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Gutiérrez-Guerrero YT, Phifer-Rixey M, Nachman MW. Across two continents: The genomic basis of environmental adaptation in house mice (Mus musculus domesticus) from the Americas. PLoS Genet 2024; 20:e1011036. [PMID: 38968323 PMCID: PMC11253941 DOI: 10.1371/journal.pgen.1011036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 07/17/2024] [Accepted: 06/10/2024] [Indexed: 07/07/2024] Open
Abstract
Replicated clines across environmental gradients can be strong evidence of adaptation. House mice (Mus musculus domesticus) were introduced to the Americas by European colonizers and are now widely distributed from Tierra del Fuego to Alaska. Multiple aspects of climate, such as temperature, vary predictably across latitude in the Americas. Past studies of North American populations across latitudinal gradients provided evidence of environmental adaptation in traits related to body size, metabolism, and behavior and identified candidate genes using selection scans. Here, we investigate genomic signals of environmental adaptation on a second continent, South America, and ask whether there is evidence of parallel adaptation across multiple latitudinal transects in the Americas. We first identified loci across the genome showing signatures of selection related to climatic variation in mice sampled across a latitudinal transect in South America, accounting for neutral population structure. Consistent with previous results, most candidate SNPs were in putatively regulatory regions. Genes that contained the most extreme outliers relate to traits such as body weight or size, metabolism, immunity, fat, eye function, and the cardiovascular system. We then compared these results with the results of analyses of published data from two transects in North America. While most candidate genes were unique to individual transects, we found significant overlap among candidate genes identified independently in the three transects. These genes are diverse, with functions relating to metabolism, immunity, cardiac function, and circadian rhythm, among others. We also found parallel shifts in allele frequency in candidate genes across latitudinal gradients. Finally, combining data from all three transects, we identified several genes associated with variation in body weight. Overall, our results provide strong evidence of shared responses to selection and identify genes that likely underlie recent environmental adaptation in house mice across North and South America.
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Affiliation(s)
- Yocelyn T. Gutiérrez-Guerrero
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
| | - Megan Phifer-Rixey
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Michael W. Nachman
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
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2
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Dumont BL, Gatti DM, Ballinger MA, Lin D, Phifer-Rixey M, Sheehan MJ, Suzuki TA, Wooldridge LK, Frempong HO, Lawal RA, Churchill GA, Lutz C, Rosenthal N, White JK, Nachman MW. Into the Wild: A novel wild-derived inbred strain resource expands the genomic and phenotypic diversity of laboratory mouse models. PLoS Genet 2024; 20:e1011228. [PMID: 38598567 PMCID: PMC11034653 DOI: 10.1371/journal.pgen.1011228] [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: 11/28/2023] [Revised: 04/22/2024] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
The laboratory mouse has served as the premier animal model system for both basic and preclinical investigations for over a century. However, laboratory mice capture only a subset of the genetic variation found in wild mouse populations, ultimately limiting the potential of classical inbred strains to uncover phenotype-associated variants and pathways. Wild mouse populations are reservoirs of genetic diversity that could facilitate the discovery of new functional and disease-associated alleles, but the scarcity of commercially available, well-characterized wild mouse strains limits their broader adoption in biomedical research. To overcome this barrier, we have recently developed, sequenced, and phenotyped a set of 11 inbred strains derived from wild-caught Mus musculus domesticus. Each of these "Nachman strains" immortalizes a unique wild haplotype sampled from one of five environmentally distinct locations across North and South America. Whole genome sequence analysis reveals that each strain carries between 4.73-6.54 million single nucleotide differences relative to the GRCm39 mouse reference, with 42.5% of variants in the Nachman strain genomes absent from current classical inbred mouse strain panels. We phenotyped the Nachman strains on a customized pipeline to assess the scope of disease-relevant neurobehavioral, biochemical, physiological, metabolic, and morphological trait variation. The Nachman strains exhibit significant inter-strain variation in >90% of 1119 surveyed traits and expand the range of phenotypic diversity captured in classical inbred strain panels. These novel wild-derived inbred mouse strain resources are set to empower new discoveries in both basic and preclinical research.
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Affiliation(s)
- Beth L. Dumont
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
| | - Daniel M. Gatti
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Mallory A. Ballinger
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
| | - Dana Lin
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Megan Phifer-Rixey
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Michael J. Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, United States of America
| | - Taichi A. Suzuki
- College of Health Solutions and Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, Arizona, United States of America
| | - Lydia K. Wooldridge
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Hilda Opoku Frempong
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
| | - Raman Akinyanju Lawal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Gary A. Churchill
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
| | - Cathleen Lutz
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Nadia Rosenthal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Jacqueline K. White
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Michael W. Nachman
- Department of Integrative Biology, Museum of Vertebrate Zoology, and Center for Computational Biology, University of California, Berkeley, Berkeley, California, United States of America
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3
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Manahan DN, Nachman MW. Alternative splicing and environmental adaptation in wild house mice. Heredity (Edinb) 2024; 132:133-141. [PMID: 38012302 PMCID: PMC10923775 DOI: 10.1038/s41437-023-00663-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/29/2023] Open
Abstract
A major goal of evolutionary genetics is to understand the genetic and molecular mechanisms underlying adaptation. Previous work has established that changes in gene regulation may contribute to adaptive evolution, but most studies have focused on mRNA abundance and only a few studies have investigated the role of post-transcriptional processing. Here, we use a combination of exome sequences and short-read RNA-Seq data from wild house mice (Mus musculus domesticus) collected along a latitudinal transect in eastern North America to identify candidate genes for local adaptation through alternative splicing. First, we identified alternatively spliced transcripts that differ in frequency between mice from the northern-most and southern-most populations in this transect. We then identified the subset of these transcripts that exhibit clinal patterns of variation among all populations in the transect. Finally, we conducted association studies to identify cis-acting splicing quantitative trait loci (cis-sQTL), and we identified cis-sQTL that overlapped with previously ascertained targets of selection from genome scans. Together, these analyses identified a small set of alternatively spliced transcripts that may underlie environmental adaptation in house mice. Many of these genes have known phenotypes associated with body size, a trait that varies clinally in these populations. We observed no overlap between these genes and genes previously identified by changes in mRNA abundance, indicating that alternative splicing and changes in mRNA abundance may provide separate molecular mechanisms of adaptation.
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Affiliation(s)
- David N Manahan
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720, USA.
| | - Michael W Nachman
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720, USA
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4
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Durkin SM, Ballinger MA, Nachman MW. Tissue-specific and cis-regulatory changes underlie parallel, adaptive gene expression evolution in house mice. PLoS Genet 2024; 20:e1010892. [PMID: 38306396 PMCID: PMC10866503 DOI: 10.1371/journal.pgen.1010892] [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: 07/31/2023] [Revised: 02/14/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024] Open
Abstract
Changes in gene regulation have long been appreciated as a driving force of adaptive evolution, however the relative contributions of cis- and trans-acting changes to gene regulation over short evolutionary timescales remain unclear. Instances of recent, parallel phenotypic evolution provide an opportunity to assess whether parallel patterns are seen at the level of gene expression, and to assess the relative contribution of cis- and trans- changes to gene regulation in the early stages of divergence. Here, we studied gene expression in liver and brown adipose tissue in two wild-derived strains of house mice that independently adapted to cold, northern environments, and we compared them to a strain of house mice from a warm, tropical environment. To investigate gene regulatory evolution, we studied expression in parents and allele-specific expression in F1 hybrids of crosses between warm-adapted and cold-adapted strains. First, we found that the different cold-adapted mice showed both unique and shared changes in expression, but that the proportion of shared changes (i.e. parallelism) was greater than expected by chance. Second, we discovered that expression evolution occurred largely at tissue-specific and cis-regulated genes, and that these genes were over-represented in parallel cases of evolution. Finally, we integrated the expression data with scans for selection in natural populations and found substantial parallelism in the two northern populations for genes under selection. Furthermore, selection outliers were associated with cis-regulated genes more than expected by chance; cis-regulated genes under selection influenced phenotypes such as body size, immune functioning, and activity level. These results demonstrate that parallel patterns of gene expression in mice that have independently adapted to cold environments are driven largely by tissue-specific and cis-regulatory changes, providing insight into the mechanisms of adaptive gene regulatory evolution at the earliest stages of divergence.
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Affiliation(s)
- Sylvia M. Durkin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Mallory A. Ballinger
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Michael W. Nachman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
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5
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Dumont BL, Gatti D, Ballinger MA, Lin D, Phifer-Rixey M, Sheehan MJ, Suzuki TA, Wooldridge LK, Frempong HO, Churchill G, Lutz C, Rosenthal N, White JK, Nachman MW. Into the Wild: A novel wild-derived inbred strain resource expands the genomic and phenotypic diversity of laboratory mouse models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558738. [PMID: 37790321 PMCID: PMC10542534 DOI: 10.1101/2023.09.21.558738] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The laboratory mouse has served as the premier animal model system for both basic and preclinical investigations for a century. However, laboratory mice capture a narrow subset of the genetic variation found in wild mouse populations. This consideration inherently restricts the scope of potential discovery in laboratory models and narrows the pool of potentially identified phenotype-associated variants and pathways. Wild mouse populations are reservoirs of predicted functional and disease-associated alleles, but the sparsity of commercially available, well-characterized wild mouse strains limits their broader adoption in biomedical research. To overcome this barrier, we have recently imported, sequenced, and phenotyped a set of 11 wild-derived inbred strains developed from wild-caught Mus musculus domesticus. Each of these "Nachman strains" immortalizes a unique wild haplotype sampled from five environmentally diverse locations across North and South America: Saratoga Springs, New York, USA; Gainesville, Florida, USA; Manaus, Brazil; Tucson, Arizona, USA; and Edmonton, Alberta, Canada. Whole genome sequence analysis reveals that each strain carries between 4.73-6.54 million single nucleotide differences relative to the mouse reference assembly, with 42.5% of variants in the Nachman strain genomes absent from classical inbred mouse strains. We phenotyped the Nachman strains on a customized pipeline to assess the scope of disease-relevant neurobehavioral, biochemical, physiological, metabolic, and morphological trait variation. The Nachman strains exhibit significant inter-strain variation in >90% of 1119 surveyed traits and expand the range of phenotypic diversity captured in classical inbred strain panels alone. Taken together, our work introduces a novel wild-derived inbred mouse strain resource that will enable new discoveries in basic and preclinical research. These strains are currently available through The Jackson Laboratory Repository under laboratory code NachJ.
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Affiliation(s)
- Beth L Dumont
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA
- The University of Maine, Graduate School of Biomedical Science and Engineering, 5775 Stodder Hall, Room 46, Orono, ME, 04469, USA
| | - Daniel Gatti
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Mallory A Ballinger
- Department of Integrative Biology, Center for Computational Biology, and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dana Lin
- Department of Integrative Biology, Center for Computational Biology, and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Michael J Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Taichi A Suzuki
- College of Health Solutions and Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, USA 85281
| | | | - Hilda Opoku Frempong
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- The University of Maine, Graduate School of Biomedical Science and Engineering, 5775 Stodder Hall, Room 46, Orono, ME, 04469, USA
| | - Gary Churchill
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA
- The University of Maine, Graduate School of Biomedical Science and Engineering, 5775 Stodder Hall, Room 46, Orono, ME, 04469, USA
| | - Cathleen Lutz
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Nadia Rosenthal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA
- The University of Maine, Graduate School of Biomedical Science and Engineering, 5775 Stodder Hall, Room 46, Orono, ME, 04469, USA
| | | | - Michael W Nachman
- Department of Integrative Biology, Center for Computational Biology, and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
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6
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Miller CH, Hillock MF, Yang J, Carlson-Clarke B, Haxhillari K, Lee AY, Warden MR, Sheehan MJ. Dynamic changes to signal allocation rules in response to variable social environments in house mice. Commun Biol 2023; 6:297. [PMID: 36941412 PMCID: PMC10027867 DOI: 10.1038/s42003-023-04672-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 03/07/2023] [Indexed: 03/23/2023] Open
Abstract
Urine marking is central to mouse social behavior. Males use depletable and costly urine marks in intrasexual competition and mate attraction. We investigate how males alter signaling decisions across variable social landscapes using thermal imaging to capture spatiotemporal marking data. Thermal recording reveals fine-scale adjustments in urinary motor patterns in response to competition and social odors. Males demonstrate striking winner-loser effects in scent mark allocation effort and timing. Competitive experience primes temporal features of marking and modulates responses to scent familiarity. Males adjust signaling effort, mark latency, and marking rhythm, depending on the scent identities in the environment. Notably, recent contest outcome affects how males respond to familiar and unfamiliar urine. Winners increase marking effort toward unfamiliar relative to familiar male scents, whereas losers reduce marking effort to unfamiliar but increase to familiar rival scents. All males adjust their scent mark timing after a contest regardless of fight outcome, and deposit marks in more rapid bursts during marking bouts. In contrast to this dynamism, initial signal investment predicts aspects of scent marking days later, revealing the possibility of alternative marking strategies among competitive males. These data show that mice flexibly update their signaling decisions in response to changing social landscapes.
