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Sosa CC, Arenas C, García-Merchán VH. Human Population Density Influences Genetic Diversity of Two Rattus Species Worldwide: A Macrogenetic Approach. Genes (Basel) 2023; 14:1442. [PMID: 37510346 PMCID: PMC10379283 DOI: 10.3390/genes14071442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/18/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
On a planet experiencing constant human population growth, it is necessary to explore the anthropogenic effects on the genetic diversity of species, and specifically invasive species. Using an analysis that integrates comparative phylogeography, urban landscape genetics, macrogenetics and a systematic review, we explore the worldwide genetic diversity of the human commensal and anthropogenic species Rattus rattus and Rattus norvegicus. Based on metadata obtained considering 35 selected studies related to observed heterozygosity, measured by nuclear molecular markers (microsatellites, Single Nucleotide Polymorphisms-SNPs-, restrictition site-associated DNA sequencing -RAD-Seq-), socioeconomic and mobility anthropogenic factors were used as predictors of genetic diversity of R. rattus and R. norvegicus, using the Gini index, principal component analysis and Random Forest Regression as analysis methodology. Population density was on average the best predictor of genetic diversity in the Rattus species analyzed, indicating that the species respond in a particular way to the characteristics present in urban environments because of a combination of life history characteristics and human-mediated migration and colonization processes. To create better management and control strategies for these rodents and their associated diseases, it is necessary to fill the existing information gap in urban landscape genetics studies with more metadata repositories, with emphasis on tropical and subtropical regions of the world.
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Affiliation(s)
- Chrystian C Sosa
- Evolution, Ecology and Conservation Research Group-EECO, Biology Program, Faculty of Basic Sciences and Technologies, Universidad del Quindío, Armenia 630004, Colombia
- Department of Natural Sciences and Mathematics, Pontificia Universidad Javeriana, Cali 7 #40-62, Bogotá 110311, Colombia
| | - Catalina Arenas
- Evolution, Ecology and Conservation Research Group-EECO, Biology Program, Faculty of Basic Sciences and Technologies, Universidad del Quindío, Armenia 630004, Colombia
| | - Víctor Hugo García-Merchán
- Evolution, Ecology and Conservation Research Group-EECO, Biology Program, Faculty of Basic Sciences and Technologies, Universidad del Quindío, Armenia 630004, Colombia
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2
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Kalbfleisch TS, Hussien AbouEl Ela NA, Li K, Brashear WA, Kochan KJ, Hillhouse AE, Zhu Y, Dhande IS, Kline EJ, Hudson EA, Murphy TD, Thibaud-Nissen F, Smith ML, Doris PA. The Assembled Genome of the Stroke-Prone Spontaneously Hypertensive Rat. Hypertension 2023; 80:138-146. [PMID: 36330812 PMCID: PMC9814308 DOI: 10.1161/hypertensionaha.122.20140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND We report the creation and evaluation of a de novo assembly of the genome of the spontaneously hypertensive rat, the most widely used model of human cardiovascular disease. METHODS The genome is assembled from long read sequencing (PacBio HiFi and continuous long read data [CLR]) and scaffolded with long-range structural information obtained from Bionano optical maps and proximity ligation sequencing proximity analysis of the genome. The genome assembly was polished with Illumina short reads. Completeness of the assembly was investigated using Benchmarking Universal Single Copy Orthologs analysis. The genome assembly was also evaluated with the rat reference gene set, using NCBI automated protocols. We also generated orthogonal single molecule transcript sequence reads (Iso-Seq) from 8 tissues and used them to validate the coding assembly, to annotate the assembly with RNA transcripts representing unique full length transcript isoforms for each gene and to determine whether divergences between RefSeq sequences and the assembly were attributable to assembly errors or polymorphisms. RESULTS The assembly analysis indicates that this assembly is comparable in contiguity and completeness to the current rat reference assembly, while the use of HiFi sequencing yields an assembly that is more correct at the single base level. Synteny analysis was performed to uncover the extent of synteny and the presence and distribution of chromosomal rearrangements between the reference and this assembly. CONCLUSION The resulting genome assembly is reference quality and captures significant structural variation.
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Affiliation(s)
- Theodore S Kalbfleisch
- Department of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky, Lexington, KY (T.S.K., N.A.H., K.L.)
| | - Nahla A Hussien AbouEl Ela
- Department of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky, Lexington, KY (T.S.K., N.A.H., K.L.)
| | - Kai Li
- Department of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky, Lexington, KY (T.S.K., N.A.H., K.L.)
| | - Wesley A Brashear
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX (W.A.B., K.J.K., A.E.H.)
| | - Kelli J Kochan
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX (W.A.B., K.J.K., A.E.H.)
| | - Andrew E Hillhouse
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX (W.A.B., K.J.K., A.E.H.)
| | - Yaming Zhu
- Center for Human Genetics, Brown Foundation Institute of Molecular Medicine, University of Texas McGovern School of Medicine, Houston, TX (Y.Z., I.S.D., P.A.D.)
| | - Isha S Dhande
- Center for Human Genetics, Brown Foundation Institute of Molecular Medicine, University of Texas McGovern School of Medicine, Houston, TX (Y.Z., I.S.D., P.A.D.)
| | - Eric J Kline
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY (E.J.K., E.A.H, M.L.S.)
| | - Elizabeth A Hudson
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY (E.J.K., E.A.H, M.L.S.)
