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Payseur BA, Anderson S, James RT, Parmenter MD, Gray MM, Vinyard CJ. Genetics of evolved load resistance in the skeletons of unusually large mice from Gough Island. Genetics 2023; 225:iyad137. [PMID: 37477896 PMCID: PMC10471205 DOI: 10.1093/genetics/iyad137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 07/22/2023] Open
Abstract
A primary function of the skeleton is to resist the loads imparted by body weight. Genetic analyses have identified genomic regions that contribute to differences in skeletal load resistance between laboratory strains of mice, but these studies are usually restricted to 1 or 2 bones and leave open the question of how load resistance evolves in natural populations. To address these challenges, we examined the genetics of bone structure using the largest wild house mice on record, which live on Gough Island (GI). We measured structural traits connected to load resistance in the femur, tibia, scapula, humerus, radius, ulna, and mandible of GI mice, a smaller-bodied reference strain from the mainland, and 760 of their F2s. GI mice have bone geometries indicative of greater load resistance abilities but show no increase in bone mineral density compared to the mainland strain. Across traits and bones, we identified a total of 153 quantitative trait loci (QTL) that span all but one of the autosomes. The breadth of QTL detection ranges from a single bone to all 7 bones. Additive effects of QTL are modest. QTL for bone structure show limited overlap with QTL for bone length and width and QTL for body weight mapped in the same cross, suggesting a distinct genetic architecture for load resistance. Our findings provide a rare genetic portrait of the evolution of load resistance in a natural population with extreme body size.
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Affiliation(s)
- Bret A Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sara Anderson
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Roy T James
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | | | - Melissa M Gray
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Christopher J Vinyard
- Department of Biomedical Sciences, Ohio University - Heritage College of Osteopathic Medicine, Athens, OH 45701, USA
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2
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Stratton JA, Nolte MJ, Payseur BA. Genetics of behavioural evolution in giant mice from Gough Island. Proc Biol Sci 2023; 290:20222603. [PMID: 37161324 PMCID: PMC10170209 DOI: 10.1098/rspb.2022.2603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/14/2023] [Indexed: 05/11/2023] Open
Abstract
The evolution of behaviour on islands is a pervasive phenomenon that contributed to Darwin's theory of natural selection. Island populations frequently show increased boldness and exploration compared with their mainland counterparts. Despite the generality of this pattern, the genetic basis of island-associated behaviours remains a mystery. To address this gap in knowledge, we genetically dissected behaviour in 613 F2s generated by crossing inbred mouse strains from Gough Island (where they live without predators or human commensals) and a mainland conspecific. We used open field and light/dark box tests to measure seven behaviours related to boldness and exploration in juveniles and adults. Across all assays, we identified a total of 41 quantitative trait loci (QTL) influencing boldness and exploration. QTL have moderate effects and are often unique to specific behaviours or ages. Function-valued trait mapping revealed changes in estimated effects of QTL during assays, providing a rare dynamic window into the genetics of behaviour often missed by standard approaches. The genomic locations of QTL are distinct from those found in laboratory strains of mice, indicating different genetic paths to the evolution of similar behaviours. We combine our mapping results with extensive phenotypic and genetic information available for laboratory mice to nominate candidate genes for the evolution of behaviour on islands.
