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Caraballo L, Rangel Y, Reyna-Bello A, Muñoz M, Figueroa-Espinosa R, Sanz-Rodriquez CE, Guerrero E, Loureiro CL, Liu Q, Takiff HE. Outbreak of Intermediate Species Leptospira venezuelensis Spread by Rodents to Cows and Humans in L. interrogans-Endemic Region, Venezuela. Emerg Infect Dis 2024; 30:1514-1522. [PMID: 39043385 PMCID: PMC11286060 DOI: 10.3201/eid3008.231562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024] Open
Abstract
Leptospirosis is a common but underdiagnosed zoonosis. We conducted a 1-year prospective study in La Guaira State, Venezuela, analyzing 71 hospitalized patients who had possible leptospirosis and sampling local rodents and dairy cows. Leptospira rrs gene PCR test results were positive in blood or urine samples from 37/71 patients. Leptospira spp. were isolated from cultured blood or urine samples of 36/71 patients; 29 had L. interrogans, 3 L. noguchii, and 4 L. venezuelensis. Conjunctival suffusion was the most distinguishing clinical sign, many patients had liver involvement, and 8/30 patients with L. interrogans infections died. The Leptospira spp. found in humans were also isolated from local rodents; L. interrogans and L. venezuelensis were isolated from cows on a nearby, rodent-infested farm. Phylogenetic clustering of L. venezuelensis isolates suggested a recently expanded outbreak strain spread by rodents. Increased awareness of leptospirosis prevalence and rapid diagnostic tests are needed to improve patient outcomes.
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Li J, Huang E, Wu Y, Zhu C, Li W, Ai L, Xie Q, Tian Z, Zhong W, Sun G, Zhang L, Tan W. Population structure, dispersion patterns and genetic diversity of two major invasive and commensal zoonotic disease hosts ( Rattus norvegicus and Rattus tanezumi) from the southeastern coast of China. Front Genet 2024; 14:1174584. [PMID: 38259625 PMCID: PMC10800861 DOI: 10.3389/fgene.2023.1174584] [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: 02/26/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
Background: The invasive brownrat (Rattus norvegicus) and the Oriental rats (Rattus tanezumi) are common commensal murid that are important hosts for rodent-borne diseases in southeast Asia. Understanding their population structure and genetic diversity is essential to uncover their invasion biology and distribution dynamics that are essential for controlling rodent-borne diseases. Methods: TA total of 103 R. norvegicus and 85 R. tanezumi were collected from 13 to 9 coastal areas of six provincial monitoring sentinel sites, respectivelyto assess patterns in their microsatellite loci and their mitochondrial coxl gene region. Results: Eleven sampled populations of R. norvegicus were divided into two major clusters by region. The observed heterozygosity values of all regional populations were smaller than expected genetic diversity heterozygosity values and deviated from Hardy-Weinberg equilibrium Nine sample populations of R. tanezumi were divided into three clusters; two that included sample from Hainan and Fujian provinces, and one that included samples from the other provinces and cities. The genetic diversity of R. tanezumi was highest in samples from Jiangsu and Guangdong provinces. Conclusion: The data in this paper confirm the two invasive rodent species from the southeastern coastal region of China may have relied on maritime transport to spread from the southern region of China to the Yangtze River basin. R. tanezumi may then hanve migrated unidirectionally, along the southeastern provinces of China towards the north, while R. norvegicus spread in a complex and multidirectional manner in Hainan, Fujian, Zhejiang and Jiangsu Provinces of the country.
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Affiliation(s)
- Jiaqiao Li
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
- School of Resources and Chemical Engineering, Sanming University, Sanming, China
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Enjiong Huang
- Technology Center of Fuzhou Customs, Fuzhou, Fujian, China
| | - Yifan Wu
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Changqiang Zhu
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Wenhao Li
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Lele Ai
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Qinghua Xie
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhi Tian
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Weiwen Zhong
- Center for Disease Control and Prevention, Longquan, Zhejiang, China
| | - Gang Sun
- School of Resources and Chemical Engineering, Sanming University, Sanming, China
| | - Lingling Zhang
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weilong Tan
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
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3
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Koppes EA, Johnson MA, Moresco JJ, Luppi P, Lewis DW, Stolz DB, Diedrich JK, Yates JR, Wek RC, Watkins SC, Gollin SM, Park HJ, Drain P, Nicholls RD. Insulin secretion deficits in a Prader-Willi syndrome β-cell model are associated with a concerted downregulation of multiple endoplasmic reticulum chaperones. PLoS Genet 2023; 19:e1010710. [PMID: 37068109 PMCID: PMC10138222 DOI: 10.1371/journal.pgen.1010710] [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: 06/18/2022] [Revised: 04/27/2023] [Accepted: 03/21/2023] [Indexed: 04/18/2023] Open
Abstract