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD (T.D.M., F.T.-N.)
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD (T.D.M., F.T.-N.)
| | - Melissa L Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY (E.J.K., E.A.H, M.L.S.)
| | - Peter A Doris
- Center for Human Genetics, Brown Foundation Institute of Molecular Medicine, University of Texas McGovern School of Medicine, Houston, TX (Y.Z., I.S.D., P.A.D.)
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Hulme-Beaman A, Orton D, Cucchi T. The origins of the domesticate brown rat ( Rattus norvegicus) and its pathways to domestication. Anim Front 2021; 11:78-86. [PMID: 34158992 PMCID: PMC8214441 DOI: 10.1093/af/vfab020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Ardern Hulme-Beaman
- Department of Archaeology, Classics and Egyptology, University of Liverpool, 12–14 Abercromby Square, Liverpool, L69 7WZ, UK
| | - David Orton
- BioArCh, Department of Archaeology, University of York, York YO10 5DD, UK
| | - Thomas Cucchi
- Archaeozoology, Archaeobotany, Societies, Practices, Environments (AASPE-UMR7209), CNRS, National Museum of Natural History (MNHN), Paris, France
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Li Y, Fujiwara K, Osada N, Kawai Y, Takada T, Kryukov AP, Abe K, Yonekawa H, Shiroishi T, Moriwaki K, Saitou N, Suzuki H. House mouse Mus musculus dispersal in East Eurasia inferred from 98 newly determined complete mitochondrial genome sequences. Heredity (Edinb) 2021; 126:132-147. [PMID: 32934361 PMCID: PMC7852662 DOI: 10.1038/s41437-020-00364-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 11/09/2022] Open
Abstract
The Eurasian house mouse Mus musculus is useful for tracing prehistorical human movement related to the spread of farming. We determined whole mitochondrial DNA (mtDNA) sequences (ca. 16,000 bp) of 98 wild-derived individuals of two subspecies, M. m. musculus (MUS) and M. m. castaneus (CAS). We revealed directional dispersals reaching as far as the Japanese Archipelago from their homelands. Our phylogenetic analysis indicated that the eastward movement of MUS was characterised by five step-wise regional extension events: (1) broad spatial expansion into eastern Europe and the western part of western China, (2) dispersal to the eastern part of western China, (3) dispersal to northern China, (4) dispersal to the Korean Peninsula and (5) colonisation and expansion in the Japanese Archipelago. These events were estimated to have occurred during the last 2000-18,000 years. The dispersal of CAS was characterised by three events: initial divergences (ca. 7000-9000 years ago) of haplogroups in northernmost China and the eastern coast of India, followed by two population expansion events that likely originated from the Yangtze River basin to broad areas of South and Southeast Asia, including Sri Lanka, Bangladesh and Indonesia (ca. 4000-6000 years ago) and to Yunnan, southern China and the Japanese Archipelago (ca. 2000-3500). This study provides a solid framework for the spatiotemporal movement of the human-associated organisms in Holocene Eastern Eurasia using whole mtDNA sequences, reliable evolutionary rates and accurate branching patterns. The information obtained here contributes to the analysis of a variety of animals and plants associated with prehistoric human migration.
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Affiliation(s)
- Yue Li
- Graduate School of Environmental Science, Hokkaido University, North 10, West 5, Kita-ku, Sapporo, 060-0810, Japan
| | - Kazumichi Fujiwara
- Graduate School of Information Science and Technology, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, 060-0814, Japan
- Global Station for Big Data and Cybersecurity, GI-CoRE, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, 060-0814, Japan
| | - Naoki Osada
- Graduate School of Information Science and Technology, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, 060-0814, Japan
- Global Station for Big Data and Cybersecurity, GI-CoRE, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, 060-0814, Japan
| | - Yosuke Kawai
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine, 1-21-1, Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Toyoyuki Takada
- Integrated Bioresource Information Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, 305-0074, Japan
| | - Alexey P Kryukov
- Far Eastern Branch of the Russian Academy of Sciences, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Vladivostok, 690022, Russia
| | - Kuniya Abe
- Technology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, 305-0074, Japan
| | - Hiromichi Yonekawa
- Laboratory for Transgenic Technology, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kami-kitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | | | - Kazuo Moriwaki
- RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, 305-0074, Japan
- National Institute of Genetics, 1111 Yata, Mishima, 411-8540, Japan
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, 411-8540, Japan
- School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, 903-0215, Japan
| | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, North 10, West 5, Kita-ku, Sapporo, 060-0810, Japan.