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Affiliation(s)
- Caitlin H Miller
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA.
| | - Matthew F Hillock
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA
| | - Jay Yang
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA
| | | | - Klaudio Haxhillari
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA
| | - Annie Y Lee
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA
| | - Melissa R Warden
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA
| | - Michael J Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA.
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7
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von Takach B, Sargent H, Penton CE, Rick K, Murphy BP, Neave G, Davies HF, Hill BM, Banks SC. Population genomics and conservation management of the threatened black-footed tree-rat (Mesembriomys gouldii) in northern Australia. Heredity (Edinb) 2023; 130:278-288. [PMID: 36899176 PMCID: PMC10162988 DOI: 10.1038/s41437-023-00601-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 03/12/2023] Open
Abstract
Genomic diversity is a fundamental component of Earth's total biodiversity, and requires explicit consideration in efforts to conserve biodiversity. To conserve genomic diversity, it is necessary to measure its spatial distribution, and quantify the contribution that any intraspecific evolutionary lineages make to overall genomic diversity. Here, we describe the range-wide population genomic structure of a threatened Australian rodent, the black-footed tree-rat (Mesembriomys gouldii), aiming to provide insight into the timing and extent of population declines across a large region with a dearth of long-term monitoring data. By estimating recent trajectories in effective population sizes at four localities, we confirm widespread population decline across the species' range, but find that the population in the peri-urban area of the Darwin region has been more stable. Based on current sampling, the Melville Island population made the greatest contribution to overall allelic richness of the species, and the prioritisation analysis suggested that conservation of the Darwin and Cobourg Peninsula populations would be the most cost-effective scenario to retain more than 90% of all alleles. Our results broadly confirm current sub-specific taxonomy, and provide crucial data on the spatial distribution of genomic diversity to help prioritise limited conservation resources. Along with additional sampling and genomic analysis from the far eastern and western edges of the black-footed tree-rat distribution, we suggest a range of conservation and research priorities that could help improve black-footed tree-rat population trajectories at large and fine spatial scales, including the retention and expansion of structurally complex habitat patches.
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Affiliation(s)
- Brenton von Takach
- School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia.,Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, 0909, Australia
| | - Holly Sargent
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, 0909, Australia
| | - Cara E Penton
- Warddeken Land Management Ltd, Darwin, NT, Australia
| | - Kate Rick
- School of Biological Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Brett P Murphy
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, 0909, Australia
| | - Georgina Neave
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, 0909, Australia
| | - Hugh F Davies
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, 0909, Australia
| | - Brydie M Hill
- Flora and Fauna Division, Department of Environment, Parks and Water Security, Northern Territory Government, Berrimah, NT, 0831, Australia
| | - Sam C Banks
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, 0909, Australia.
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8
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Li X, Sun M, Qi H, Ju C, Chen Z, Gao X, Lin Z. Identification of a Chromosome 1 Substitution Line B6-Chr1BLD as a Novel Hyperlipidemia Model via Phenotyping Screening. Metabolites 2022; 12:metabo12121276. [PMID: 36557314 PMCID: PMC9781061 DOI: 10.3390/metabo12121276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Hyperlipidemia is a chronic disease that seriously affects human health. Due to the fact that traditional animal models cannot fully mimic hyperlipidemia in humans, new animal models are urgently needed for basic drug research on hyperlipidemia. Previous studies have demonstrated that the genomic diversity of the wild mice chromosome 1 substitution lines was significantly different from that of laboratory mice, suggesting that it might be accompanied by phenotypic diversity. We first screened the blood lipid-related phenotype of chromosome 1 substitution lines. We found that the male HFD-fed B6-Chr1BLD mice showed more severe hyperlipidemia-related phenotypes in body weight, lipid metabolism and liver lesions. By RNA sequencing and whole-genome sequencing results of B6-Chr1BLD, we found that several differentially expressed single nucleotide polymorphism enriched genes were associated with lipid metabolism-related pathways. Lipid metabolism-related genes, mainly including Aida, Soat1, Scly and Ildr2, might play an initial and upstream role in the abnormal metabolic phenotype of male B6-Chr1BLD mice. Taken together, male B6-Chr1BLD mice could serve as a novel, polygenic interaction-based hyperlipidemia model. This study could provide a novel animal model for accurate clinical diagnosis and precise medicine of hyperlipidemia.
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Affiliation(s)
- Xu Li
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animals for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center, National Resource Center for Mutant Mice of China, Nanjing Drum Tower Hospital, School of Medicine, Nanjing University, Nanjing 210061, China
| | - Minli Sun
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animals for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center, National Resource Center for Mutant Mice of China, Nanjing Drum Tower Hospital, School of Medicine, Nanjing University, Nanjing 210061, China
| | - Hao Qi
- GemPharmatech Inc., 12 Xuefu Road, Jiangbei New Area, Nanjing 210061, China
- Correspondence: (H.Q.); (Z.L.)
| | - Cunxiang Ju
- GemPharmatech Inc., 12 Xuefu Road, Jiangbei New Area, Nanjing 210061, China
| | - Zhong Chen
- GemPharmatech Inc., 12 Xuefu Road, Jiangbei New Area, Nanjing 210061, China
| | - Xiang Gao
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animals for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center, National Resource Center for Mutant Mice of China, Nanjing Drum Tower Hospital, School of Medicine, Nanjing University, Nanjing 210061, China
| | - Zhaoyu Lin
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animals for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center, National Resource Center for Mutant Mice of China, Nanjing Drum Tower Hospital, School of Medicine, Nanjing University, Nanjing 210061, China
- Correspondence: (H.Q.); (Z.L.)
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9
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Morgan AP, Hughes JJ, Didion JP, Jolley WJ, Campbell KJ, Threadgill DW, Bonhomme F, Searle JB, de Villena FPM. Population structure and inbreeding in wild house mice (Mus musculus) at different geographic scales. Heredity (Edinb) 2022; 129:183-194. [PMID: 35764696 PMCID: PMC9411160 DOI: 10.1038/s41437-022-00551-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 11/08/2022] Open
Abstract
House mice (Mus musculus) have spread globally as a result of their commensal relationship with humans. In the form of laboratory strains, both inbred and outbred, they are also among the most widely used model organisms in biomedical research. Although the general outlines of house mouse dispersal and population structure are well known, details have been obscured by either limited sample size or small numbers of markers. Here we examine ancestry, population structure, and inbreeding using SNP microarray genotypes in a cohort of 814 wild mice spanning five continents and all major subspecies of Mus, with a focus on M. m. domesticus. We find that the major axis of genetic variation in M. m. domesticus is a south-to-north gradient within Europe and the Mediterranean. The dominant ancestry component in North America, Australia, New Zealand, and various small offshore islands are of northern European origin. Next we show that inbreeding is surprisingly pervasive and highly variable, even between nearby populations. By inspecting the length distribution of homozygous segments in individual genomes, we find that inbreeding in commensal populations is mostly due to consanguinity. Our results offer new insight into the natural history of an important model organism for medicine and evolutionary biology.
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Affiliation(s)
- Andrew P Morgan
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
- Department of Medicine, Duke University Hospital, Durham, NC, USA.
| | - Jonathan J Hughes
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - John P Didion
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Independent Scientist, San Diego, CA, USA
| | | | | | - David W Threadgill
- Institute for Genome Sciences and Society, Texas A&M University, College Station, TX, USA
| | - Francois Bonhomme
- Institut des Sciences de l'Évolution Montpellier, Université de Montpellier, Montpellier, France
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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10
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Palma-Vera SE, Reyer H, Langhammer M, Reinsch N, Derezanin L, Fickel J, Qanbari S, Weitzel JM, Franzenburg S, Hemmrich-Stanisak G, Schoen J. Genomic characterization of the world's longest selection experiment in mouse reveals the complexity of polygenic traits. BMC Biol 2022; 20:52. [PMID: 35189878 PMCID: PMC8862358 DOI: 10.1186/s12915-022-01248-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 02/07/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Long-term selection experiments are a powerful tool to understand the genetic background of complex traits. The longest of such experiments has been conducted in the Research Institute for Farm Animal Biology (FBN), generating extreme mouse lines with increased fertility, body mass, protein mass and endurance. For >140 generations, these lines have been maintained alongside an unselected control line, representing a valuable resource for understanding the genetic basis of polygenic traits. However, their history and genomes have not been reported in a comprehensive manner yet. Therefore, the aim of this study is to provide a summary of the breeding history and phenotypic traits of these lines along with their genomic characteristics. We further attempt to decipher the effects of the observed line-specific patterns of genetic variation on each of the selected traits. RESULTS Over the course of >140 generations, selection on the control line has given rise to two extremely fertile lines (>20 pups per litter each), two giant growth lines (one lean, one obese) and one long-distance running line. Whole genome sequencing analysis on 25 animals per line revealed line-specific patterns of genetic variation among lines, as well as high levels of homozygosity within lines. This high degree of distinctiveness results from the combined effects of long-term continuous selection, genetic drift, population bottleneck and isolation. Detection of line-specific patterns of genetic differentiation and structural variation revealed multiple candidate genes behind the improvement of the selected traits. CONCLUSIONS The genomes of the Dummerstorf trait-selected mouse lines display distinct patterns of genomic variation harbouring multiple trait-relevant genes. Low levels of within-line genetic diversity indicate that many of the beneficial alleles have arrived to fixation alongside with neutral alleles. This study represents the first step in deciphering the influence of selection and neutral evolutionary forces on the genomes of these extreme mouse lines and depicts the genetic complexity underlying polygenic traits.
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Affiliation(s)
- Sergio E Palma-Vera
- Institute of Reproductive Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.
| | - Henry Reyer
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Martina Langhammer
- Institute of Genetics and Biometry, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Norbert Reinsch
- Institute of Genetics and Biometry, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Lorena Derezanin
- Institute of Reproductive Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
- Department of Evolutionary Genetics, Research Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Joerns Fickel
- Department of Evolutionary Genetics, Research Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- University of Potsdam, Institute for Biochemistry and Biology, Potsdam, Germany
| | - Saber Qanbari
- Institute of Genetics and Biometry, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Joachim M Weitzel
- Institute of Reproductive Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | | | | | - Jennifer Schoen
- Institute of Reproductive Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
- Department of Reproduction Biology, Research Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
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11
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Beckman EJ, Martins F, Suzuki TA, Bi K, Keeble S, Good JM, Chavez AS, Ballinger MA, Agwamba K, Nachman MW. The genomic basis of high-elevation adaptation in wild house mice (Mus musculus domesticus) from South America. Genetics 2022; 220:iyab226. [PMID: 34897431 PMCID: PMC9097263 DOI: 10.1093/genetics/iyab226] [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: 09/29/2021] [Accepted: 12/04/2021] [Indexed: 11/14/2022] Open
Abstract
Understanding the genetic basis of environmental adaptation in natural populations is a central goal in evolutionary biology. The conditions at high elevation, particularly the low oxygen available in the ambient air, impose a significant and chronic environmental challenge to metabolically active animals with lowland ancestry. To understand the process of adaptation to these novel conditions and to assess the repeatability of evolution over short timescales, we examined the signature of selection from complete exome sequences of house mice (Mus musculus domesticus) sampled across two elevational transects in the Andes of South America. Using phylogenetic analysis, we show that house mice colonized high elevations independently in Ecuador and Bolivia. Overall, we found distinct responses to selection in each transect and largely nonoverlapping sets of candidate genes, consistent with the complex nature of traits that underlie adaptation to low oxygen availability (hypoxia) in other species. Nonetheless, we also identified a small subset of the genome that appears to be under parallel selection at the gene and SNP levels. In particular, three genes (Col22a1, Fgf14, and srGAP1) bore strong signatures of selection in both transects. Finally, we observed several patterns that were common to both transects, including an excess of derived alleles at high elevation, and a number of hypoxia-associated genes exhibiting a threshold effect, with a large allele frequency change only at the highest elevations. This threshold effect suggests that selection pressures may increase disproportionately at high elevations in mammals, consistent with observations of some high-elevation diseases in humans.