Prader-Willi syndrome (PWS) is a multisystem disorder with neurobehavioral, metabolic, and hormonal phenotypes, caused by loss of expression of a paternally-expressed imprinted gene cluster. Prior evidence from a PWS mouse model identified abnormal pancreatic islet development with retention of aged insulin and deficient insulin secretion. To determine the collective roles of PWS genes in β-cell biology, we used genome-editing to generate isogenic, clonal INS-1 insulinoma lines having 3.16 Mb deletions of the silent, maternal- (control) and active, paternal-allele (PWS). PWS β-cells demonstrated a significant cell autonomous reduction in basal and glucose-stimulated insulin secretion. Further, proteomic analyses revealed reduced levels of cellular and secreted hormones, including all insulin peptides and amylin, concomitant with reduction of at least ten endoplasmic reticulum (ER) chaperones, including GRP78 and GRP94. Critically, differentially expressed genes identified by whole transcriptome studies included reductions in levels of mRNAs encoding these secreted peptides and the group of ER chaperones. In contrast to the dosage compensation previously seen for ER chaperones in Grp78 or Grp94 gene knockouts or knockdown, compensation is precluded by the stress-independent deficiency of ER chaperones in PWS β-cells. Consistent with reduced ER chaperones levels, PWS INS-1 β-cells are more sensitive to ER stress, leading to earlier activation of all three arms of the unfolded protein response. Combined, the findings suggest that a chronic shortage of ER chaperones in PWS β-cells leads to a deficiency of protein folding and/or delay in ER transit of insulin and other cargo. In summary, our results illuminate the pathophysiological basis of pancreatic β-cell hormone deficits in PWS, with evolutionary implications for the multigenic PWS-domain, and indicate that PWS-imprinted genes coordinate concerted regulation of ER chaperone biosynthesis and β-cell secretory pathway function.
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Affiliation(s)
- Erik A Koppes
- Division of Genetic and Genomic Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Marie A Johnson
- Division of Genetic and Genomic Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - James J Moresco
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Patrizia Luppi
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Dale W Lewis
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Donna B Stolz
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Jolene K Diedrich
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - John R Yates
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ronald C Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Simon C Watkins
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Susanne M Gollin
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Hyun Jung Park
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Peter Drain
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Robert D Nicholls
- Division of Genetic and Genomic Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history. Nat Commun 2022; 13:2399. [PMID: 35504912 PMCID: PMC9064997 DOI: 10.1038/s41467-022-30009-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 03/18/2022] [Indexed: 11/29/2022] Open
Abstract
The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we first generate a de novo genome assembly of the black rat. We then sequence 67 ancient and three modern black rat mitogenomes, and 36 ancient and three modern nuclear genomes from archaeological sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of our newly reported sequences, together with published mitochondrial DNA sequences, confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling. ‘Archaeogenetic analysis of black rat remains reveals that this species was introduced into temperate Europe twice, in the Roman and medieval periods. This population turnover was likely associated with multiple historical and environmental factors.’
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Liu S, Li F, Zhou J, Lv J, Tan Z, Zhang Y, Ge X. The phylogeny of the Anderson's White‐bellied Rat (
Niviventer andersoni
) based on complete mitochondrial genomes. Ecol Evol 2022; 12:e8663. [PMID: 35261750 PMCID: PMC8890005 DOI: 10.1002/ece3.8663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 01/29/2022] [Accepted: 02/04/2022] [Indexed: 11/07/2022] Open
Affiliation(s)
- Shu‐Jing Liu
- College of BiologyHunan Provincial Key Laboratory of Medical VirologyHunan UniversityChangshaChina
| | - Fu‐Li Li
- Institute of Preventive MedicineSchool of Public HealthDali UniversityDaliChina
| | - Ji‐Hua Zhou
- Yunnan Provincial Key Laboratory for Zoonosis Control and PreventionYunnan Institute of Endemic Diseases Control and PreventionDaliChina
| | - Ji‐Zhou Lv
- Institute of Animal QuarantineChinese Academy of Inspection and QuarantineBeijingChina
| | - Zhong‐Yang Tan
- College of BiologyHunan Provincial Key Laboratory of Medical VirologyHunan UniversityChangshaChina
| | - Yun‐Zhi Zhang
- Institute of Preventive MedicineSchool of Public HealthDali UniversityDaliChina
| | - Xing‐Yi Ge
- College of BiologyHunan Provincial Key Laboratory of Medical VirologyHunan UniversityChangshaChina
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Probing the genomic limits of de-extinction in the Christmas Island rat. Curr Biol 2022; 32:1650-1656.e3. [PMID: 35271794 PMCID: PMC9044923 DOI: 10.1016/j.cub.2022.02.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/24/2022] [Accepted: 02/07/2022] [Indexed: 12/17/2022]
Abstract
Three principal methods are under discussion as possible pathways to “true” de-extinction; i.e., back-breeding, cloning, and genetic engineering.1,2 Of these, while the latter approach is most likely to apply to the largest number of extinct species, its potential is constrained by the degree to which the extinct species genome can be reconstructed. We explore this question using the extinct Christmas Island rat (Rattus macleari) as a model, an endemic rat species that was driven extinct between 1898 and 1908.3, 4, 5 We first re-sequenced its genome to an average of >60× coverage, then mapped it to the reference genomes of different Rattus species. We then explored how evolutionary divergence from the extant reference genome affected the fraction of the Christmas Island rat genome that could be recovered. Our analyses show that even when the extremely high-quality Norway brown rat (R. norvegicus) is used as a reference, nearly 5% of the genome sequence is unrecoverable, with 1,661 genes recovered at lower than 90% completeness, and 26 completely absent. Furthermore, we find the distribution of regions affected is not random, but for example, if 90% completeness is used as the cutoff, genes related to immune response and olfaction are excessively affected. Ultimately, our approach demonstrates the importance of applying similar analyses to candidates for de-extinction through genome editing in order to provide critical baseline information about how representative the edited form would be of the extinct species. Evolutionary divergence limits the completeness of extinct species genomes The extinct Christmas Island rat was re-sequenced to ca. 60× coverage Nevertheless, 4.85% of the Norway brown rat genome remains absent after mapping Absences are not random; immune response and olfaction are excessively affected