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Carter CS, Richardson A, Huffman DM, Austad S. Bring Back the Rat! J Gerontol A Biol Sci Med Sci 2020; 75:405-415. [PMID: 31894235 DOI: 10.1093/gerona/glz298] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Indexed: 12/12/2022] Open
Abstract
As 2020 is "The Year of the Rat" in the Chinese astrological calendar, it seems an appropriate time to consider whether we should bring back the laboratory rat to front-and-center in research on the basic biology of mammalian aging. Beginning in the 1970s, aging research with rats became common, peaking in 1992 but then declined dramatically by 2018 as the mouse became preeminent. The purpose of this review is to highlight some of the historical contributions as well as current advantages of the rat as a mammalian model of human aging, because we suspect at least a generation of researchers is no longer aware of this history or these advantages. Herein, we compare and contrast the mouse and rat in the context of several biological domains relevant to their use as appropriate models of aging: phylogeny/domestication, longevity interventions, pathology/physiology, and behavior/cognition. It is not the goal of this review to give a complete characterization of the differences between mice and rats, but to provide important examples of why using rats as well as mice is important to advance our understanding of the biology of aging.
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Affiliation(s)
- Christy S Carter
- Department of Medicine, Division of Gerontology, Geriatrics and Palliative Care, School of Medicine, University of Alabama at Birmingham
| | - Arlan Richardson
- Department of Biochemistry and Molecular Biology, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Science Center, and the Oklahoma City VA Medical Center
| | - Derek M Huffman
- Department of Molecular Pharmacology, Department of Medicine, and Institute for Aging Research, Albert Einstein College of Medicine, Bronx, New York
| | - Steven Austad
- Department of Biology, College of Arts and Sciences, University of Alabama at Birmingham
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7
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Puckett EE, Orton D, Munshi‐South J. Commensal Rats and Humans: Integrating Rodent Phylogeography and Zooarchaeology to Highlight Connections between Human Societies. Bioessays 2020; 42:e1900160. [DOI: 10.1002/bies.201900160] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/09/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Emily E. Puckett
- Department of Biological SciencesUniversity of Memphis Memphis TN 38152 USA
| | - David Orton
- BioArChDepartment of ArchaeologyUniversity of York York YO10 5DD UK
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Parsons MH, Jardine CM, Crowther MS, Himsworth CG. Editorial: Trends in Urban Rodent Monitoring and Mitigation: Improving Our Understanding of Population and Disease Ecology, Surveillance and Control. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2019.00522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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9
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Parsons MH, Deutsch MA, Dumitriu D, Munshi-South J. Differential responses by urban brown rats (Rattus norvegicus) toward male or female-produced scents in sheltered and high-risk presentations. JOURNAL OF URBAN ECOLOGY 2019. [DOI: 10.1093/jue/juz009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Wild rats (Rattus norvegicus) are among the most ubiquitous and consequential organisms in the urban environment. However, collecting data from city rats is difficult, and there has been little research to determine the influence, or valence, of rat scents on urban conspecifics. Using a mark-release-monitor protocol, we previously learned rats can be attracted to remote-sensing points when baited with mixed-bedding from male and female laboratory rats. It was thus essential that we disambiguate which scents were eliciting attraction (+ valence), inspection, a conditioned response whereby attraction may be followed by avoidance (–valence), or null-response (0 valence). We used radio-frequency identification tagging and scent-baited antennas to assess extended (>40 days) responses to either male or female scents against two risk presentations (near-shelter and exposed to predators). In response to male scents, rats (n = 8) visited both treatments (shelter, exposed) more than controls (0.2 visits/day treatment vs. 0.1/day; P < 0.05) indicating scents accounted for response more so than risk. Dwell-times, however, did not differ (1.2 s/visit treatment vs. 0.9 s/visit; P > 0.5). These outcomes are consistent with inspection (–valence). In response to female scents, rats (n = 7) increased visitation (5.02 visits/day vs. 0.1/day controls; P < 0.05), while dwell-times also increased 6.8 s/visit vs. 0.2 s/visit in both risk-settings. The latter is consistent with persistent attraction (+valence), but was also influenced by shelter, as runway visits (1.1 visits/day) were a magnitude more common than predator-exposed (0.1 visits/day). Further understanding and exploiting the mobility of city rats is necessary for improvements in basic and applied research, including city pathogen-surveillance and urban wildlife management.