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Affiliation(s)
- Elizabeth J Beckman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Felipe Martins
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Taichi A Suzuki
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sara Keeble
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
- Wildlife Biology Program, University of Montana, Missoula, MT 59812, USA
| | - Andreas S Chavez
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Evolution, Ecology, and Organismal Biology and the Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Mallory A Ballinger
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kennedy Agwamba
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael W Nachman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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12
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A continent-wide high genetic load in African buffalo revealed by clines in the frequency of deleterious alleles, genetic hitchhiking and linkage disequilibrium. PLoS One 2021; 16:e0259685. [PMID: 34882683 PMCID: PMC8659316 DOI: 10.1371/journal.pone.0259685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/24/2021] [Indexed: 11/19/2022] Open
Abstract
A high genetic load can negatively affect population viability and increase susceptibility to diseases and other environmental stressors. Prior microsatellite studies of two African buffalo (Syncerus caffer) populations in South Africa indicated substantial genome-wide genetic load due to high-frequency occurrence of deleterious alleles. The occurrence of these alleles, which negatively affect male body condition and bovine tuberculosis resistance, throughout most of the buffalo's range were evaluated in this study. Using available microsatellite data (2-17 microsatellite loci) for 1676 animals from 34 localities (from 25°S to 5°N), we uncovered continent-wide frequency clines of microsatellite alleles associated with the aforementioned male traits. Frequencies decreased over a south-to-north latitude range (average per-locus Pearson r = -0.22). The frequency clines coincided with a multilocus-heterozygosity cline (adjusted R2 = 0.84), showing up to a 16% decrease in southern Africa compared to East Africa. Furthermore, continent-wide linkage disequilibrium (LD) at five linked locus pairs was detected, characterized by a high fraction of positive interlocus associations (0.66, 95% CI: 0.53, 0.77) between male-deleterious-trait-associated alleles. Our findings suggest continent-wide and genome-wide selection of male-deleterious alleles driven by an earlier observed sex-chromosomal meiotic drive system, resulting in frequency clines, reduced heterozygosity due to hitchhiking effects and extensive LD due to male-deleterious alleles co-occurring in haplotypes. The selection pressures involved must be high to prevent destruction of allele-frequency clines and haplotypes by LD decay. Since most buffalo populations are stable, these results indicate that natural mammal populations, depending on their genetic background, can withstand a high genetic load.
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13
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Lawal RA, Arora UP, Dumont BL. Selection shapes the landscape of functional variation in wild house mice. BMC Biol 2021; 19:239. [PMID: 34794440 PMCID: PMC8603481 DOI: 10.1186/s12915-021-01165-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 10/14/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Through human-aided dispersal over the last ~ 10,000 years, house mice (Mus musculus) have recently colonized diverse habitats across the globe, promoting the emergence of new traits that confer adaptive advantages in distinct environments. Despite their status as the premier mammalian model system, the impact of this demographic and selective history on the global patterning of disease-relevant trait variation in wild mouse populations is poorly understood. RESULTS Here, we leveraged 154 whole-genome sequences from diverse wild house mouse populations to survey the geographic organization of functional variation and systematically identify signals of positive selection. We show that a significant proportion of wild mouse variation is private to single populations, including numerous predicted functional alleles. In addition, we report strong signals of positive selection at many genes associated with both complex and Mendelian diseases in humans. Notably, we detect a significant excess of selection signals at disease-associated genes relative to null expectations, pointing to the important role of adaptation in shaping the landscape of functional variation in wild mouse populations. We also uncover strong signals of selection at multiple genes involved in starch digestion, including Mgam and Amy1. We speculate that the successful emergence of the human-mouse commensalism may have been facilitated, in part, by dietary adaptations at these loci. Finally, our work uncovers multiple cryptic structural variants that manifest as putative signals of positive selection, highlighting an important and under-appreciated source of false-positive signals in genome-wide selection scans. CONCLUSIONS Overall, our findings highlight the role of adaptation in shaping wild mouse genetic variation at human disease-associated genes. Our work also highlights the biomedical relevance of wild mouse genetic diversity and underscores the potential for targeted sampling of mice from specific populations as a strategy for developing effective new mouse models of both rare and common human diseases.
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Affiliation(s)
| | - Uma P Arora
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA
| | - Beth L Dumont
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA.
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA.
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14
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Saxenhofer M, Labutin A, White TA, Heckel G. Host genetic factors associated with the range limit of a European hantavirus. Mol Ecol 2021; 31:252-265. [PMID: 34614264 PMCID: PMC9298007 DOI: 10.1111/mec.16211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/30/2021] [Accepted: 09/22/2021] [Indexed: 11/30/2022]
Abstract
The natural host ranges of many viruses are restricted to very specific taxa. Little is known about the molecular barriers between species that lead to the establishment of this restriction or generally prevent virus emergence in new hosts. Here, we identify genomic polymorphisms in a natural rodent host associated with a strong genetic barrier to the transmission of European Tula orthohantavirus (TULV). We analysed the very abrupt spatial transition between two major phylogenetic clades in TULV across the comparatively much wider natural hybrid zone between evolutionary lineages of their reservoir host, the common vole (Microtus arvalis). Genomic scans of 79,225 single nucleotide polymorphisms (SNPs) in 323 TULV‐infected host individuals detected 30 SNPs that were consistently associated with the TULV clades CEN.S or EST.S in two replicate sampling transects. Focusing the analysis on 199 voles with evidence of genomic admixture at the individual level (0.1–0.9) supported statistical significance for all 30 loci. Host genomic variation at these SNPs explained up to 37.6% of clade‐specific TULV infections. Genes in the vicinity of associated SNPs include SAHH, ITCH and two members of the Syngr gene family, which are involved in functions related to immune response or membrane transport. This study demonstrates the relevance of natural hybrid zones as systems not only for studying processes of evolutionary divergence and speciation, but also for the detection of evolving genetic barriers for specialized parasites.
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Affiliation(s)
- Moritz Saxenhofer
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Génopode, Lausanne, Switzerland
| | - Anton Labutin
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Thomas A White
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Génopode, Lausanne, Switzerland
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15
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Managing the Health of Captive Herds of Exotic Companion Mammals. Vet Clin North Am Exot Anim Pract 2021; 24:547-566. [PMID: 34366010 DOI: 10.1016/j.cvex.2021.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Common medical problems diagnosed and treated in individual companion exotic mammals are relevant in a herd-health setting. Many of these problems are often associated with poor husbandry and/or inappropriate nutrition. Rabbits, ferrets, chinchillas, and rodents have been domesticated alongside humans and an understanding of their ethology gives veterinarians a base knowledge in making recommendations for animals in their care. This article briefly reviews the ethology and husbandry in such species, but detailed needs are beyond the scope of this article.
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16
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Geibel J, Reimer C, Pook T, Weigend S, Weigend A, Simianer H. How imputation can mitigate SNP ascertainment Bias. BMC Genomics 2021; 22:340. [PMID: 33980139 PMCID: PMC8114708 DOI: 10.1186/s12864-021-07663-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 12/30/2022] Open
Abstract
Background Population genetic studies based on genotyped single nucleotide polymorphisms (SNPs) are influenced by a non-random selection of the SNPs included in the used genotyping arrays. The resulting bias in the estimation of allele frequency spectra and population genetics parameters like heterozygosity and genetic distances relative to whole genome sequencing (WGS) data is known as SNP ascertainment bias. Full correction for this bias requires detailed knowledge of the array design process, which is often not available in practice. This study suggests an alternative approach to mitigate ascertainment bias of a large set of genotyped individuals by using information of a small set of sequenced individuals via imputation without the need for prior knowledge on the array design. Results The strategy was first tested by simulating additional ascertainment bias with a set of 1566 chickens from 74 populations that were genotyped for the positions of the Affymetrix Axiom™ 580 k Genome-Wide Chicken Array. Imputation accuracy was shown to be consistently higher for populations used for SNP discovery during the simulated array design process. Reference sets of at least one individual per population in the study set led to a strong correction of ascertainment bias for estimates of expected and observed heterozygosity, Wright’s Fixation Index and Nei’s Standard Genetic Distance. In contrast, unbalanced reference sets (overrepresentation of populations compared to the study set) introduced a new bias towards the reference populations. Finally, the array genotypes were imputed to WGS by utilization of reference sets of 74 individuals (one per population) to 98 individuals (additional commercial chickens) and compared with a mixture of individually and pooled sequenced populations. The imputation reduced the slope between heterozygosity estimates of array data and WGS data from 1.94 to 1.26 when using the smaller balanced reference panel and to 1.44 when using the larger but unbalanced reference panel. This generally supported the results from simulation but was less favorable, advocating for a larger reference panel when imputing to WGS. Conclusions The results highlight the potential of using imputation for mitigation of SNP ascertainment bias but also underline the need for unbiased reference sets. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07663-6.
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Affiliation(s)
- Johannes Geibel
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany. .,Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany.
| | - Christian Reimer
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany.,Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany
| | - Torsten Pook
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany.,Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany
| | - Steffen Weigend
- Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany.,Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Höltystrasse 10, 31535, Neustadt-Mariensee, Germany
| | - Annett Weigend
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Höltystrasse 10, 31535, Neustadt-Mariensee, Germany
| | - Henner Simianer
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany.,Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany
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17
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von Takach B, Penton CE, Murphy BP, Radford IJ, Davies HF, Hill BM, Banks SC. Population genomics and conservation management of a declining tropical rodent. Heredity (Edinb) 2021; 126:763-775. [PMID: 33664461 PMCID: PMC8102610 DOI: 10.1038/s41437-021-00418-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 01/31/2023] Open
Abstract
Conservation management is improved by incorporating information about the spatial distribution of population genetic diversity into planning strategies. Northern Australia is the location of some of the world's most severe ongoing declines of endemic mammal species, yet we have little genetic information from this regional mammal assemblage to inform a genetic perspective on conservation assessment and planning. We used next-generation sequencing data from remnant populations of the threatened brush-tailed rabbit-rat (Conilurus penicillatus) to compare patterns of genomic diversity and differentiation across the landscape and investigate standardised hierarchical genomic diversity metrics to better understand brush-tailed rabbit-rat population genomic structure. We found strong population structuring, with high levels of differentiation between populations (FST = 0.21-0.78). Two distinct genomic lineages between the Tiwi Islands and mainland are also present. Prioritisation analysis showed that one population in both lineages would need to be conserved to retain at least ~80% of alleles for the species. Analysis of standardised genomic diversity metrics showed that approximately half of the total diversity occurs among lineages (δ = 0.091 from grand total γ = 0.184). We suggest that a focus on conserving remnant island populations may not be appropriate for the preservation of species-level genomic diversity and adaptive potential, as these populations represent a small component of the total diversity and a narrow subset of the environmental conditions in which the species occurs. We also highlight the importance of considering both genomic and ecological differentiation between source and receiving populations when considering translocations for conservation purposes.
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Affiliation(s)
- Brenton von Takach
- grid.1043.60000 0001 2157 559XResearch Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory Australia
| | - Cara E. Penton
- grid.1043.60000 0001 2157 559XResearch Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory Australia
| | - Brett P. Murphy
- grid.1043.60000 0001 2157 559XResearch Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory Australia ,grid.1043.60000 0001 2157 559XNESP Threatened Species Recovery Hub, Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory Australia
| | - Ian J. Radford
- grid.452589.70000 0004 1799 3491Department of Biodiversity, Conservation and Attractions, Kununurra, WA Australia
| | - Hugh F. Davies
- grid.1043.60000 0001 2157 559XResearch Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory Australia ,grid.1043.60000 0001 2157 559XNESP Threatened Species Recovery Hub, Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory Australia
| | - Brydie M. Hill
- grid.483876.60000 0004 0394 3004Flora and Fauna Division, Department of Environment, Parks and Water Security, Northern Territory Government, Darwin, Northern Territory Australia
| | - Sam C. Banks
- grid.1043.60000 0001 2157 559XResearch Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory Australia
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18
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Ferris KG, Chavez AS, Suzuki TA, Beckman EJ, Phifer-Rixey M, Bi K, Nachman MW. The genomics of rapid climatic adaptation and parallel evolution in North American house mice. PLoS Genet 2021; 17:e1009495. [PMID: 33914747 PMCID: PMC8084166 DOI: 10.1371/journal.pgen.1009495] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 03/17/2021] [Indexed: 12/23/2022] Open
Abstract
Parallel changes in genotype and phenotype in response to similar selection pressures in different populations provide compelling evidence of adaptation. House mice (Mus musculus domesticus) have recently colonized North America and are found in a wide range of environments. Here we measure phenotypic and genotypic differentiation among house mice from five populations sampled across 21° of latitude in western North America, and we compare our results to a parallel latitudinal cline in eastern North America. First, we show that mice are genetically differentiated between transects, indicating that they have independently colonized similar environments in eastern and western North America. Next, we find genetically-based differences in body weight and nest building behavior between mice from the ends of the western transect which mirror differences seen in the eastern transect, demonstrating parallel phenotypic change. We then conduct genome-wide scans for selection and a genome-wide association study to identify targets of selection and candidate genes for body weight. We find some genomic signatures that are unique to each transect, indicating population-specific responses to selection. However, there is significant overlap between genes under selection in eastern and western house mouse transects, providing evidence of parallel genetic evolution in response to similar selection pressures across North America.