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7
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Zhu L, Qing-Qing W, Xue-Ting J, Wen-Jing J, Xin-Xu Z, Qian-Qian Y, Jun-Sheng Z, Zhong-Wan P. Sequencing and analysis of the complete mitochondrial genome of the lesser bandicoot rat ( Bandicota bengalensis) from China and its phylogenetic analysis. Mitochondrial DNA B Resour 2021; 6:2063-2065. [PMID: 34212099 PMCID: PMC8218843 DOI: 10.1080/23802359.2021.1942273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
The complete mitogenome sequence of the lesser bandicoot rat (Bandicota bengalensis Gray and Hardwicke, 1833) was determined using long PCR. The genome was 16,327 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 origin of L strand replication and 1 control region. The overall base composition of the heavy strand is A (34.2%), C (24.9%), T (28.5%) and G (12.4%). The base compositions present clearly the A-T skew, which is most obviously in the control region and protein-coding genes. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees. This study verifies the evolutionary status of Bandicota bengalensis in Muridae at the molecular level. The mitochondrial genome would be a significant supplement for the Bandicota bengalensis genetic background. The two Bandicota species formed a monophyletic group with the high bootstrap value (100%) in all examinations.
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Affiliation(s)
- Liu Zhu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Wang Qing-Qing
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Jiang Xue-Ting
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Jiang Wen-Jing
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Zhao Xin-Xu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Yao Qian-Qian
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Zhang Jun-Sheng
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Piao Zhong-Wan
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
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8
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Cai H, Wang QQ, Zhao XX, Yao QQ, Wu N, Zhang JS, Liu Z. Sequencing and analysis of the complete mitochondrial genome of Micromys erythrotis from China and its phylogenetic analysis. Mitochondrial DNA B Resour 2021; 6:1617-1620. [PMID: 34027072 PMCID: PMC8118456 DOI: 10.1080/23802359.2021.1926353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 05/02/2021] [Indexed: 11/04/2022] Open
Abstract
The complete mitogenome sequence of Micromys erythrotis was determined using long PCR. The genome was 16,238 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 origin of L strand replication and 1 control region. The overall base composition of the heavy strand is A (33.7%), C (24.8%), T (29.1%) and G (12.4%). The base compositions present clearly the A-T skew, which is most obviously in the control region and protein-coding genes. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees. This study verifies the evolutionary status of Micromys erythrotis in Muridae at the molecular level. The mitochondrial genome would be a significant supplement for the Micromys erythrotis genetic background.
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Affiliation(s)
- He Cai
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Qing-Qing Wang
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Xin-Xu Zhao
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Qian-Qian Yao
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Ning Wu
- Ningan Jiangnan School, Ningan, P.R. China
| | - Jun-Sheng Zhang
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Zhu Liu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
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9
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Camacho-Sanchez M, Leonard JA. Mitogenomes Reveal Multiple Colonization of Mountains by Rattus in Sundaland. J Hered 2021; 111:392-404. [PMID: 32485737 PMCID: PMC7423070 DOI: 10.1093/jhered/esaa014] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 05/25/2020] [Indexed: 01/16/2023] Open
Abstract
Tropical mountains are cradles of biodiversity and endemism. Sundaland, tropical Southeast Asia, hosts 3 species of Rattus endemic to elevations above 2000 m with an apparent convergence in external morphology: Rattus korinchi and R. hoogerwerfi from Sumatra, and R. baluensis from Borneo. A fourth one, R. tiomanicus, is restricted to lowland elevations across the whole region. The origins of these endemics are little known due to the absence of a robust phylogenetic framework. We use complete mitochondrial genomes from the 3 high altitude Rattus, and several related species to determine their relationships, date divergences, reconstruct their history of colonization, and test for selection on the mitochondrial DNA. We show that mountain colonization happened independently in Borneo (<390 Kya) and Sumatra (~1.38 Mya), likely from lowland lineages. The origin of the Bornean endemic R. baluensis is very recent and its genetic diversity is nested within the diversity of R. tiomanicus. We found weak evidence of positive selection in the high-elevation lineages and attributed the greater nonsynonymous mutations on these branches (specially R. baluensis) to lesser purifying selection having acted on the terminal branches in the phylogeny.