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Affiliation(s)
- Michael H Parsons
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Michael A Deutsch
- Medical and Applied Entomology, Arrow Exterminating Company, Inc., Lynbrook, NY, USA
| | - Dani Dumitriu
- Departments of Pediatrics and Psychiatry, the Zuckerman Institute, and the Columbia Population Research Center, Columbia University, New York, NY, USA
| | - Jason Munshi-South
- Department of Biological Sciences and the Louis Calder Center—Biological Field Station, Fordham University, Armonk, NY, USA
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Puckett EE, Magnussen E, Khlyap LA, Strand TM, Lundkvist Å, Munshi-South J. Genomic analyses reveal three independent introductions of the invasive brown rat (Rattus norvegicus) to the Faroe Islands. Heredity (Edinb) 2019; 124:15-27. [PMID: 31399718 DOI: 10.1038/s41437-019-0255-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 07/10/2019] [Accepted: 07/20/2019] [Indexed: 11/09/2022] Open
Abstract
Population genomics offers innovative approaches to test hypotheses related to the source and timing of introduction of invasive species. These approaches are particularly appropriate to study colonization of island ecosystems. The brown rat is a cold-hardy global invasive that has reached most of the world's island ecosystems, including even highly isolated archipelagoes such as the Faroe Islands in the North Atlantic Ocean. Historic records tell of rats rafting to the southern island of Suðuroy in 1768 following a shipwreck off the coast of Scotland, then expanding across the archipelago. We investigated the demographic history of brown rats in the Faroes using 50,174 SNPs. We inferred three independent introductions of rats, including to Suðuroy, the islands of Borðoy and Viðoy, and onto Streymoy from which they expanded to Eysturoy and Vágar. All Faroese populations showed signs of strong bottlenecks and declining effective population size. We inferred that these founder events removed low frequency alleles, the exact data needed to estimate recent demographic histories. Therefore, we were unable to accurately estimate the timing of each invasion. The difficulties with demographic inference may be applicable to other invasive species, particularly those with extreme and recent bottlenecks. We identified three invasions of brown rats to the Faroe Islands that resulted in highly differentiated populations that will be useful for future studies of life history variation and genomic adaptation.
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Affiliation(s)
- Emily E Puckett
- Department of Biological Sciences, University of Memphis, Memphis, TN, USA. .,Louis Calder Center- Biological Field Station, Fordham University, Armonk, NY, USA.
| | - Eyðfinn Magnussen
- Faculty of Science and Technology, University of the Faroe Islands, Tórshavn, Faroe Islands
| | - Liudmila A Khlyap
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Tanja M Strand
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden.,National Veterinary Institute (SVA), Department of Microbiology, Uppsala, Sweden
| | - Åke Lundkvist
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Jason Munshi-South
- Louis Calder Center- Biological Field Station, Fordham University, Armonk, NY, USA
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Puckett EE, Munshi-South J. Brown rat demography reveals pre-commensal structure in eastern Asia before expansion into Southeast Asia. Genome Res 2019; 29:762-770. [PMID: 30910795 PMCID: PMC6499317 DOI: 10.1101/gr.235754.118] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/21/2019] [Indexed: 01/26/2023]
Abstract
Fossil evidence indicates that the globally distributed brown rat (Rattus norvegicus) originated in northern China and Mongolia. Historical records report the human-mediated invasion of rats into Europe in the 1500s, followed by global spread because of European imperialist activity during the 1600s–1800s. We analyzed 14 genomes representing seven previously identified evolutionary clusters, and tested alternative demographic models to infer patterns of range expansion, divergence times, and changes in effective population (Ne) size for this globally important pest species. We observed three range expansions from the ancestral population that produced the Pacific (diverged ∼16.1 kya), eastern China (∼17.5 kya), and Southeast (SE) Asia (∼0.86 kya) lineages. Our model shows a rapid range expansion from SE Asia into the Middle East and then continued expansion into central Europe 788 yr ago (1227 AD). We observed declining Ne within all brown rat lineages from 150–1 kya, reflecting population contractions during glacial cycles. Ne increased since 1 kya in Asian and European, but not in Pacific, evolutionary clusters. Our results support the hypothesis that northern Asia was the ancestral range for brown rats. We suggest that southward human migration across China between the 800s–1550s AD resulted in the introduction of rats to SE Asia, from which they rapidly expanded via existing maritime trade routes. Finally, we discovered that North America was colonized separately on both the Atlantic and Pacific seaboards, by evolutionary clusters of vastly different ages and genomic diversity levels. Our results should stimulate discussions among historians and zooarcheologists regarding the relationship between humans and rats.
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Affiliation(s)
- Emily E Puckett
- Louis Calder Center, Fordham University, Armonk, New York 10504, USA.,Department of Biological Sciences, University of Memphis, Memphis, Tennessee 38152, USA
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