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Affiliation(s)
- Jered A. Stratton
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Mark J. Nolte
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Bret A. Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
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3
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Oh RY, Deshwar AR, Marwaha A, Sabha N, Tropak M, Hou H, Yuki KE, Wilson MD, Rump P, Lunsing R, Elserafy N, Chung CWT, Hewson S, Klein-Rodewald T, Calzada-Wack J, Sanz-Moreno A, Kraiger M, Marschall S, Fuchs H, Gailus-Durner V, Hrabe de Angelis M, Dowling J, Schulze A. Biallelic loss-of-function variants in RABGAP1 cause a novel neurodevelopmental syndrome. Genet Med 2022; 24:2399-2407. [PMID: 36083289 DOI: 10.1016/j.gim.2022.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022] Open
Abstract
PURPOSE RABGAP1 is a GTPase-activating protein implicated in a variety of cellular and molecular processes, including mitosis, cell migration, vesicular trafficking, and mTOR signaling. There are no known Mendelian diseases caused by variants in RABGAP1. METHODS Through GeneMatcher, we identified 5 patients from 3 unrelated families with homozygous variants in the RABGAP1 gene found on exome sequencing. We established lymphoblastoid cells lines derived from an affected individual and her parents and performed RNA sequencing and functional studies. Rabgap1 knockout mice were generated and phenotyped. RESULTS We report 5 patients presenting with a common constellation of features, including global developmental delay/intellectual disability, microcephaly, bilateral sensorineural hearing loss, and seizures, as well as overlapping dysmorphic features. Neuroimaging revealed common features, including delayed myelination, white matter volume loss, ventriculomegaly, and thinning of the corpus callosum. Functional analysis of patient cells revealed downregulated mTOR signaling and abnormal localization of early endosomes and lysosomes. Rabgap1 knockout mice exhibited several features in common with the patient cohort, including microcephaly, thinning of the corpus callosum, and ventriculomegaly. CONCLUSION Collectively, our results provide evidence of a novel neurodevelopmental syndrome caused by biallelic loss-of-function variants in RABGAP1.
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Affiliation(s)
- Rachel Youjin Oh
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ashish R Deshwar
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada; Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ashish Marwaha
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
| | - Nesrin Sabha
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael Tropak
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Huayun Hou
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kyoko E Yuki
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael D Wilson
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Patrick Rump
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Roelineke Lunsing
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Noha Elserafy
- Department of Clinical Genetics, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Clara W T Chung
- Department of Clinical Genetics, Liverpool Hospital, Sydney, New South Wales, Australia; School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Stacy Hewson
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tanja Klein-Rodewald
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße, Neuherberg, Germany
| | - Julia Calzada-Wack
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße, Neuherberg, Germany
| | - Adrián Sanz-Moreno
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße, Neuherberg, Germany
| | - Markus Kraiger
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße, Neuherberg, Germany
| | - Susan Marschall
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße, Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße, Neuherberg, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße, Neuherberg, Germany
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße, Neuherberg, Germany; Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Freising, Germany; German Center for Diabetes Research (DZD), Ingolstaedter Landstraße, Neuherberg, Germany
| | - James Dowling
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andreas Schulze
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada; Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada; Departments of Paediatrics and Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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4
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Parmenter MD, Nelson JP, Gray MM, Weigel S, Vinyard CJ, Payseur BA. A complex genetic architecture underlies mandibular evolution in big mice from Gough Island. Genetics 2022; 220:iyac023. [PMID: 35137059 PMCID: PMC8982026 DOI: 10.1093/genetics/iyac023] [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: 11/30/2021] [Accepted: 01/31/2022] [Indexed: 01/29/2023] Open
Abstract
Some of the most compelling examples of morphological evolution come from island populations. Alterations in the size and shape of the mandible have been repeatedly observed in murid rodents following island colonization. Despite this pattern and the significance of the mandible for dietary adaptation, the genetic basis of island-mainland divergence in mandibular form remains uninvestigated. To fill this gap, we examined mandibular morphology in 609 F2s from a cross between Gough Island mice, the largest wild house mice on record, and mice from a mainland reference strain (WSB). Univariate genetic mapping identifies 3 quantitative trait loci (QTL) for relative length of the temporalis lever arm and 2 distinct QTL for relative condyle length, 2 traits expected to affect mandibular function that differ between Gough Island mice and WSB mice. Multivariate genetic mapping of coordinates from geometric morphometric analyses identifies 27 QTL contributing to overall mandibular shape. Quantitative trait loci show a complex mixture of modest, additive effects dispersed throughout the mandible, with landmarks including the coronoid process and the base of the ascending ramus frequently modulated by QTL. Additive effects of most shape quantitative trait loci do not align with island-mainland divergence, suggesting that directional selection played a limited role in the evolution of mandibular shape. In contrast, Gough Island mouse alleles at QTL for centroid size and QTL for jaw length increase these measures, suggesting selection led to larger mandibles, perhaps as a correlated response to the evolution of larger bodies.