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Affiliation(s)
- Miguel Camacho-Sanchez
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
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10
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Liu Y, Yao L, Ci Y, Cao X, Zhao M, Li Y, Zhang X. Genetic differentiation of geographic populations of Rattus tanezumi based on the mitochondrial Cytb gene. PLoS One 2021; 16:e0248102. [PMID: 33735257 PMCID: PMC7971478 DOI: 10.1371/journal.pone.0248102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 02/21/2021] [Indexed: 11/18/2022] Open
Abstract
Rattus tanezumi is a common domestic rat and host of the bubonic plague pathogen in China and Southeast Asia (SEA). The origin, genetic differentiation and dispersal of R. tanezumi have received increasing attention from researchers. The population genetics of R. tanezumi based on its mitochondrial cytochrome b gene have been studied to explain the origin, relationships and dispersal of populations. In this study, we captured a total of 229 rats; morphological and molecular biological identification cytochrome oxidase subunit I (COI) confirmed 131 R. tanezumi individuals collected from 6 provincial areas, and their Cytb gene sequences were analyzed. The results showed that the population in Mohan (MH), Yunnan, had the highest genetic diversity, while that in Ningde (ND), Fujian, had the lowest. Tajima’s D statistic for all populations was negative and nonsignificant, indicating the possible expansion of R. tanezumi populations. Low gene flow occurred between the Zhangmu (ZM) R. tanezumi population and other populations, and the genetic differentiation among them was high. Furthermore, our analyses revealed the ZM lineage was the oldest lineage among the groups and diverged ~1.06 Mya, followed by the Luoyang (LY) lineages (~0.51 Mya) and Yunnan lineage (~0.33 Mya). In southeastern Yunnan, the Jinshuihe (JSH) and MH populations were more closely related to the populations in southeastern China (Fuzhou (FZ), ND, Quanzhou (QZ), Nanchang (NC)) and inland areas (Chongqing (CQ), LY) than to those in other areas of Yunnan (Jiegao (JG) and Qingshuihe (QSH)), indicating that R. tanezumi may have spread from southeastern Yunnan to the interior of China. In summary, R. tanezumi may have originated in ZM and adjacent areas, spread to Yunnan, and then spread from the southeast of Yunnan inland or directly eastward from ZM to inland China.
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Affiliation(s)
- Yingying Liu
- Institute of Health Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Lisi Yao
- Institute of Health Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Ying Ci
- Institute of Health Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Xiaomei Cao
- Institute of Health Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Minghui Zhao
- Jiangxi International Travel Health Care Center, Nanchang, Jiangxi, China
| | - Ying Li
- Institute of Health Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - XiaoLong Zhang
- Institute of Health Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
- * E-mail:
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11
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Charbonnel N, Galan M, Tatard C, Loiseau A, Diagne C, Dalecky A, Parrinello H, Rialle S, Severac D, Brouat C. Differential immune gene expression associated with contemporary range expansion in two invasive rodents in Senegal. Sci Rep 2020; 10:18257. [PMID: 33106535 PMCID: PMC7589499 DOI: 10.1038/s41598-020-75060-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 06/28/2020] [Indexed: 01/09/2023] Open
Abstract
Biological invasions are major anthropogenic changes associated with threats to biodiversity and health. However, what determines the successful establishment and spread of introduced populations remains unclear. Here, we explore several hypotheses linking invasion success and immune phenotype traits, including those based on the evolution of increased competitive ability concept. We compared gene expression profiles between anciently and recently established populations of two major invading species, the house mouse Mus musculus domesticus and the black rat Rattus rattus, in Senegal (West Africa). Transcriptome analyses identified differential expression between anciently and recently established populations for 364 mouse genes and 83 rat genes. All immune-related genes displaying differential expression along the mouse invasion route were overexpressed at three of the four recently invaded sites studied. Complement activation pathway genes were overrepresented among these genes. By contrast, no particular immunological process was found to be overrepresented among the differentially expressed genes of black rat. Changes in transcriptome profiles were thus observed along invasion routes, but with different specific patterns between the two invasive species. These changes may be driven by increases in infection risks at sites recently invaded by the house mouse, and by stochastic events associated with colonization history for the black rat. These results constitute a first step toward the identification of immune eco-evolutionary processes potentially involved in the invasion success of these two rodent species.