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Affiliation(s)
- Kathleen G. Ferris
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Andreas S. Chavez
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Taichi A. Suzuki
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Elizabeth J. Beckman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Megan Phifer-Rixey
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Michael W. Nachman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
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19
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Geibel J, Reimer C, Weigend S, Weigend A, Pook T, Simianer H. How array design creates SNP ascertainment bias. PLoS One 2021; 16:e0245178. [PMID: 33784304 PMCID: PMC8009414 DOI: 10.1371/journal.pone.0245178] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/22/2020] [Indexed: 12/30/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs), genotyped with arrays, have become a widely used marker type in population genetic analyses over the last 10 years. However, compared to whole genome re-sequencing data, arrays are known to lack a substantial proportion of globally rare variants and tend to be biased towards variants present in populations involved in the development process of the respective array. This affects population genetic estimators and is known as SNP ascertainment bias. We investigated factors contributing to ascertainment bias in array development by redesigning the Axiom™ Genome-Wide Chicken Array in silico and evaluating changes in allele frequency spectra and heterozygosity estimates in a stepwise manner. A sequential reduction of rare alleles during the development process was shown. This was mainly caused by the identification of SNPs in a limited set of populations and a within-population selection of common SNPs when aiming for equidistant spacing. These effects were shown to be less severe with a larger discovery panel. Additionally, a generally massive overestimation of expected heterozygosity for the ascertained SNP sets was shown. This overestimation was 24% higher for populations involved in the discovery process than not involved populations in case of the original array. The same was observed after the SNP discovery step in the redesign. However, an unequal contribution of populations during the SNP selection can mask this effect but also adds uncertainty. Finally, we make suggestions for the design of specialized arrays for large scale projects where whole genome re-sequencing techniques are still too expensive.
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Affiliation(s)
- Johannes Geibel
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Göttingen, Germany
- * E-mail:
| | - Christian Reimer
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Göttingen, Germany
| | - Steffen Weigend
- Center for Integrated Breeding Research, University of Goettingen, Göttingen, Germany
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt-Mariensee, Germany
| | - Annett Weigend
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt-Mariensee, Germany
| | - Torsten Pook
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Göttingen, Germany
| | - Henner Simianer
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Göttingen, Germany
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20
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Benjelloun B, Boyer F, Streeter I, Zamani W, Engelen S, Alberti A, Alberto FJ, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Rezaei HR, Naderi S, Stella A, Chikhi A, Clarke L, Kijas J, Flicek P, Taberlet P, Pompanon F. An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity. Mol Ecol Resour 2019; 19:1497-1515. [PMID: 31359622 PMCID: PMC7115901 DOI: 10.1111/1755-0998.13070] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 06/30/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022]
Abstract
Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low-coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high-density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low-density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.
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Affiliation(s)
- Badr Benjelloun
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
- National Institute of Agronomic Research (INRA Maroc), Regional Centre of Agronomic Research, 23000 Beni-Mellal, Morocco
| | - Frédéric Boyer
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Wahid Zamani
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
- Department of Environmental Sciences, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, 46417-76489 Noor, Mazandaran, Iran
| | - Stefan Engelen
- CEA - Institut de biologie François-Jacob, Genoscope, 2 Rue Gaston Cremieux 91057 Evry Cedex, France
| | - Adriana Alberti
- CEA - Institut de biologie François-Jacob, Genoscope, 2 Rue Gaston Cremieux 91057 Evry Cedex, France
| | - Florian J. Alberto
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Mohamed BenBati
- National Institute of Agronomic Research (INRA Maroc), Regional Centre of Agronomic Research, 23000 Beni-Mellal, Morocco
| | - Mustapha Ibnelbachyr
- National Institute of Agronomic Research (INRA Maroc), CRRA Errachidia, 52000 Errachidia, Morocco
| | - Mouad Chentouf
- National Institute of Agronomic Research (INRA Maroc), CRRA Tangier, 90010 Tangier, Morocco
| | - Abdelmajid Bechchari
- National Institute of Agronomic Research (INRA Maroc), CRRA Oujda, 60000 Oujda, Morocco
| | - Hamid R. Rezaei
- Department of Environmental Sci, Gorgan University of Agricultural Sciences & Natural Resources, 41996-13776 Gorgan, Iran
| | - Saeid Naderi
- Environmental Sciences Department, Natural Resources Faculty, University of Guilan, 49138-15749 Guilan, Iran
| | - Alessandra Stella
- PTP Science Park, Bioinformatics Unit, Via Einstein-Loc. Cascina Codazza, 26900 Lodi, Italy
| | - Abdelkader Chikhi
- National Institute of Agronomic Research (INRA Maroc), CRRA Errachidia, 52000 Errachidia, Morocco
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - James Kijas
- Commonwealth Scientific and Industrial Research Organisation Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Pierre Taberlet
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - François Pompanon
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
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21
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Phifer-Rixey M, Bi K, Ferris KG, Sheehan MJ, Lin D, Mack KL, Keeble SM, Suzuki TA, Good JM, Nachman MW. The genomic basis of environmental adaptation in house mice. PLoS Genet 2018; 14:e1007672. [PMID: 30248095 PMCID: PMC6171964 DOI: 10.1371/journal.pgen.1007672] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 10/04/2018] [Accepted: 08/30/2018] [Indexed: 01/18/2023] Open
Abstract
House mice (Mus musculus) arrived in the Americas only recently in association with European colonization (~400-600 generations), but have spread rapidly and show evidence of local adaptation. Here, we take advantage of this genetic model system to investigate the genomic basis of environmental adaptation in house mice. First, we documented clinal patterns of phenotypic variation in 50 wild-caught mice from a latitudinal transect in Eastern North America. Next, we found that progeny of mice from different latitudes, raised in a common laboratory environment, displayed differences in a number of complex traits related to fitness. Consistent with Bergmann's rule, mice from higher latitudes were larger and fatter than mice from lower latitudes. They also built bigger nests and differed in aspects of blood chemistry related to metabolism. Then, combining exomic, genomic, and transcriptomic data, we identified specific candidate genes underlying adaptive variation. In particular, we defined a short list of genes with cis-eQTL that were identified as candidates in exomic and genomic analyses, all of which have known ties to phenotypes that vary among the studied populations. Thus, wild mice and the newly developed strains represent a valuable resource for future study of the links between genetic variation, phenotypic variation, and climate.
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Affiliation(s)
- Megan Phifer-Rixey
- Department of Biology, Monmouth University, West Long Branch, New Jersey, United States of America
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States of America
| | - Ke Bi
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States of America
- Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, United States of America
| | - Kathleen G. Ferris
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States of America
| | - Michael J. Sheehan
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States of America
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, United States of America
| | - Dana Lin
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States of America
| | - Katya L. Mack
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States of America
| | - Sara M. Keeble
- Division of Biological Sciences, University of Montana, Missoula, Missoula, Montana, United States of America
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, Los Angeles, California, United States of America
| | - Taichi A. Suzuki
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States of America
| | - Jeffrey M. Good
- Division of Biological Sciences, University of Montana, Missoula, Missoula, Montana, United States of America
| | - Michael W. Nachman
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States of America
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22
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Wittenburg D, Liebscher V. An approximate Bayesian significance test for genomic evaluations. Biom J 2018; 60:1096-1109. [PMID: 30101421 PMCID: PMC6282823 DOI: 10.1002/bimj.201700219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 03/06/2018] [Accepted: 04/10/2018] [Indexed: 11/12/2022]
Abstract
Genomic information can be used to study the genetic architecture of some trait. Not only the size of the genetic effect captured by molecular markers and their position on the genome but also the mode of inheritance, which might be additive or dominant, and the presence of interactions are interesting parameters. When searching for interacting loci, estimating the effect size and determining the significant marker pairs increases the computational burden in terms of speed and memory allocation dramatically. This study revisits a rapid Bayesian approach (fastbayes). As a novel contribution, a measure of evidence is derived to select markers with effect significantly different from zero. It is based on the credibility of the highest posterior density interval next to zero in a marginalized manner. This methodology is applied to simulated data resembling a dairy cattle population in order to verify the sensitivity of testing for a given range of type-I error levels. A real data application complements this study. Sensitivity and specificity of fastbayes were similar to a variational Bayesian method, and a further reduction of computing time could be achieved. More than 50% of the simulated causative variants were identified. The most complex model containing different kinds of genetic effects and their pairwise interactions yielded the best outcome over a range of type-I error levels. The validation study showed that fastbayes is a dual-purpose tool for genomic inferences - it is applicable to predict future outcome of not-yet phenotyped individuals with high precision as well as to estimate and test single-marker effects. Furthermore, it allows the estimation of billions of interaction effects.
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Affiliation(s)
- Dörte Wittenburg
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - Volkmar Liebscher
- Department of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Str. 47, D-17489, Greifswald, Germany
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23
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Abolins S, Lazarou L, Weldon L, Hughes L, King EC, Drescher P, Pocock MJO, Hafalla JCR, Riley EM, Viney M. The ecology of immune state in a wild mammal, Mus musculus domesticus. PLoS Biol 2018; 16:e2003538. [PMID: 29652925 PMCID: PMC5919074 DOI: 10.1371/journal.pbio.2003538] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 04/25/2018] [Accepted: 03/09/2018] [Indexed: 01/08/2023] Open
Abstract
The immune state of wild animals is largely unknown. Knowing this and what affects it is important in understanding how infection and disease affects wild animals. The immune state of wild animals is also important in understanding the biology of their pathogens, which is directly relevant to explaining pathogen spillover among species, including to humans. The paucity of knowledge about wild animals' immune state is in stark contrast to our exquisitely detailed understanding of the immunobiology of laboratory animals. Making an immune response is costly, and many factors (such as age, sex, infection status, and body condition) have individually been shown to constrain or promote immune responses. But, whether or not these factors affect immune responses and immune state in wild animals, their relative importance, and how they interact (or do not) are unknown. Here, we have investigated the immune ecology of wild house mice-the same species as the laboratory mouse-as an example of a wild mammal, characterising their adaptive humoral, adaptive cellular, and innate immune state. Firstly, we show how immune variation is structured among mouse populations, finding that there can be extensive immune discordance among neighbouring populations. Secondly, we identify the principal factors that underlie the immunological differences among mice, showing that body condition promotes and age constrains individuals' immune state, while factors such as microparasite infection and season are comparatively unimportant. By applying a multifactorial analysis to an immune system-wide analysis, our results bring a new and unified understanding of the immunobiology of a wild mammal.
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Affiliation(s)
- Stephen Abolins
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Luke Lazarou
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Laura Weldon
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Louise Hughes
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Elizabeth C. King
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Paul Drescher
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | | | - Julius C. R. Hafalla
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Eleanor M. Riley
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Mark Viney
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
- * E-mail:
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24
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Škrabar N, Turner LM, Pallares LF, Harr B, Tautz D. Using the
Mus musculus
hybrid zone to assess covariation and genetic architecture of limb bone lengths. Mol Ecol Resour 2018. [DOI: 10.1111/1755-0998.12776] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Neva Škrabar
- Max‐Planck Institute for Evolutionary Biology Plön Germany
| | - Leslie M. Turner
- Max‐Planck Institute for Evolutionary Biology Plön Germany
- Department of Biology and Biochemistry Milner Centre for Evolution University of Bath Bath UK
| | - Luisa F. Pallares
- Max‐Planck Institute for Evolutionary Biology Plön Germany
- Lewis‐Sigler Institute for Integrative Genomics Princeton University Princeton NJ USA
| | - Bettina Harr
- Max‐Planck Institute for Evolutionary Biology Plön Germany
| | - Diethard Tautz
- Max‐Planck Institute for Evolutionary Biology Plön Germany
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25
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Radder JE, Gregory AD, Leme AS, Cho MH, Chu Y, Kelly NJ, Bakke P, Gulsvik A, Litonjua AA, Sparrow D, Beaty TH, Crapo JD, Silverman EK, Zhang Y, Berndt A, Shapiro SD. Variable Susceptibility to Cigarette Smoke-Induced Emphysema in 34 Inbred Strains of Mice Implicates Abi3bp in Emphysema Susceptibility. Am J Respir Cell Mol Biol 2017; 57:367-375. [PMID: 28441029 DOI: 10.1165/rcmb.2016-0220oc] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is caused by a complex interaction of environmental exposures, most commonly cigarette smoke, and genetic factors. Chronic cigarette smoke exposure in the mouse is a commonly used animal model of COPD. We aimed to expand our knowledge about the variable susceptibility of inbred strains to this model and test for genetic variants associated with this trait. To that end, we sought to measure differential susceptibility to cigarette smoke-induced emphysema in the mouse, identify genetic loci associated with this quantitative trait, and find homologous human genes associated with COPD. Alveolar chord length (CL) in 34 inbred strains of mice was measured after 6 months of exposure to cigarette smoke. After testing for association, we connected a murine candidate locus to a published meta-analysis of moderate-to-severe COPD. We identified deleterious mutations in a candidate gene in silico and measured gene expression in extreme strains. A/J was the most susceptible strain in our survey (Δ CL 7.0 ± 2.2 μm) and CBA/J was the least susceptible (Δ CL -0.3 ± 1.2 μm). By integrating mouse and human genome-wide scans, we identified the candidate gene Abi3bp. CBA/J mice harbor predicted deleterious variants in Abi3bp, and expression of the gene differs significantly between CBA/J and A/J mice. This is the first report of susceptibility to cigarette smoke-induced emphysema in 34 inbred strains of mice, and Abi3bp is identified as a potential contributor to this phenotype.