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Affiliation(s)
| | - Jacob P Nelson
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - Melissa M Gray
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - Sara Weigel
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Christopher J Vinyard
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA
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5
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Linking genetic, morphological, and behavioural divergence between inland island and mainland deer mice. Heredity (Edinb) 2022; 128:97-106. [PMID: 34952930 PMCID: PMC8814197 DOI: 10.1038/s41437-021-00492-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 02/03/2023] Open
Abstract
The island syndrome hypothesis (ISH) stipulates that, as a result of local selection pressures and restricted gene flow, individuals from island populations should differ from individuals within mainland populations. Specifically, island populations are predicted to contain individuals that are larger, less aggressive, more sociable, and that invest more in their offspring. To date, tests of the ISH have mainly compared oceanic islands to continental sites, and rarely smaller spatial scales such as inland watersheds. Here, using a novel set of genome-wide SNP markers in wild deer mice (Peromyscus maniculatus) we conducted a genomic assessment of predictions underlying the ISH in an inland riverine island system: analysing island-mainland population structure, and quantifying heritability of phenotypes thought to underlie the ISH. We found clear genomic differentiation between the island and mainland populations and moderate to high marker-based heritability estimates for overall variation in traits previously found to differ in line with the ISH between mainland and island locations. FST outlier analyses highlighted 12 loci associated with differentiation between mainland and island populations. Together these results suggest that the island populations examined are on independent evolutionary trajectories, the traits considered have a genetic basis (rather than phenotypic variation being solely due to phenotypic plasticity). Coupled with the previous results showing significant phenotypic differentiation between the island and mainland groups in this system, this study suggests that the ISH can hold even on a small spatial scale.
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Unger CM, Devine J, Hallgrímsson B, Rolian C. Selection for increased tibia length in mice alters skull shape through parallel changes in developmental mechanisms. eLife 2021; 10:67612. [PMID: 33899741 PMCID: PMC8118654 DOI: 10.7554/elife.67612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/23/2021] [Indexed: 12/18/2022] Open
Abstract
Bones in the vertebrate cranial base and limb skeleton grow by endochondral ossification, under the control of growth plates. Mechanisms of endochondral ossification are conserved across growth plates, which increases covariation in size and shape among bones, and in turn may lead to correlated changes in skeletal traits not under direct selection. We used micro-CT and geometric morphometrics to characterize shape changes in the cranium of the Longshanks mouse, which was selectively bred for longer tibiae. We show that Longshanks skulls became longer, flatter, and narrower in a stepwise process. Moreover, we show that these morphological changes likely resulted from developmental changes in the growth plates of the Longshanks cranial base, mirroring changes observed in its tibia. Thus, indirect and non-adaptive morphological changes can occur due to developmental overlap among distant skeletal elements, with important implications for interpreting the evolutionary history of vertebrate skeletal form.