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Affiliation(s)
- Nathalie Charbonnel
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France.
| | - Maxime Galan
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Caroline Tatard
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Anne Loiseau
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Christophe Diagne
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
- Départment de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Fann, Dakar, Senegal
| | | | - Hugues Parrinello
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Stephanie Rialle
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Dany Severac
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Carine Brouat
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
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12
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Ancient DNA of Guinea Pigs (Cavia spp.) Indicates a Probable New Center of Domestication and Pathways of Global Distribution. Sci Rep 2020; 10:8901. [PMID: 32483316 PMCID: PMC7264122 DOI: 10.1038/s41598-020-65784-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/08/2020] [Indexed: 11/08/2022] Open
Abstract
Guinea pigs (Cavia spp.) have a long association with humans. From as early as 10,000 years ago they were a wild food source. Later, domesticated Cavia porcellus were dispersed well beyond their native range through pre-Columbian exchange networks and, more recently, widely across the globe. Here we present 46 complete mitogenomes of archaeological guinea pigs from sites in Peru, Bolivia, Colombia, the Caribbean, Belgium and the United States to elucidate their evolutionary history, origins and paths of dispersal. Our results indicate an independent centre of domestication of Cavia in the eastern Colombian Highlands. We identify a Peruvian origin for the initial introduction of domesticated guinea pigs (Cavia porcellus) beyond South America into the Caribbean. We also demonstrate that Peru was the probable source of the earliest known guinea pigs transported, as part of the exotic pet trade, to both Europe and the southeastern United States. Finally, we identify a modern reintroduction of guinea pigs to Puerto Rico, where local inhabitants use them for food. This research demonstrates that the natural and cultural history of guinea pigs is more complex than previously known and has implications for other studies regarding regional to global-scale studies of mammal domestication, translocation, and distribution.
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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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Modlinska K, Pisula W. The Norway rat, from an obnoxious pest to a laboratory pet. eLife 2020; 9:50651. [PMID: 31948542 PMCID: PMC6968928 DOI: 10.7554/elife.50651] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 12/11/2019] [Indexed: 12/03/2022] Open
Abstract
The laboratory rat was the first mammal domesticated for research purposes. It is descended from wild Norway rats, Rattus norvegicus, which despite their name likely originated in Asia. Exceptionally adaptable, these rodents now inhabit almost all environments on Earth, especially near human settlements where they are often seen as pests. The laboratory rat thrives in captivity, and its domestication has produced many inbred and outbred lines that are used for different purposes, including medical trials and behavioral studies. Differences between wild Norway rats and their laboratory counterparts were first noted in the early 20th century and led some researchers to later question its value as a model organism. While these views are probably unjustified, the advanced domestication of the laboratory rat does suggest that resuming studies of wild rats could benefit the wider research community.
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Affiliation(s)
- Klaudia Modlinska
- Institute of Psychology, Polish Academy of Sciences, Warszawa, Poland
| | - Wojciech Pisula
- Institute of Psychology, Polish Academy of Sciences, Warszawa, Poland
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Gatto-Almeida F, Pichlmueller F, Micheletti T, Abrahão CR, Mangini PR, Russell JC. Using genetics to plan black rat (Rattus rattus) management in Fernando de Noronha archipelago, Brazil. Perspect Ecol Conserv 2020. [DOI: 10.1016/j.pecon.2020.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Hulme-Beaman A, Cucchi T, Evin A, Searle JB, Dobney K. Exploring Rattus praetor (Rodentia, Muridae) as a possible species complex using geometric morphometrics on dental morphology. Mamm Biol 2018; 92:62-67. [PMID: 30177868 PMCID: PMC6067089 DOI: 10.1016/j.mambio.2018.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Taxonomic uncertainties in the Rattus genus persist due to among-species morphological conservatism coupled with within-species environmental variation in morphology. As a result, this genus contains a number of possible cryptic species. One important example can be found in R. praetor, where morphological studies indicate it is a possible species complex. Genetic studies of R. praetor (limited to analysis of mitochondrial DNA) have been inconclusive, but do indicate such subdivision. Here we use geometric morphometrics to explore this possible species complex by analysing the dental traits of 48 specimens from New Guinea and neighbouring regions. We find separate molar morphologies for Bougainsville Island, central New Guinea and west New Guinea which cannot be easily explained by different environmental factors (climate, precipitation and altitude), strongly suggesting the existence of a number of evolutionarily distinct taxa within what is currently called R. praetor thus supporting previous suggestions that R. praetor is a species complex. Our findings demonstrate the potential of advanced morphological analyses in identifying separate species, contrary to the claims of morphological conservatism. Future analyses should combine geometric morphometrics with genetic analyses over the species range and include sub-fossil specimens from the Bismarck archipelago and Solomon Islands to resolve the evolutionary history of R. praetor.