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Affiliation(s)
- Josiah E Radder
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Alyssa D Gregory
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Adriana S Leme
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Michael H Cho
- 2 Channing Division of Network Medicine, and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Yanxia Chu
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Neil J Kelly
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Per Bakke
- 4 Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Amund Gulsvik
- 4 Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Augusto A Litonjua
- 2 Channing Division of Network Medicine, and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - David Sparrow
- 5 School of Public Health and.,6 School of Medicine, Boston University, Boston, Massachusetts.,7 Veterans Affairs Boston Healthcare System, Boston, Massachusetts
| | - Terri H Beaty
- 8 Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland; and
| | - James D Crapo
- 9 Department of Radiology, National Jewish Health, Denver, Colorado
| | - Edwin K Silverman
- 2 Channing Division of Network Medicine, and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Yingze Zhang
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Annerose Berndt
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Steven D Shapiro
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
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26
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Affiliation(s)
| | - Michael J. Wade
- Department of Biology; Indiana University; Bloomington IN USA
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27
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Chang PL, Kopania E, Keeble S, Sarver BAJ, Larson E, Orth A, Belkhir K, Boursot P, Bonhomme F, Good JM, Dean MD. Whole exome sequencing of wild-derived inbred strains of mice improves power to link phenotype and genotype. Mamm Genome 2017; 28:416-425. [PMID: 28819774 DOI: 10.1007/s00335-017-9704-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/23/2017] [Indexed: 12/30/2022]
Abstract
The house mouse is a powerful model to dissect the genetic basis of phenotypic variation, and serves as a model to study human diseases. Despite a wealth of discoveries, most classical laboratory strains have captured only a small fraction of genetic variation known to segregate in their wild progenitors, and existing strains are often related to each other in complex ways. Inbred strains of mice independently derived from natural populations have the potential to increase power in genetic studies with the addition of novel genetic variation. Here, we perform exome-enrichment and high-throughput sequencing (~8× coverage) of 26 wild-derived strains known in the mouse research community as the "Montpellier strains." We identified 1.46 million SNPs in our dataset, approximately 19% of which have not been detected from other inbred strains. This novel genetic variation is expected to contribute to phenotypic variation, as they include 18,496 nonsynonymous variants and 262 early stop codons. Simulations demonstrate that the higher density of genetic variation in the Montpellier strains provides increased power for quantitative genetic studies. Inasmuch as the power to connect genotype to phenotype depends on genetic variation, it is important to incorporate these additional genetic strains into future research programs.
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Affiliation(s)
- Peter L Chang
- Molecular and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
| | - Emily Kopania
- Molecular and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA.,Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Sara Keeble
- Molecular and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA.,Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Brice A J Sarver
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Erica Larson
- Division of Biological Sciences, University of Montana, Missoula, MT, USA.,Department of Biological Sciences, University of Denver, Denver, CO, 80210, USA
| | - Annie Orth
- Institut des Sciences de l'Evolution, CNRS UMR554, Université de Montpellier, Montpellier, France
| | - Khalid Belkhir
- Institut des Sciences de l'Evolution, CNRS UMR554, Université de Montpellier, Montpellier, France
| | - Pierre Boursot
- Institut des Sciences de l'Evolution, CNRS UMR554, Université de Montpellier, Montpellier, France
| | - François Bonhomme
- Institut des Sciences de l'Evolution, CNRS UMR554, Université de Montpellier, Montpellier, France
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Matthew D Dean
- Molecular and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA.
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28
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Sequence analysis of chromosome 1 revealed different selection patterns between Chinese wild mice and laboratory strains. Mol Genet Genomics 2017. [PMID: 28631230 DOI: 10.1007/s00438-017-1335-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Both natural and artificial selection play a critical role in animals' adaptation to the environment. Detection of the signature of selection in genomic regions can provide insights for understanding the function of specific phenotypes. It is generally assumed that laboratory mice may experience intense artificial selection while wild mice more natural selection. However, the differences of selection signature in the mouse genome and underlying genes between wild and laboratory mice remain unclear. In this study, we used two mouse populations: chromosome 1 (Chr 1) substitution lines (C1SLs) derived from Chinese wild mice and mouse genome project (MGP) sequenced inbred strains and two selection detection statistics: Fst and Tajima's D to identify the signature of selection footprint on Chr 1. For the differentiation between the C1SLs and MGP, 110 candidate selection regions containing 47 protein coding genes were detected. A total of 149 selection regions which encompass 7.215 Mb were identified in the C1SLs by Tajima's D approach. While for the MGP, we identified nearly twice selection regions (243) compared with the C1SLs which accounted for 13.27 Mb Chr 1 sequence. Through functional annotation, we identified several biological processes with significant enrichment including seven genes in the olfactory transduction pathway. In addition, we searched the phenotypes associated with the 47 candidate selection genes identified by Fst. These genes were involved in behavior, growth or body weight, mortality or aging, and immune systems which align well with the phenotypic differences between wild and laboratory mice. Therefore, the findings would be helpful for our understanding of the phenotypic differences between wild and laboratory mice and applications for using this new mouse resource (C1SLs) for further genetics studies.
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29
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Lowry DB, Hoban S, Kelley JL, Lotterhos KE, Reed LK, Antolin MF, Storfer A. Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation. Mol Ecol Resour 2016; 17:142-152. [PMID: 27860289 DOI: 10.1111/1755-0998.12635] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/23/2016] [Accepted: 09/02/2016] [Indexed: 12/26/2022]
Abstract
Understanding how and why populations evolve is of fundamental importance to molecular ecology. Restriction site-associated DNA sequencing (RADseq), a popular reduced representation method, has ushered in a new era of genome-scale research for assessing population structure, hybridization, demographic history, phylogeography and migration. RADseq has also been widely used to conduct genome scans to detect loci involved in adaptive divergence among natural populations. Here, we examine the capacity of those RADseq-based genome scan studies to detect loci involved in local adaptation. To understand what proportion of the genome is missed by RADseq studies, we developed a simple model using different numbers of RAD-tags, genome sizes and extents of linkage disequilibrium (length of haplotype blocks). Under the best-case modelling scenario, we found that RADseq using six- or eight-base pair cutting restriction enzymes would fail to sample many regions of the genome, especially for species with short linkage disequilibrium. We then surveyed recent studies that have used RADseq for genome scans and found that the median density of markers across these studies was 4.08 RAD-tag markers per megabase (one marker per 245 kb). The length of linkage disequilibrium for many species is one to three orders of magnitude less than density of the typical recent RADseq study. Thus, we conclude that genome scans based on RADseq data alone, while useful for studies of neutral genetic variation and genetic population structure, will likely miss many loci under selection in studies of local adaptation.
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Affiliation(s)
- David B Lowry
- Plant Biology Laboratories, Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI, 48824, USA.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - Sean Hoban
- The Morton Arboretum, Lisle, IL, USA.,National Institute for Mathematical and Biological Synthesis (NIMBioS), Knoxville, TN, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, 430 Nahant Rd., Nahant, MA, 01908, USA
| | - Laura K Reed
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35406, USA
| | - Michael F Antolin
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
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30
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Genome Sequencing of Chromosome 1 Substitution Lines Derived from Chinese Wild Mice Revealed a Unique Resource for Genetic Studies of Complex Traits. G3-GENES GENOMES GENETICS 2016; 6:3571-3580. [PMID: 27605517 PMCID: PMC5100856 DOI: 10.1534/g3.116.033902] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mouse resources such as Collaborative Cross, outbred stocks, Hybrid Mouse Diversity Panel, and chromosome substitution strains have been instrumental to many progresses in the studies of complex traits genetics. We have established a population of chromosome 1 (Chr 1) substitution lines (C1SLs) in which donor chromosomes were derived from Chinese wild mice. Genome sequencing of 18 lines of this population showed that Chr 1 had been replaced by the donor chromosome. About 4.5 million unique single nucleotide polymorphisms and indels were discovered on Chr 1, of which 1.3 million were novel. Compared with sequenced classical inbred strains, Chr 1 of each C1SL had fivefold more variants, and more loss of function and potentially regulatory variants. Further haplotype analysis showed that the donor chromosome accumulated more historical recombination events, with the largest haplotype block being only 100 kb, and about 57% of the blocks were <1 kb. Subspecies origin analysis showed that these chromosomes had a mosaic genome structure that dominantly originated from Mus musculus musculus and M. m. castaneus subspecies, except for the C57BL/6J-Chr1KM line from M. m. domesticus. In addition, phenotyping four of these lines on blood biochemistry suggested that there were substantial phenotypic variations among our lines, especially line C57BL/6J-Chr1HZ and donor strain C57BL/6J. Further gene ontology enrichment revealed that the differentially expressed genes among liver-expressed genes between C57BL/6J and C57BL/6J-Chr1HZ were enriched in lipid metabolism biological processes. All these characteristics enable C1SLs to be a unique resource for identifying and fine mapping quantitative trait loci on mouse Chr 1, and carrying out systems genetics studies of complex traits.
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31
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Parker CC, Gopalakrishnan S, Carbonetto P, Gonzales NM, Leung E, Park YJ, Aryee E, Davis J, Blizard DA, Ackert-Bicknell CL, Lionikas A, Pritchard JK, Palmer AA. Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice. Nat Genet 2016; 48:919-26. [PMID: 27376237 PMCID: PMC4963286 DOI: 10.1038/ng.3609] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/08/2016] [Indexed: 12/15/2022]
Abstract
Although mice are the most widely used mammalian model organism, genetic studies have suffered from limited mapping resolution due to extensive linkage disequilibrium (LD) that is characteristic of crosses among inbred strains. Carworth Farms White (CFW) mice are a commercially available outbred mouse population that exhibit rapid LD decay in comparison to other available mouse populations. We performed a genome-wide association study (GWAS) of behavioral, physiological and gene expression phenotypes using 1,200 male CFW mice. We used genotyping by sequencing (GBS) to obtain genotypes at 92,734 SNPs. We also measured gene expression using RNA sequencing in three brain regions. Our study identified numerous behavioral, physiological and expression quantitative trait loci (QTLs). We integrated the behavioral QTL and eQTL results to implicate specific genes, including Azi2 in sensitivity to methamphetamine and Zmynd11 in anxiety-like behavior. The combination of CFW mice, GBS and RNA sequencing constitutes a powerful approach to GWAS in mice.