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Affiliation(s)
- Colton M Unger
- Department of Biological Sciences, University of Calgary, Calgary, Canada.,McCaig Institute for Bone and Joint Health, Calgary, Canada
| | - Jay Devine
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, Canada
| | - Benedikt Hallgrímsson
- McCaig Institute for Bone and Joint Health, Calgary, Canada.,Department of Cell Biology and Anatomy, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Canada
| | - Campbell Rolian
- McCaig Institute for Bone and Joint Health, Calgary, Canada.,Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
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7
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Abstract
Island populations are hallmarks of extreme phenotypic evolution. Radical changes in resource availability and predation risk accompanying island colonization drive changes in behavior, which Darwin likened to tameness in domesticated animals. Although many examples of animal boldness are found on islands, the heritability of observed behaviors, a requirement for evolution, remains largely unknown. To fill this gap, we profiled anxiety and exploration in island and mainland inbred strains of house mice raised in a common laboratory environment. The island strain was descended from mice on Gough Island, the largest wild house mice on record. Experiments utilizing open environments across two ages showed that Gough Island mice are bolder and more exploratory, even when a shelter is provided. Concurrently, Gough Island mice retain an avoidance response to predator urine. F1 offspring from crosses between these two strains behave more similarly to the mainland strain for most traits, suggesting recessive mutations contributed to behavioral evolution on the island. Our results provide a rare example of novel, inherited behaviors in an island population and demonstrate that behavioral evolution can be specific to different forms of perceived danger. Our discoveries pave the way for a genetic understanding of how island populations evolve unusual behaviors.
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8
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Abstract
A key challenge in understanding how organisms adapt to their environments is to identify the mutations and genes that make it possible. By comparing patterns of sequence variation to neutral predictions across genomes, the targets of positive selection can be located. We applied this logic to house mice that invaded Gough Island (GI), an unusual population that shows phenotypic and ecological hallmarks of selection. We used massively parallel short-read sequencing to survey the genomes of 14 GI mice. We computed a set of summary statistics to capture diverse aspects of variation across these genome sequences, used approximate Bayesian computation to reconstruct a null demographic model, and then applied machine learning to estimate the posterior probability of positive selection in each region of the genome. Using a conservative threshold, 1,463 5-kb windows show strong evidence for positive selection in GI mice but not in a mainland reference population of German mice. Disproportionate shares of these selection windows contain genes that harbor derived nonsynonymous mutations with large frequency differences. Over-represented gene ontologies in selection windows emphasize neurological themes. Inspection of genomic regions harboring many selection windows with high posterior probabilities pointed to genes with known effects on exploratory behavior and body size as potential targets. Some genes in these regions contain candidate adaptive variants, including missense mutations and/or putative regulatory mutations. Our results provide a genomic portrait of adaptation to island conditions and position GI mice as a powerful system for understanding the genetic component of natural selection.
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Affiliation(s)
- Bret A Payseur
- Laboratory of Genetics, University of Wisconsin – Madison, Madison, WI
| | - Peicheng Jing
- Laboratory of Genetics, University of Wisconsin – Madison, Madison, WI
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9
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Wilches R, Beluch WH, McConnell E, Tautz D, Chan YF. Independent evolution toward larger body size in the distinctive Faroe Island mice. G3-GENES GENOMES GENETICS 2021; 11:6062402. [PMID: 33561246 PMCID: PMC8022703 DOI: 10.1093/g3journal/jkaa051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/10/2020] [Indexed: 11/29/2022]
Abstract
Most phenotypic traits in nature involve the collective action of many genes. Traits that evolve repeatedly are particularly useful for understanding how selection may act on changing trait values. In mice, large body size has evolved repeatedly on islands and under artificial selection in the laboratory. Identifying the loci and genes involved in this process may shed light on the evolution of complex, polygenic traits. Here, we have mapped the genetic basis of body size variation by making a genetic cross between mice from the Faroe Islands, which are among the largest and most distinctive natural populations of mice in the world, and a laboratory mouse strain selected for small body size, SM/J. Using this F2 intercross of 841 animals, we have identified 111 loci controlling various aspects of body size, weight and growth hormone levels. By comparing against other studies, including the use of a joint meta-analysis, we found that the loci involved in the evolution of large size in the Faroese mice were largely independent from those of a different island population or other laboratory strains. We hypothesize that colonization bottleneck, historical hybridization, or the redundancy between multiple loci have resulted in the Faroese mice achieving an outwardly similar phenotype through a distinct evolutionary path.