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Affiliation(s)
- Ardern Hulme-Beaman
- Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK.,Research Centre in Evolutionary Anthropology and Palaeoecology, School of Natural Sciences and Psychology, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Thomas Cucchi
- CNRS-Muséum National d'Histoire Naturelle, UMR 7209, Archéozoologie, Archéobotanique Sociétés, Pratiques et Environnement, 55 Rue Buffon, 75005 Paris, France
| | - Allowen Evin
- Institut des Sciences de l'Evolution, Université de Montpellier, UMR CNRS, UM, EPHE, IRD 2 Place Eugène Bataillon, CC065, 34095 Montpellier, Cedex 5, France
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY 14853-2701, USA
| | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK.,Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
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Puckett EE, Micci‐Smith O, Munshi‐South J. Genomic analyses identify multiple Asian origins and deeply diverged mitochondrial clades in inbred brown rats ( Rattus norvegicus). Evol Appl 2018; 11:718-726. [PMID: 29875813 PMCID: PMC5979757 DOI: 10.1111/eva.12572] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/27/2017] [Indexed: 01/05/2023] Open
Abstract
Over 500 strains of inbred brown rats (Rattus norvegicus) have been developed for use as a biomedical model organism. Most of these inbred lines were derived from the colony established at the Wistar Institute in 1906 or its descendants following worldwide distribution to research and breeding centers. The geographic source of the animals that founded the Wistar colony has been lost to history; thus, we compared 25 inbred rat strains to 326 wild rats from a global diversity dataset at 32 k SNPs, and 47 mitochondrial genomes to identify the source populations. We analyzed nuclear genomic data using principal component analyses and co-ancestry heat maps, and mitogenomes using phylogenetic trees and networks. In the nuclear genome, inbred rats clustered together indicating a single geographic origin for the strains studied and showed admixed ancestral variation with wild rats in eastern Asia and western North America. The Sprague Dawley derived, Wistar derived, and Brown Norway strains each had mitogenomes from different clades which diverged between 13 and 139 kya. Thus, we posit that rats originally collected for captive breeding had high mitochondrial diversity that became fixed through genetic drift and/or artificial selection. Our results show that these important medical models share common genomic ancestry from a few source populations, and opportunities exist to create new strains with diverse genomic backgrounds to provide novel insight into the genomic basis of disease phenotypes.
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Affiliation(s)
- Emily E. Puckett
- Louis Calder Center – Biological Field StationFordham UniversityArmonkNYUSA
| | - Olivia Micci‐Smith
- Louis Calder Center – Biological Field StationFordham UniversityArmonkNYUSA
| | - Jason Munshi‐South
- Louis Calder Center – Biological Field StationFordham UniversityArmonkNYUSA
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Prendergast ME, Buckley M, Crowther A, Frantz L, Eager H, Lebrasseur O, Hutterer R, Hulme-Beaman A, Van Neer W, Douka K, Veall MA, Quintana Morales EM, Schuenemann VJ, Reiter E, Allen R, Dimopoulos EA, Helm RM, Shipton C, Mwebi O, Denys C, Horton M, Wynne-Jones S, Fleisher J, Radimilahy C, Wright H, Searle JB, Krause J, Larson G, Boivin NL. Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets. PLoS One 2017; 12:e0182565. [PMID: 28817590 PMCID: PMC5560628 DOI: 10.1371/journal.pone.0182565] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/20/2017] [Indexed: 02/02/2023] Open
Abstract
Human-mediated biological exchange has had global social and ecological impacts. In sub-Saharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first millennium CE, while another posits introduction dating back to 3000 BCE. These distinct scenarios have implications for understanding the emergence of long-distance maritime connectivity, and the ecological and economic impacts of introduced species. Resolution of this longstanding debate requires new efforts, given the lack of well-dated fauna from high-precision excavations, and ambiguous osteomorphological identifications. We analysed faunal remains from 22 eastern African sites spanning a wide geographic and chronological range, and applied biomolecular techniques to confirm identifications of two Asian taxa: domestic chicken (Gallus gallus) and black rat (Rattus rattus). Our approach included ancient DNA (aDNA) analysis aided by BLAST-based bioinformatics, Zooarchaeology by Mass Spectrometry (ZooMS) collagen fingerprinting, and direct AMS (accelerator mass spectrometry) radiocarbon dating. Our results support a late, mid-first millennium CE introduction of these species. We discuss the implications of our findings for models of biological exchange, and emphasize the applicability of our approach to tropical areas with poor bone preservation.