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Affiliation(s)
- Clarissa C. Parker
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Department of Psychology, Middlebury College, Middlebury, VT 05753, USA
- Program in Neuroscience, Middlebury College, Middlebury, VT 05753, USA
| | - Shyam Gopalakrishnan
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Museum of Natural History, Copenhagen University, Copenhagen, Denmark
| | - Peter Carbonetto
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- AncestryDNA, San Francisco, CA 94105, USA
| | | | - Emily Leung
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Yeonhee J Park
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Emmanuel Aryee
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Joe Davis
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - David A. Blizard
- Department of Biobehavioral Health, Pennsylvania State University, University Park, PA 16802, USA
| | - Cheryl L. Ackert-Bicknell
- Center for Musculoskeletal Research, University of Rochester, Rochester, NY 14624, USA
- Department of Orthopaedics and Rehabilitation, University of Rochester, Rochester, NY 14624, USA
| | - Arimantas Lionikas
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill Aberdeen, Scotland UK
| | - Jonathan K. Pritchard
- Department of Genetics, Stanford University, Palo Alto, CA 94305, USA
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Palo Alto, CA 94305, USA
| | - Abraham A. Palmer
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92103, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92103, USA
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32
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Didion JP, Morgan AP, Yadgary L, Bell TA, McMullan RC, Ortiz de Solorzano L, Britton-Davidian J, Bult CJ, Campbell KJ, Castiglia R, Ching YH, Chunco AJ, Crowley JJ, Chesler EJ, Förster DW, French JE, Gabriel SI, Gatti DM, Garland T, Giagia-Athanasopoulou EB, Giménez MD, Grize SA, Gündüz İ, Holmes A, Hauffe HC, Herman JS, Holt JM, Hua K, Jolley WJ, Lindholm AK, López-Fuster MJ, Mitsainas G, da Luz Mathias M, McMillan L, Ramalhinho MDGM, Rehermann B, Rosshart SP, Searle JB, Shiao MS, Solano E, Svenson KL, Thomas-Laemont P, Threadgill DW, Ventura J, Weinstock GM, Pomp D, Churchill GA, Pardo-Manuel de Villena F. R2d2 Drives Selfish Sweeps in the House Mouse. Mol Biol Evol 2016; 33:1381-95. [PMID: 26882987 PMCID: PMC4868115 DOI: 10.1093/molbev/msw036] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A selective sweep is the result of strong positive selection driving newly occurring or standing genetic variants to fixation, and can dramatically alter the pattern and distribution of allelic diversity in a population. Population-level sequencing data have enabled discoveries of selective sweeps associated with genes involved in recent adaptations in many species. In contrast, much debate but little evidence addresses whether “selfish” genes are capable of fixation—thereby leaving signatures identical to classical selective sweeps—despite being neutral or deleterious to organismal fitness. We previously described R2d2, a large copy-number variant that causes nonrandom segregation of mouse Chromosome 2 in females due to meiotic drive. Here we show population-genetic data consistent with a selfish sweep driven by alleles of R2d2 with high copy number (R2d2HC) in natural populations. We replicate this finding in multiple closed breeding populations from six outbred backgrounds segregating for R2d2 alleles. We find that R2d2HC rapidly increases in frequency, and in most cases becomes fixed in significantly fewer generations than can be explained by genetic drift. R2d2HC is also associated with significantly reduced litter sizes in heterozygous mothers, making it a true selfish allele. Our data provide direct evidence of populations actively undergoing selfish sweeps, and demonstrate that meiotic drive can rapidly alter the genomic landscape in favor of mutations with neutral or even negative effects on overall Darwinian fitness. Further study will reveal the incidence of selfish sweeps, and will elucidate the relative contributions of selfish genes, adaptation and genetic drift to evolution.
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Affiliation(s)
- John P Didion
- Department of Genetics, The University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill Carolina Center for Genome Science, The University of North Carolina at Chapel Hill
| | - Andrew P Morgan
- Department of Genetics, The University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill Carolina Center for Genome Science, The University of North Carolina at Chapel Hill
| | - Liran Yadgary
- Department of Genetics, The University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill Carolina Center for Genome Science, The University of North Carolina at Chapel Hill
| | - Timothy A Bell
- Department of Genetics, The University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill Carolina Center for Genome Science, The University of North Carolina at Chapel Hill
| | - Rachel C McMullan
- Department of Genetics, The University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill Carolina Center for Genome Science, The University of North Carolina at Chapel Hill
| | - Lydia Ortiz de Solorzano
- Department of Genetics, The University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill Carolina Center for Genome Science, The University of North Carolina at Chapel Hill
| | - Janice Britton-Davidian
- Institut des Sciences de l'Evolution, Université De Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | | | - Karl J Campbell
- Island Conservation, Puerto Ayora, Galápagos Island, Ecuador School of Geography, Planning & Environmental Management, The University of Queensland, St Lucia, QLD, Australia
| | - Riccardo Castiglia
- Department of Biology and Biotechnologies "Charles Darwin", University of Rome "La Sapienza", Rome, Italy
| | - Yung-Hao Ching
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Hualien City, Taiwan
| | | | - James J Crowley
- Department of Genetics, The University of North Carolina at Chapel Hill
| | | | - Daniel W Förster
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany
| | - John E French
- National Toxicology Program, National Institute of Environmental Sciences, NIH, Research Triangle Park, NC
| | - Sofia I Gabriel
- Department of Animal Biology & CESAM - Centre for Environmental and Marine Studies, Faculty of Sciences, University of Lisbon, Lisboa, Portugal
| | | | | | | | - Mabel D Giménez
- Instituto de Biología Subtropical, CONICET - Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - Sofia A Grize
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - İslam Gündüz
- Department of Biology, Faculty of Arts and Sciences, University of Ondokuz Mayis, Samsun, Turkey
| | - Andrew Holmes
- Laboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD
| | - Heidi C Hauffe
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'adige, TN, Italy
| | - Jeremy S Herman
- Department of Natural Sciences, National Museums Scotland, Edinburgh, United Kingdom
| | - James M Holt
- Department of Computer Science, The University of North Carolina at Chapel Hill
| | - Kunjie Hua
- Department of Genetics, The University of North Carolina at Chapel Hill
| | | | - Anna K Lindholm
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | | | - George Mitsainas
- Section of Animal Biology, Department of Biology, University of Patras, Patras, Greece
| | - Maria da Luz Mathias
- Department of Animal Biology & CESAM - Centre for Environmental and Marine Studies, Faculty of Sciences, University of Lisbon, Lisboa, Portugal
| | - Leonard McMillan
- Department of Computer Science, The University of North Carolina at Chapel Hill
| | - Maria da Graça Morgado Ramalhinho
- Department of Animal Biology & CESAM - Centre for Environmental and Marine Studies, Faculty of Sciences, University of Lisbon, Lisboa, Portugal
| | - Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD
| | - Stephan P Rosshart
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY
| | - Meng-Shin Shiao
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Emanuela Solano
- Department of Biology and Biotechnologies "Charles Darwin", University of Rome "La Sapienza", Rome, Italy
| | | | | | - David W Threadgill
- Department of Veterinary Pathobiology, Texas A&M University, College Station Department of Molecular and Cellular Medicine, Texas A&M University, College Station
| | - Jacint Ventura
- Departament de Biologia Animal, de Biologia Vegetal y de Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Daniel Pomp
- Department of Genetics, The University of North Carolina at Chapel Hill Carolina Center for Genome Science, The University of North Carolina at Chapel Hill
| | | | - Fernando Pardo-Manuel de Villena
- Department of Genetics, The University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill Carolina Center for Genome Science, The University of North Carolina at Chapel Hill
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Miller JM, Poissant J, Malenfant RM, Hogg JT, Coltman DW. Temporal dynamics of linkage disequilibrium in two populations of bighorn sheep. Ecol Evol 2015; 5:3401-12. [PMID: 26380673 PMCID: PMC4569035 DOI: 10.1002/ece3.1612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Linkage disequilibrium (LD) is the nonrandom association of alleles at two markers. Patterns of LD have biological implications as well as practical ones when designing association studies or conservation programs aimed at identifying the genetic basis of fitness differences within and among populations. However, the temporal dynamics of LD in wild populations has received little empirical attention. In this study, we examined the overall extent of LD, the effect of sample size on the accuracy and precision of LD estimates, and the temporal dynamics of LD in two populations of bighorn sheep (Ovis canadensis) with different demographic histories. Using over 200 microsatellite loci, we assessed two metrics of multi-allelic LD, D', and χ ('2). We found that both populations exhibited high levels of LD, although the extent was much shorter in a native population than one that was founded via translocation, experienced a prolonged bottleneck post founding, followed by recent admixture. In addition, we observed significant variation in LD in relation to the sample size used, with small sample sizes leading to depressed estimates of the extent of LD but inflated estimates of background levels of LD. In contrast, there was not much variation in LD among yearly cross-sections within either population once sample size was accounted for. Lack of pronounced interannual variability suggests that researchers may not have to worry about interannual variation when estimating LD in a population and can instead focus on obtaining the largest sample size possible.
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Affiliation(s)
- Joshua M Miller
- Department of Biological Sciences, University of Alberta Edmonton, Alberta, Canada
| | - Jocelyn Poissant
- Centre for Ecology and Conservation, University of Exeter Penryn Campus, UK
| | - René M Malenfant
- Department of Biological Sciences, University of Alberta Edmonton, Alberta, Canada
| | - John T Hogg
- Montana Conservation Science Institute 5200 Upper Miller Creek Road, Missoula, Montana, USA
| | - David W Coltman
- Department of Biological Sciences, University of Alberta Edmonton, Alberta, Canada
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34
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Storz JF, Bridgham JT, Kelly SA, Garland T. Genetic approaches in comparative and evolutionary physiology. Am J Physiol Regul Integr Comp Physiol 2015; 309:R197-214. [PMID: 26041111 PMCID: PMC4525326 DOI: 10.1152/ajpregu.00100.2015] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/23/2015] [Indexed: 01/04/2023]
Abstract
Whole animal physiological performance is highly polygenic and highly plastic, and the same is generally true for the many subordinate traits that underlie performance capacities. Quantitative genetics, therefore, provides an appropriate framework for the analysis of physiological phenotypes and can be used to infer the microevolutionary processes that have shaped patterns of trait variation within and among species. In cases where specific genes are known to contribute to variation in physiological traits, analyses of intraspecific polymorphism and interspecific divergence can reveal molecular mechanisms of functional evolution and can provide insights into the possible adaptive significance of observed sequence changes. In this review, we explain how the tools and theory of quantitative genetics, population genetics, and molecular evolution can inform our understanding of mechanism and process in physiological evolution. For example, lab-based studies of polygenic inheritance can be integrated with field-based studies of trait variation and survivorship to measure selection in the wild, thereby providing direct insights into the adaptive significance of physiological variation. Analyses of quantitative genetic variation in selection experiments can be used to probe interrelationships among traits and the genetic basis of physiological trade-offs and constraints. We review approaches for characterizing the genetic architecture of physiological traits, including linkage mapping and association mapping, and systems approaches for dissecting intermediary steps in the chain of causation between genotype and phenotype. We also discuss the promise and limitations of population genomic approaches for inferring adaptation at specific loci. We end by highlighting the role of organismal physiology in the functional synthesis of evolutionary biology.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska;
| | - Jamie T Bridgham
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon
| | - Scott A Kelly
- Department of Zoology, Ohio Wesleyan University, Delaware, Ohio; and
| | - Theodore Garland
- Department of Biology, University of California, Riverside, Riverside, California
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35
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Smadja CM, Loire E, Caminade P, Thoma M, Latour Y, Roux C, Thoss M, Penn DJ, Ganem G, Boursot P. Seeking signatures of reinforcement at the genetic level: a hitchhiking mapping and candidate gene approach in the house mouse. Mol Ecol 2015; 24:4222-4237. [PMID: 26132782 DOI: 10.1111/mec.13301] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 06/12/2015] [Accepted: 06/17/2015] [Indexed: 12/11/2022]
Abstract
Reinforcement is the process by which prezygotic isolation is strengthened as a response to selection against hybridization. Most empirical support for reinforcement comes from the observation of its possible phenotypic signature: an accentuated degree of prezygotic isolation in the hybrid zone as compared to allopatry. Here, we implemented a novel approach to this question by seeking for the signature of reinforcement at the genetic level. In the house mouse, selection against hybrids and enhanced olfactory-based assortative mate preferences are observed in a hybrid zone between the two European subspecies Mus musculus musculus and M. m. domesticus, suggesting a possible recent reinforcement event. To test for the genetic signature of reinforcing selection and identify genes involved in sexual isolation, we adopted a hitchhiking mapping approach targeting genomic regions containing candidate genes for assortative mating in mice. We densely scanned these genomic regions in hybrid zone and allopatric samples using a large number of fast evolving microsatellite loci that allow the detection of recent selection events. We found a handful of loci showing the expected pattern of significant reduction in variability in populations close to the hybrid zone, showing assortative odour preference in mate choice experiments as compared to populations further away and displaying no such preference. These loci lie close to genes that we pinpoint as testable candidates for further investigation.