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Affiliation(s)
- Ricardo Wilches
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
| | - William H Beluch
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
| | - Ellen McConnell
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Genetics, 24306 Plön, Germany
| | - Diethard Tautz
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Genetics, 24306 Plön, Germany
| | - Yingguang Frank Chan
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
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10
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Phifer-Rixey M, Harr B, Hey J. Further resolution of the house mouse (Mus musculus) phylogeny by integration over isolation-with-migration histories. BMC Evol Biol 2020; 20:120. [PMID: 32933487 PMCID: PMC7493149 DOI: 10.1186/s12862-020-01666-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/27/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The three main subspecies of house mice, Mus musculus castaneus, Mus musculus domesticus, and Mus musculus musculus, are estimated to have diverged ~ 350-500KYA. Resolution of the details of their evolutionary history is complicated by their relatively recent divergence, ongoing gene flow among the subspecies, and complex demographic histories. Previous studies have been limited to some extent by the number of loci surveyed and/or by the scope of the method used. Here, we apply a method (IMa3) that provides an estimate of a population phylogeny while allowing for complex histories of gene exchange. RESULTS Results strongly support a topology with M. m. domesticus as sister to M. m. castaneus and M. m. musculus. In addition, we find evidence of gene flow between all pairs of subspecies, but that gene flow is most restricted from M. m. musculus into M. m. domesticus. Estimates of other key parameters are dependent on assumptions regarding generation time and mutation rate in house mice. Nevertheless, our results support previous findings that the effective population size, Ne, of M. m. castaneus is larger than that of the other two subspecies, that the three subspecies began diverging ~ 130 - 420KYA, and that the time between divergence events was short. CONCLUSIONS Joint demographic and phylogenetic analyses of genomic data provide a clearer picture of the history of divergence in house mice.
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Affiliation(s)
| | - Bettina Harr
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany
| | - Jody Hey
- Department of Biology, Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, USA
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11
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Nolte MJ, Jing P, Dewey CN, Payseur BA. Giant Island Mice Exhibit Widespread Gene Expression Changes in Key Metabolic Organs. Genome Biol Evol 2020; 12:1277-1301. [PMID: 32531054 PMCID: PMC7487164 DOI: 10.1093/gbe/evaa118] [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] [Accepted: 06/06/2020] [Indexed: 12/02/2022] Open
Abstract
Island populations repeatedly evolve extreme body sizes, but the genomic basis of this pattern remains largely unknown. To understand how organisms on islands evolve gigantism, we compared genome-wide patterns of gene expression in Gough Island mice, the largest wild house mice in the world, and mainland mice from the WSB/EiJ wild-derived inbred strain. We used RNA-seq to quantify differential gene expression in three key metabolic organs: gonadal adipose depot, hypothalamus, and liver. Between 4,000 and 8,800 genes were significantly differentially expressed across the evaluated organs, representing between 20% and 50% of detected transcripts, with 20% or more of differentially expressed transcripts in each organ exhibiting expression fold changes of at least 2×. A minimum of 73 candidate genes for extreme size evolution, including Irs1 and Lrp1, were identified by considering differential expression jointly with other data sets: 1) genomic positions of published quantitative trait loci for body weight and growth rate, 2) whole-genome sequencing of 16 wild-caught Gough Island mice that revealed fixed single-nucleotide differences between the strains, and 3) publicly available tissue-specific regulatory elements. Additionally, patterns of differential expression across three time points in the liver revealed that Arid5b potentially regulates hundreds of genes. Functional enrichment analyses pointed to cell cycling, mitochondrial function, signaling pathways, inflammatory response, and nutrient metabolism as potential causes of weight accumulation in Gough Island mice. Collectively, our results indicate that extensive gene regulatory evolution in metabolic organs accompanied the rapid evolution of gigantism during the short time house mice have inhabited Gough Island.