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Affiliation(s)
- Mary E. Prendergast
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA, United States of America
- * E-mail:
| | - Michael Buckley
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Alison Crowther
- School of Social Science, The University of Queensland, Brisbane Queensland, Australia
| | - Laurent Frantz
- Palaeogenomics & Bio-Archaeology Research Network, Oxford University, Oxford, United Kingdom
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, United Kingdom
| | - Heidi Eager
- Dept. Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States of America
- Research Laboratory for Archaeology and the History of Art, Oxford University, Oxford, United Kingdom
| | - Ophélie Lebrasseur
- Palaeogenomics & Bio-Archaeology Research Network, Oxford University, Oxford, United Kingdom
| | - Rainer Hutterer
- Dept. Vertebrates, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | | | - Wim Van Neer
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Dept. Biology, University of Leuven, Leuven, Belgium
| | - Katerina Douka
- Research Laboratory for Archaeology and the History of Art, Oxford University, Oxford, United Kingdom
| | - Margaret-Ashley Veall
- Research Laboratory for Archaeology and the History of Art, Oxford University, Oxford, United Kingdom
| | | | | | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Richard Allen
- Palaeogenomics & Bio-Archaeology Research Network, Oxford University, Oxford, United Kingdom
- Research Laboratory for Archaeology and the History of Art, Oxford University, Oxford, United Kingdom
| | - Evangelos A. Dimopoulos
- Palaeogenomics & Bio-Archaeology Research Network, Oxford University, Oxford, United Kingdom
| | | | - Ceri Shipton
- McDonald Institute for Archaeological Research, Cambridge, United Kingdom
- British Institute in Eastern Africa, Nairobi, Kenya
| | - Ogeto Mwebi
- Dept. Zoology, Osteology Section, National Museums of Kenya, Nairobi, Kenya
| | - Christiane Denys
- Dept. Systématique & Evolution, Muséum National d’Histoire Naturelle, Paris, France
| | - Mark Horton
- Dept. Archaeology and Anthropology, University of Bristol, Bristol, United Kingdom
| | | | - Jeffrey Fleisher
- Dept. Anthropology, Rice University, Houston, United States of America
| | - Chantal Radimilahy
- Musée d’Art et d’Archéologie, Université d’Antananarivo, Antananarivo, Madagascar
| | - Henry Wright
- Museum of Anthropology, University of Michigan, Ann Arbor, United States of America
- Santa Fe Institute, Santa Fe NM, United States of America
| | - Jeremy B. Searle
- Dept. Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States of America
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Greger Larson
- Palaeogenomics & Bio-Archaeology Research Network, Oxford University, Oxford, United Kingdom
| | - Nicole L. Boivin
- Max Planck Institute for the Science of Human History, Jena, Germany
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Camacho-Sanchez M, Leonard JA, Fitriana Y, Tilak MK, Fabre PH. The generic status of Rattus annandalei (Bonhote, 1903) (Rodentia, Murinae) and its evolutionary implications. J Mammal 2017. [DOI: 10.1093/jmammal/gyx081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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20
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West K, Collins C, Kardailsky O, Kahn J, Hunt TL, Burley DV, Matisoo-Smith E. The Pacific Rat Race to Easter Island: Tracking the Prehistoric Dispersal of Rattus exulans Using Ancient Mitochondrial Genomes. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00052] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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21
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Guo HL, Teng HJ, Zhang JH, Zhang JX, Zhang YH. Asian house rats may facilitate their invasive success through suppressing brown rats in chronic interaction. Front Zool 2017; 14:20. [PMID: 28413431 PMCID: PMC5389004 DOI: 10.1186/s12983-017-0202-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 03/02/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The Asian house rat (Rattus tanezumi) and the brown rat (Rattus norvegicus) are closely related species and are partially sympatric in southern China. Over the past 20 years, R. tanezumi has significantly expanded northward in China and partially replaced the native brown rat subspecies, R. n. humiliatus. Although invasive species are often more aggressive than native species, we did not observe interspecific physical aggression between R. tanezumi and R. n. humiliatus. Here, we focused on whether or not R. tanezumi was superior to R. n. humiliatus in terms of nonphysical competition, which is primarily mediated by chemical signals. RESULTS We performed two laboratory experiments to test different paradigms in domesticated R. tanezumi and R. n. humiliatus. In Experiment 1, we caged adult male rats of each species for 2 months in heterospecific or conspecific pairs, partitioned by perforated galvanized iron sheets, allowing exchange of chemical stimuli and ultrasonic vocalization. The sexual attractiveness of male urine odor showed a tendency (marginal significance) to increase in R. tanezumi caged with R. n. humiliatus, compared with those in conspecific pairs. Hippocampal glucocorticoid receptor (GR) and brain-derived nutrition factor (BDNF) mRNA were upregulated in R. n. humiliatus and R. tanezumi, respectively, when the rats were caged in heterospecific pairs. In Experiment 2, we kept juvenile male rats in individual cages in rooms with either the same or the different species for 2 months, allowing chemical interaction. The sexual attractiveness of male urine was significantly enhanced in R. tanezumi, but reduced in R. n. humiliatus by heterospecific cues and mRNA expression of hippocampal GR and BDNF were upregulated by heterospecific cues in R. n. humiliatus and R. tanezumi, respectively. Although not identical, the results from Experiments 1 and 2 were generally consistent. CONCLUSIONS The results of both experiments indicate that nonphysical/chronic interspecific stimuli, particularly scent signals, between R. n. humiliatus and R. tanezumi may negatively affect R. n. humiliatus and positively affect R. tanezumi. We infer that chronic interspecific interactions may have contributed to the invasion of R. tanezumi into the range of R. n. humiliatus in natural habitats.