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Affiliation(s)
- Carole M Smadja
- Institut des Sciences de l'Evolution UMR 5554 (Centre National de la Recherche Scientifique CNRS, Institut pour la Recherche et le Développement IRD, Université de Montpellier), cc065 Université de Montpellier, Campus Triolet, 34095 Montpellier, France
| | - Etienne Loire
- Institut des Sciences de l'Evolution UMR 5554 (Centre National de la Recherche Scientifique CNRS, Institut pour la Recherche et le Développement IRD, Université de Montpellier), cc065 Université de Montpellier, Campus Triolet, 34095 Montpellier, France
| | - Pierre Caminade
- Institut des Sciences de l'Evolution UMR 5554 (Centre National de la Recherche Scientifique CNRS, Institut pour la Recherche et le Développement IRD, Université de Montpellier), cc065 Université de Montpellier, Campus Triolet, 34095 Montpellier, France
| | - Marios Thoma
- Institut des Sciences de l'Evolution UMR 5554 (Centre National de la Recherche Scientifique CNRS, Institut pour la Recherche et le Développement IRD, Université de Montpellier), cc065 Université de Montpellier, Campus Triolet, 34095 Montpellier, France
| | - Yasmin Latour
- Institut des Sciences de l'Evolution UMR 5554 (Centre National de la Recherche Scientifique CNRS, Institut pour la Recherche et le Développement IRD, Université de Montpellier), cc065 Université de Montpellier, Campus Triolet, 34095 Montpellier, France
| | - Camille Roux
- Institut des Sciences de l'Evolution UMR 5554 (Centre National de la Recherche Scientifique CNRS, Institut pour la Recherche et le Développement IRD, Université de Montpellier), cc065 Université de Montpellier, Campus Triolet, 34095 Montpellier, France
| | - Michaela Thoss
- University of Veterinary Medicine Vienna, Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, Vienna, Austria
| | - Dustin J Penn
- University of Veterinary Medicine Vienna, Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, Vienna, Austria
| | - Guila Ganem
- Institut des Sciences de l'Evolution UMR 5554 (Centre National de la Recherche Scientifique CNRS, Institut pour la Recherche et le Développement IRD, Université de Montpellier), cc065 Université de Montpellier, Campus Triolet, 34095 Montpellier, France
| | - Pierre Boursot
- Institut des Sciences de l'Evolution UMR 5554 (Centre National de la Recherche Scientifique CNRS, Institut pour la Recherche et le Développement IRD, Université de Montpellier), cc065 Université de Montpellier, Campus Triolet, 34095 Montpellier, France
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36
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Phifer-Rixey M, Nachman MW. Insights into mammalian biology from the wild house mouse Mus musculus. eLife 2015; 4. [PMID: 25875302 PMCID: PMC4397906 DOI: 10.7554/elife.05959] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/26/2015] [Indexed: 12/22/2022] Open
Abstract
The house mouse, Mus musculus, was established in the early 1900s as one of the first genetic model organisms owing to its short generation time, comparatively large litters, ease of husbandry, and visible phenotypic variants. For these reasons and because they are mammals, house mice are well suited to serve as models for human phenotypes and disease. House mice in the wild consist of at least three distinct subspecies and harbor extensive genetic and phenotypic variation both within and between these subspecies. Wild mice have been used to study a wide range of biological processes, including immunity, cancer, male sterility, adaptive evolution, and non-Mendelian inheritance. Despite the extensive variation that exists among wild mice, classical laboratory strains are derived from a limited set of founders and thus contain only a small subset of this variation. Continued efforts to study wild house mice and to create new inbred strains from wild populations have the potential to strengthen house mice as a model system. DOI:http://dx.doi.org/10.7554/eLife.05959.001
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Affiliation(s)
- Megan Phifer-Rixey
- Department of Integrative Biology, University of California, Berkeley, Berkeley, United States and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, United States
| | - Michael W Nachman
- Department of Integrative Biology, University of California, Berkeley, Berkeley, United States and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, United States
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37
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Maga AM, Navarro N, Cunningham ML, Cox TC. Quantitative trait loci affecting the 3D skull shape and size in mouse and prioritization of candidate genes in-silico. Front Physiol 2015; 6:92. [PMID: 25859222 PMCID: PMC4374467 DOI: 10.3389/fphys.2015.00092] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/05/2015] [Indexed: 11/17/2022] Open
Abstract
We describe the first application of high-resolution 3D micro-computed tomography, together with 3D landmarks and geometric morphometrics, to map QTL responsible for variation in skull shape and size using a backcross between C57BL/6J and A/J inbred strains. Using 433 animals, 53 3D landmarks, and 882 SNPs from autosomes, we identified seven QTL responsible for the skull size (SCS.qtl) and 30 QTL responsible for the skull shape (SSH.qtl). Size, sex, and direction-of-cross were all significant factors and included in the analysis as covariates. All autosomes harbored at least one SSH.qtl, sometimes up to three. Effect sizes of SSH.qtl appeared to be small, rarely exceeding 1% of the overall shape variation. However, they account for significant amount of variation in some specific directions of the shape space. Many QTL have stronger effect on the neurocranium than expected from a random vector that will parcellate uniformly across the four cranial regions. On the contrary, most of QTL have an effect on the palate weaker than expected. Combined interval length of 30 SSH.qtl was about 315 MB and contained 2476 known protein coding genes. We used a bioinformatics approach to filter these candidate genes and identified 16 high-priority candidates that are likely to play a role in the craniofacial development and disorders. Thus, coupling the QTL mapping approach in model organisms with candidate gene enrichment approaches appears to be a feasible way to identify high-priority candidates genes related to the structure or tissue of interest.
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Affiliation(s)
- A Murat Maga
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington Seattle, WA, USA ; Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute Seattle, WA, USA
| | - Nicolas Navarro
- Laboratoire PALEVO, Ecole Pratique des Hautes Etudes Dijon, France ; UMR uB/CNRS 6282 - Biogéosciences, Université de Bourgogne Dijon, France
| | - Michael L Cunningham
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington Seattle, WA, USA ; Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute Seattle, WA, USA
| | - Timothy C Cox
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington Seattle, WA, USA ; Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute Seattle, WA, USA ; Department of Anatomy and Developmental Biology, Monash University Clayton, VIC, Australia
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38
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Turner LM, Harr B. Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions. eLife 2014; 3. [PMID: 25487987 PMCID: PMC4359376 DOI: 10.7554/elife.02504] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 10/23/2014] [Indexed: 12/22/2022] Open
Abstract
Mapping hybrid defects in contact zones between incipient species can identify genomic regions contributing to reproductive isolation and reveal genetic mechanisms of speciation. The house mouse features a rare combination of sophisticated genetic tools and natural hybrid zones between subspecies. Male hybrids often show reduced fertility, a common reproductive barrier between incipient species. Laboratory crosses have identified sterility loci, but each encompasses hundreds of genes. We map genetic determinants of testis weight and testis gene expression using offspring of mice captured in a hybrid zone between M. musculus musculus and M. m. domesticus. Many generations of admixture enables high-resolution mapping of loci contributing to these sterility-related phenotypes. We identify complex interactions among sterility loci, suggesting multiple, non-independent genetic incompatibilities contribute to barriers to gene flow in the hybrid zone.
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Affiliation(s)
- Leslie M Turner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Bettina Harr
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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39
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Pallares LF, Harr B, Turner LM, Tautz D. Use of a natural hybrid zone for genomewide association mapping of craniofacial traits in the house mouse. Mol Ecol 2014; 23:5756-70. [PMID: 25319559 DOI: 10.1111/mec.12968] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 09/23/2014] [Accepted: 10/03/2014] [Indexed: 02/03/2023]
Abstract
The identification of the genes involved in morphological variation in nature is still a major challenge. Here, we explore a new approach: we combine 178 samples from a natural hybrid zone between two subspecies of the house mouse (Mus musculus domesticus and Mus musculus musculus), and high coverage of the genome (~ 145K SNPs) to identify loci underlying craniofacial shape variation. Due to the long history of recombination in the hybrid zone, high mapping resolution is anticipated. The combination of genomes from subspecies allows the mapping of both, variation within subspecies and inter-subspecific differences, thereby increasing the overall amount of causal genetic variation that can be detected. Skull and mandible shape were measured using 3D landmarks and geometric morphometrics. Using principal component axes as phenotypes, and a linear mixed model accounting for genetic relatedness in the mapping populations, we identified nine genomic regions associated with skull shape and 10 with mandible shape. High mapping resolution (median size of significant regions = 148 kb) enabled identification of single or few candidate genes in most cases. Some of the genes act as regulators or modifiers of signalling pathways relevant for morphological development and bone formation, including several with known craniofacial phenotypes in mice and humans. The significant associations combined explain 13% and 7% of the skull and mandible shape variation, respectively. In addition, a positive correlation was found between chromosomal length and proportion of variation explained. Our results suggest a complex genetic architecture for shape traits and support a polygenic model.
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Affiliation(s)
- Luisa F Pallares
- Max-Planck Institute for Evolutionary Biology, Plön, 24306, Germany
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40
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Yang J, Shikano T, Li MH, Merilä J. Genome-wide linkage disequilibrium in nine-spined stickleback populations. G3 (BETHESDA, MD.) 2014; 4:1919-29. [PMID: 25122668 PMCID: PMC4199698 DOI: 10.1534/g3.114.013334] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 08/09/2014] [Indexed: 11/18/2022]
Abstract
Variation in the extent and magnitude of genome-wide linkage disequilibrium (LD) among populations residing in different habitats has seldom been studied in wild vertebrates. We used a total of 109 microsatellite markers to quantify the level and patterns of genome-wide LD in 13 Fennoscandian nine-spined stickleback (Pungitius pungitius) populations from four (viz. marine, lake, pond, and river) different habitat types. In general, high magnitude (D' > 0.5) of LD was found both in freshwater and marine populations, and the magnitude of LD was significantly greater in inland freshwater than in marine populations. Interestingly, three coastal freshwater populations located in close geographic proximity to the marine populations exhibited similar LD patterns and genetic diversity as their marine neighbors. The greater levels of LD in inland freshwater compared with marine and costal freshwater populations can be explained in terms of their contrasting demographic histories: founder events, long-term isolation, small effective sizes, and population bottlenecks are factors likely to have contributed to the high levels of LD in the inland freshwater populations. In general, these findings shed new light on the patterns and extent of variation in genome-wide LD, as well as the ecological and evolutionary factors driving them.
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Affiliation(s)
- Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Takahito Shikano
- Ecological Genetics Research Unit, Department of Biosciences, FIN-00014 University of Helsinki, Finland
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Juha Merilä
- Ecological Genetics Research Unit, Department of Biosciences, FIN-00014 University of Helsinki, Finland
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Abstract
One approach to understanding the genetic basis of speciation is to scan the genomes of recently diverged taxa to identify highly differentiated regions. The house mouse, Mus musculus, provides a useful system for the study of speciation. Three subspecies (M. m. castaneus, M. m. domesticus, and M. m. musculus) diverged ∼350 KYA, are distributed parapatrically, show varying degrees of reproductive isolation in laboratory crosses, and hybridize in nature. We sequenced the testes transcriptomes of multiple wild-derived inbred lines from each subspecies to identify highly differentiated regions of the genome, to identify genes showing high expression divergence, and to compare patterns of differentiation among subspecies that have different demographic histories and exhibit different levels of reproductive isolation. Using a sliding-window approach, we found many genomic regions with high levels of sequence differentiation in each of the pairwise comparisons among subspecies. In all comparisons, the X chromosome was more highly differentiated than the autosomes. Sequence differentiation and expression divergence were greater in the M. m. domesticus-M. m. musculus comparison than in either pairwise comparison with M. m. castaneus, which is consistent with laboratory crosses that show the greatest reproductive isolation between M. m. domesticus and M. m. musculus. Coalescent simulations suggest that differences in estimates of effective population size can account for many of the observed patterns. However, there was an excess of highly differentiated regions relative to simulated distributions under a wide range of demographic scenarios. Overlap of some highly differentiated regions with previous results from QTL mapping and hybrid zone studies points to promising candidate regions for reproductive isolation.
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42
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Gonzales NM, Palmer AA. Fine-mapping QTLs in advanced intercross lines and other outbred populations. Mamm Genome 2014; 25:271-92. [PMID: 24906874 DOI: 10.1007/s00335-014-9523-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 04/25/2014] [Indexed: 12/16/2022]
Abstract
Quantitative genetic studies in model organisms, particularly in mice, have been extremely successful in identifying chromosomal regions that are associated with a wide variety of behavioral and other traits. However, it is now widely understood that identification of the underlying genes will be far more challenging. In the last few years, a variety of populations have been utilized in an effort to more finely map these chromosomal regions with the goal of identifying specific genes. The common property of these newer populations is that linkage disequilibrium spans relatively short distances, which permits fine-scale mapping resolution. This review focuses on advanced intercross lines (AILs) which are the simplest such population. As originally proposed in 1995 by Darvasi and Soller, an AIL is the product of intercrossing two inbred strains beyond the F2 generation. Unlike recombinant inbred strains, AILs are maintained as outbred populations; brother-sister matings are specifically avoided. Each generation of intercrossing beyond the F2 further degrades linkage disequilibrium between adjacent makers, which allows for fine-scale mapping of quantitative trait loci (QTLs). Advances in genotyping technology and techniques for the statistical analysis of AILs have permitted rapid advances in the application of AILs. We review some of the analytical issues and available software, including QTLRel, EMMA, EMMAX, GEMMA, TASSEL, GRAMMAR, WOMBAT, Mendel, and others.