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Affiliation(s)
- Mark J Nolte
- Laboratory of Genetics, University of Wisconsin - Madison
| | - Peicheng Jing
- Laboratory of Genetics, University of Wisconsin - Madison
| | - Colin N Dewey
- Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin - Madison
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12
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Baier F, Hoekstra HE. The genetics of morphological and behavioural island traits in deer mice. Proc Biol Sci 2019; 286:20191697. [PMID: 31662081 DOI: 10.1098/rspb.2019.1697] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Animals on islands often exhibit dramatic differences in morphology and behaviour compared with mainland individuals, a phenomenon known as the 'island syndrome'. These differences are thought to be adaptations to island environments, but the extent to which they have a genetic basis or instead represent plastic responses to environmental extremes is often unknown. Here, we revisit a classic case of island syndrome in deer mice (Peromyscus maniculatus) from British Columbia. We first show that Saturna Island mice and those from neighbouring islands are approximately 35% (approx. 5 g) heavier than mainland mice and diverged approximately 10 000 years ago. We then establish laboratory colonies and find that Saturna Island mice are heavier both because they are longer and have disproportionately more lean mass. These trait differences are maintained in second-generation captive-born mice raised in a common environment. In addition, island-mainland hybrids reveal a maternal genetic effect on body weight. Using behavioural testing in the laboratory, we also find that wild-caught island mice are less aggressive than mainland mice; however, laboratory-raised mice born to these founders do not differ in aggression. Together, our results reveal that these mice have different responses to the environmental conditions on islands-a heritable change in a morphological trait and a plastic response in a behavioural trait.
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Affiliation(s)
- Felix Baier
- Howard Hughes Medical Institute, Museum of Comparative Zoology, Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.,Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Hopi E Hoekstra
- Howard Hughes Medical Institute, Museum of Comparative Zoology, Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.,Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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13
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Parmenter MD, Nelson JP, Weigel SE, Gray MM, Payseur BA, Vinyard CJ. Masticatory Apparatus Performance and Functional Morphology in the Extremely Large Mice from Gough Island. Anat Rec (Hoboken) 2018; 303:167-179. [PMID: 30548803 DOI: 10.1002/ar.24053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/14/2018] [Accepted: 09/03/2018] [Indexed: 11/07/2022]
Abstract
Since their arrival approximately 200 years ago, the house mice (Mus musculus) on Gough Island (GI) rapidly increased in size to become the largest wild house mice on record. Along with this extreme increase in body size, GI mice adopted a predatory diet, consuming significant quantities of seabird chicks and eggs. We studied this natural experiment to determine how evolution of extreme size and a novel diet impacted masticatory apparatus performance and functional morphology in these mice. We measured maximum bite force and jaw opening (i.e., gape) along with several musculoskeletal dimensions functionally linked to these performance measurements to test the hypotheses that GI mice evolved larger bite forces and jaw gapes as part of their extreme increase in size and/or novel diet. GI mice can bite more forcefully and open their jaws wider than a representative mainland strain of house mice. Similarly, GI mice have musculoskeletal features of the masticatory apparatus that are absolutely larger than WSB mice. However, when considered relative to body size or jaw length, as a relevant mechanical standard, GI mice show reduced performance, suggesting a size-related decrease in these abilities. Correspondingly, most musculoskeletal features are not relatively larger in GI mice. Incisor biting leverage and condylar dimensions are exceptions, suggesting relative increases in biting efficiency and condylar rotation in GI mice. Based on these results, we hypothesize that evolutionary enhancements in masticatory performance are correlated with the extreme increase in body size and associated musculoskeletal phenotypes in Gough Island mice. Anat Rec, 2019. © 2018 American Association for Anatomy.
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Affiliation(s)
| | - Jacob P Nelson
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin
| | - Sara E Weigel
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio
| | - Melissa M Gray
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin
| | - Christopher J Vinyard
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio
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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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