract lengths. We discuss the consequences of our results in interpreting the timing of the introgression of EPAS1 from Denisovans into the ancestors of Tibetans.
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Affiliation(s)
- Vladimir Shchur
- Department of Integrative Biology and Department of Statistics, UC Berkeley, Berkeley, CA
- National Research University Higher School of Economics, Russian Federation
| | - Jesper Svedberg
- Department of Biomolecular Engineering and Genomics Institute, UC Santa Cruz, California 95064
| | - Paloma Medina
- Department of Biomolecular Engineering and Genomics Institute, UC Santa Cruz, California 95064
| | - Russell Corbett-Detig
- National Research University Higher School of Economics, Russian Federation
- Department of Biomolecular Engineering and Genomics Institute, UC Santa Cruz, California 95064
| | - Rasmus Nielsen
- Department of Integrative Biology and Department of Statistics, UC Berkeley, Berkeley, CA
- National Research University Higher School of Economics, Russian Federation
- Center for GeoGenetics, Globe Institute, University of Copenhagen, 2100 Denmark
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50
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Calfee E, Agra MN, Palacio MA, Ramírez SR, Coop G. Selection and hybridization shaped the rapid spread of African honey bee ancestry in the Americas. PLoS Genet 2020; 16:e1009038. [PMID: 33075065 PMCID: PMC7595643 DOI: 10.1371/journal.pgen.1009038] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/29/2020] [Accepted: 08/09/2020] [Indexed: 02/07/2023] Open
Abstract
Recent biological invasions offer 'natural' laboratories to understand the genetics and ecology of adaptation, hybridization, and range limits. One of the most impressive and well-documented biological invasions of the 20th century began in 1957 when Apis mellifera scutellata honey bees swarmed out of managed experimental colonies in Brazil. This newly-imported subspecies, native to southern and eastern Africa, both hybridized with and out-competed previously-introduced European honey bee subspecies. Populations of scutellata-European hybrid honey bees rapidly expanded and spread across much of the Americas in less than 50 years. We use broad geographic sampling and whole genome sequencing of over 300 bees to map the distribution of scutellata ancestry where the northern and southern invasions have presently stalled, forming replicated hybrid zones with European bee populations in California and Argentina. California is much farther from Brazil, yet these hybrid zones occur at very similar latitudes, consistent with the invasion having reached a climate barrier. At these range limits, we observe genome-wide clines for scutellata ancestry, and parallel clines for wing length that span hundreds of kilometers, supporting a smooth transition from climates favoring scutellata-European hybrid bees to climates where they cannot survive winter. We find no large effect loci maintaining exceptionally steep ancestry transitions. Instead, we find most individual loci have concordant ancestry clines across South America, with a build-up of somewhat steeper clines in regions of the genome with low recombination rates, consistent with many loci of small effect contributing to climate-associated fitness trade-offs. Additionally, we find no substantial reductions in genetic diversity associated with rapid expansions nor complete dropout of scutellata ancestry at any individual loci on either continent, which suggests that the competitive fitness advantage of scutellata ancestry at lower latitudes has a polygenic basis and that scutellata-European hybrid bees maintained large population sizes during their invasion. To test for parallel selection across continents, we develop a null model that accounts for drift in ancestry frequencies during the rapid expansion. We identify several peaks within a larger genomic region where selection has pushed scutellata ancestry to high frequency hundreds of kilometers past the present cline centers in both North and South America and that may underlie high-fitness traits driving the invasion.
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Affiliation(s)
- Erin Calfee
- Center for Population Biology, University of California, Davis, California, United States of America
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | | | - María Alejandra Palacio
- Instituto Nacional de Tecnología Agropecuaria (INTA), Balcarce, Argentina
- Facultad de Ciencias Agrarias, Universidad de Mar del Plata, Balcarce, Argentina
| | - Santiago R. Ramírez
- Center for Population Biology, University of California, Davis, California, United States of America
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | - Graham Coop
- Center for Population Biology, University of California, Davis, California, United States of America
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
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