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Affiliation(s)
- Natalia M Gonzales
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
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43
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Xu J, Zhao Z, Zhang X, Zheng X, Li J, Jiang Y, Kuang Y, Zhang Y, Feng J, Li C, Yu J, Li Q, Zhu Y, Liu Y, Xu P, Sun X. Development and evaluation of the first high-throughput SNP array for common carp (Cyprinus carpio). BMC Genomics 2014; 15:307. [PMID: 24762296 PMCID: PMC4234440 DOI: 10.1186/1471-2164-15-307] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 04/17/2014] [Indexed: 12/30/2022] Open
Abstract
Background A large number of single nucleotide polymorphisms (SNPs) have been identified in common carp (Cyprinus carpio) but, as yet, no high-throughput genotyping platform is available for this species. C. carpio is an important aquaculture species that accounts for nearly 14% of freshwater aquaculture production worldwide. We have developed an array for C. carpio with 250,000 SNPs and evaluated its performance using samples from various strains of C. carpio. Results The SNPs used on the array were selected from two resources: the transcribed sequences from RNA-seq data of four strains of C. carpio, and the genome re-sequencing data of five strains of C. carpio. The 250,000 SNPs on the resulting array are distributed evenly across the reference C.carpio genome with an average spacing of 6.6 kb. To evaluate the SNP array, 1,072 C. carpio samples were collected and tested. Of the 250,000 SNPs on the array, 185,150 (74.06%) were found to be polymorphic sites. Genotyping accuracy was checked using genotyping data from a group of full-siblings and their parents, and over 99.8% of the qualified SNPs were found to be reliable. Analysis of the linkage disequilibrium on all samples and on three domestic C.carpio strains revealed that the latter had the longer haplotype blocks. We also evaluated our SNP array on 80 samples from eight species related to C. carpio, with from 53,526 to 71,984 polymorphic SNPs. An identity by state analysis divided all the samples into three clusters; most of the C. carpio strains formed the largest cluster. Conclusions The Carp SNP array described here is the first high-throughput genotyping platform for C. carpio. Our evaluation of this array indicates that it will be valuable for farmed carp and for genetic and population biology studies in C. carpio and related species.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Peng Xu
- Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
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44
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Fitzpatrick BM. Symbiote transmission and maintenance of extra-genomic associations. Front Microbiol 2014; 5:46. [PMID: 24605109 PMCID: PMC3932413 DOI: 10.3389/fmicb.2014.00046] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 01/21/2014] [Indexed: 12/02/2022] Open
Abstract
Symbiotes can be transmitted from parents to offspring or horizontally from unrelated hosts or the environment. A key question is whether symbiote transmission is similar enough to Mendelian gene transmission to generate and maintain coevolutionary associations between host and symbiote genes. Recent papers come to opposite conclusions, with some suggesting that any horizontal transmission eliminates genetic association. These studies are hard to compare owing to arbitrary differences in modeling approach, parameter values, and assumptions about selection. I show that associations between host and symbiote genes (extra-genomic associations) can be described by the same dynamic model as conventional linkage disequilibria between genes in the same genome. Thus, covariance between host and symbiote genomes depends on population history, geographic structure, selection, and co-transmission rate, just as covariance between genes within a genome. The conclusion that horizontal transmission rapidly erodes extra-genomic associations is equivalent to the conclusion that recombination rapidly erodes associations between genes within a genome. The conclusion is correct in the absence of population structure or selection. However, population structure can maintain spatial associations between host and symbiote traits, and non-additive selection (interspecific epistasis) can generate covariances between host and symbiote genotypes. These results can also be applied to cultural or other non-genetic traits. This work contributes to a growing consensus that genomic, symbiotic, and gene-culture evolution can be analyzed under a common theoretical framework. In terms of coevolutionary potential, symbiotes can be viewed as lying on a continuum between the intimacy of genes and the indifference of casually co-occurring species.
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Affiliation(s)
- Benjamin M Fitzpatrick
- Department of Ecology and Evolutionary Biology, University of Tennessee Knoxville, TN, USA
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45
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Chesler EJ. Out of the bottleneck: the Diversity Outcross and Collaborative Cross mouse populations in behavioral genetics research. Mamm Genome 2013; 25:3-11. [PMID: 24272351 PMCID: PMC3916706 DOI: 10.1007/s00335-013-9492-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/08/2013] [Indexed: 11/28/2022]
Abstract
The historical origins of classical laboratory mouse strains have led to a relatively limited range of genetic and phenotypic variation, particularly for the study of behavior. Many recent efforts have resulted in improved diversity and precision of mouse genetic resources for behavioral research, including the Collaborative Cross and Diversity Outcross population. These two populations, derived from an eight way cross of common and wild-derived strains, have high precision and allelic diversity. Behavioral variation in the population is expanded, both qualitatively and quantitatively. Variation that had once been canalized among the various inbred lines has been made amenable to genetic dissection. The genetic attributes of these complementary populations, along with advances in genetic and genomic technologies, makes a systems genetic analyses of behavior more readily tractable, enabling discovery of a greater range of neurobiological phenomena underlying behavioral variation.
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Affiliation(s)
- Elissa J Chesler
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA,
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46
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Abstract
Progress in complex trait mapping in mice has been accelerated by the development of new populations suited to high-resolution mapping and by statistical methodologies that control for population structure. When combined with newly acquired catalogs of sequence variation in inbred strains, the genetic architecture of these new populations makes it possible to dissect complex traits down to the level of single variants. These analyses have shown not only that complex traits are caused by multiple contributing loci but also that each locus is likely due to the combined effects of multiple causal DNA variants. In combination with new rapid methods for producing transgenic mice that make it efficient to test candidate genes and variants, these advances significantly enhance the mouse genetics toolbox for dissecting quantitative traits.
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Affiliation(s)
- Richard Mott
- Wellcome Trust Center for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom; ,
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47
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Linnen CR, Poh YP, Peterson BK, Barrett RDH, Larson JG, Jensen JD, Hoekstra HE. Adaptive evolution of multiple traits through multiple mutations at a single gene. Science 2013; 339:1312-6. [PMID: 23493712 DOI: 10.1126/science.1233213] [Citation(s) in RCA: 222] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The identification of precise mutations is required for a complete understanding of the underlying molecular and evolutionary mechanisms driving adaptive phenotypic change. Using plasticine models in the field, we show that the light coat color of deer mice that recently colonized the light-colored soil of the Nebraska Sand Hills provides a strong selective advantage against visually hunting predators. Color variation in an admixed population suggests that this light Sand Hills phenotype is composed of multiple traits. We identified distinct regions within the Agouti locus associated with each color trait and found that only haplotypes associated with light trait values have evidence of selection. Thus, local adaptation is the result of independent selection on many mutations within a single locus, each with a specific effect on an adaptive phenotype, thereby minimizing pleiotropic consequences.
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Affiliation(s)
- Catherine R Linnen
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA.
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48
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Davis RC, van Nas A, Bennett B, Orozco L, Pan C, Rau CD, Eskin E, Lusis AJ. Genome-wide association mapping of blood cell traits in mice. Mamm Genome 2013; 24:105-18. [PMID: 23417284 DOI: 10.1007/s00335-013-9448-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 01/11/2013] [Indexed: 12/13/2022]
Abstract
Genetic variations in blood cell parameters can impact clinical traits. We report here the mapping of blood cell traits in a panel of 100 inbred strains of mice of the Hybrid Mouse Diversity Panel (HMDP) using genome-wide association (GWA). We replicated a locus previously identified in using linkage analysis in several genetic crosses for mean corpuscular volume (MCV) and a number of other red blood cell traits on distal chromosome 7. Our peak for SNP association to MCV occurred in a linkage disequilibrium (LD) block spanning from 109.38 to 111.75 Mb that includes Hbb-b1, the likely causal gene. Altogether, we identified five loci controlling red blood cell traits (on chromosomes 1, 7, 11, 12, and 16), and four of these correspond to loci for red blood cell traits reported in a recent human GWA study. For white blood cells, including granulocytes, monocytes, and lymphocytes, a total of six significant loci were identified on chromosomes 1, 6, 8, 11, 12, and 15. An average of ten candidate genes were found at each locus and those were prioritized by examining functional variants in the HMDP such as missense and expression variants. These results provide intermediate phenotypes and candidate loci for genetic studies of atherosclerosis and cancer as well as inflammatory and immune disorders in mice.
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Affiliation(s)
- Richard C Davis
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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49
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Didion JP, de Villena FPM. Deconstructing Mus gemischus: advances in understanding ancestry, structure, and variation in the genome of the laboratory mouse. Mamm Genome 2013; 24:1-20. [PMID: 23223940 PMCID: PMC4034049 DOI: 10.1007/s00335-012-9441-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 11/05/2012] [Indexed: 01/26/2023]
Abstract
The laboratory mouse is an artificial construct with a complex relationship to its natural ancestors. In 2002, the mouse became the first mammalian model organism with a reference genome. Importantly, the mouse genome sequence was assembled from data on a single inbred laboratory strain, C57BL/6. Several large-scale genetic variant discovery efforts have been conducted, resulting in a catalog of tens of millions of SNPs and structural variants. High-density genotyping arrays covering a subset of those variants have been used to produce hundreds of millions of genotypes in laboratory stocks and a small number of wild mice. These landmark resources now enable us to determine relationships among laboratory mice, assign local ancestry at fine scale, resolve important controversies, and identify a new set of challenges-most importantly, the troubling scarcity of genetic data on the very natural populations from which the laboratory mouse was derived. Our aim with this review is to provide the reader with an historical context for the mouse as a model organism and to explain how practical decisions made in the past have influenced both the architecture of the laboratory mouse genome and the design and execution of current large-scale resources. We also provide examples on how the accomplishments of the past decade can be used by researchers to streamline the use of mice in their experiments and correctly interpret results. Finally, we propose future steps that will enable the mouse community to extend its successes in the decade to come.
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Affiliation(s)
- John P. Didion
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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50
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Neves HHR, Carvalheiro R, Queiroz SA. A comparison of statistical methods for genomic selection in a mice population. BMC Genet 2012; 13:100. [PMID: 23134637 PMCID: PMC3563460 DOI: 10.1186/1471-2156-13-100] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 10/31/2012] [Indexed: 11/16/2022] Open
Abstract
Background The availability of high-density panels of SNP markers has opened new perspectives for marker-assisted selection strategies, such that genotypes for these markers are used to predict the genetic merit of selection candidates. Because the number of markers is often much larger than the number of phenotypes, marker effect estimation is not a trivial task. The objective of this research was to compare the predictive performance of ten different statistical methods employed in genomic selection, by analyzing data from a heterogeneous stock mice population. Results For the five traits analyzed (W6W: weight at six weeks, WGS: growth slope, BL: body length, %CD8+: percentage of CD8+ cells, CD4+/ CD8+: ratio between CD4+ and CD8+ cells), within-family predictions were more accurate than across-family predictions, although this superiority in accuracy varied markedly across traits. For within-family prediction, two kernel methods, Reproducing Kernel Hilbert Spaces Regression (RKHS) and Support Vector Regression (SVR), were the most accurate for W6W, while a polygenic model also had comparable performance. A form of ridge regression assuming that all markers contribute to the additive variance (RR_GBLUP) figured among the most accurate for WGS and BL, while two variable selection methods ( LASSO and Random Forest, RF) had the greatest predictive abilities for %CD8+ and CD4+/ CD8+. RF, RKHS, SVR and RR_GBLUP outperformed the remainder methods in terms of bias and inflation of predictions. Conclusions Methods with large conceptual differences reached very similar predictive abilities and a clear re-ranking of methods was observed in function of the trait analyzed. Variable selection methods were more accurate than the remainder in the case of %CD8+ and CD4+/CD8+ and these traits are likely to be influenced by a smaller number of QTL than the remainder. Judged by their overall performance across traits and computational requirements, RR_GBLUP, RKHS and SVR are particularly appealing for application in genomic selection.
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Affiliation(s)
- Haroldo H R Neves
- Departamento de Zootecnia, FCAV, UNESP, Jaboticabal, CEP: 14,884-900, SP, Brazil.
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