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Affiliation(s)
- Hong-Ling Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, No.1-5 Beichen West Road, Chaoyang District, Beijing, 100101 China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Hua-Jing Teng
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, No.1-5 Beichen West Road, Chaoyang District, Beijing, 100101 China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jin-Hua Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, No.1-5 Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Jian-Xu Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, No.1-5 Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Yao-Hua Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, No.1-5 Beichen West Road, Chaoyang District, Beijing, 100101 China
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Affiliation(s)
- Douglas J. Richmond
- Section for Evolutionary Genomics Natural History Museum of Denmark University of Copenhagen Øster Voldgade 5–7 1350 Copenhagen Denmark
| | - Mikkel‐Holger S. Sinding
- Section for Evolutionary Genomics Natural History Museum of Denmark University of Copenhagen Øster Voldgade 5–7 1350 Copenhagen Denmark
- Natural History Museum University of Oslo P.O. Box 1172 Blindern NO‐0318 Oslo Norway
| | - M. Thomas P. Gilbert
- Section for Evolutionary Genomics Natural History Museum of Denmark University of Copenhagen Øster Voldgade 5–7 1350 Copenhagen Denmark
- Trace and Environmental DNA Laboratory Department of Environment and Agriculture Curtin University Perth WA 6102 Australia
- NTNU University Museum NO‐7491 Trondheim Norway
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Abstract
Whole-genome sequencing of wild-derived rat species can provide novel genomic resources, which may help decipher the genetics underlying complex phenotypes. As a notorious pest, reservoir of human pathogens, and colonizer, the Asian house rat, Rattus tanezumi, is successfully adapted to its habitat. However, little is known regarding genetic variation in this species. In this study, we identified over 41,000,000 single-nucleotide polymorphisms, plus insertions and deletions, through whole-genome sequencing and bioinformatics analyses. Moreover, we identified over 12,000 structural variants, including 143 chromosomal inversions. Further functional analyses revealed several fixed nonsense mutations associated with infection and immunity-related adaptations, and a number of fixed missense mutations that may be related to anticoagulant resistance. A genome-wide scan for loci under selection identified various genes related to neural activity. Our whole-genome sequencing data provide a genomic resource for future genetic studies of the Asian house rat species and have the potential to facilitate understanding of the molecular adaptations of rats to their ecological niches.
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Morand S, Bordes F, Chen HW, Claude J, Cosson JF, Galan M, Czirják GÁ, Greenwood AD, Latinne A, Michaux J, Ribas A. Global parasite and Rattus rodent invasions: The consequences for rodent-borne diseases. Integr Zool 2016; 10:409-23. [PMID: 26037785 DOI: 10.1111/1749-4877.12143] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We summarize the current knowledge on parasitism-related invasion processes of the globally invasive Rattus lineages, originating from Asia, and how these invasions have impacted the local epidemiology of rodent-borne diseases. Parasites play an important role in the invasion processes and successes of their hosts through multiple biological mechanisms such as "parasite release," "immunocompetence advantage," "biotic resistance" and "novel weapon." Parasites may also greatly increase the impact of invasions by spillover of parasites and other pathogens, introduced with invasive hosts, into new hosts, potentially leading to novel emerging diseases. Another potential impact is the ability of the invader to amplify local parasites by spillback. In both cases, local fauna and humans may be exposed to new health risks, which may decrease biodiversity and potentially cause increases in human morbidity and mortality. Here we review the current knowledge on these processes and propose some research priorities.
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Affiliation(s)
- Serge Morand
- Centre National de la Recherche Scientifique (CNRS)-Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) Animal et Gestion Intégrée des Risques, Centre d'Infectiologie Christophe Mérieux du Laos, Vientiane, Lao PDR.,Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Frédéric Bordes
- Institut des Sciences de l'Evolution, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier-Institut de Recherche pour le Développement (IRD), Montpellier, France
| | - Hsuan-Wien Chen
- Department of Biological Resources, National Chiayi University, Chiayi City, Taiwan, China
| | - Julien Claude
- Institut des Sciences de l'Evolution, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier-Institut de Recherche pour le Développement (IRD), Montpellier, France
| | - Jean-François Cosson
- Institut National de la Recherche Agronomique (INRA), Centre de Biologie et de Gestion des Populations, Baillarguet, France.,Institut National de la Recherche Agronomique (INRA), UMR Biologie et Immunologie Parasitaire Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail ses, Maisons-Alfort, France
| | - Maxime Galan
- Institut National de la Recherche Agronomique (INRA), Centre de Biologie et de Gestion des Populations, Baillarguet, France
| | - Gábor Á Czirják
- Leibniz Institute for Zoo and Wildlife Research, Department of Wildlife Diseases, 10315 Berlin, Germany
| | - Alex D Greenwood
- Leibniz Institute for Zoo and Wildlife Research, Department of Wildlife Diseases, 10315 Berlin, Germany
| | - Alice Latinne
- Institut des Sciences de l'Evolution, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier-Institut de Recherche pour le Développement (IRD), Montpellier, France.,Conservation Genetics Unit, University of Liège 4000 Liège, Belgium
| | - Johan Michaux
- Centre National de la Recherche Scientifique (CNRS)-Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) Animal et Gestion Intégrée des Risques, Centre d'Infectiologie Christophe Mérieux du Laos, Vientiane, Lao PDR.,Conservation Genetics Unit, University of Liège 4000 Liège, Belgium
| | - Alexis Ribas
- Biodiversity Research Group, Faculty of Science, Udon Thani Rajabhat University, Udon Thani, Thailand
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Buckley M, Gu M, Shameer S, Patel S, Chamberlain AT. High-throughput collagen fingerprinting of intact microfaunal remains; a low-cost method for distinguishing between murine rodent bones. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:805-12. [PMID: 27408951 PMCID: PMC4831026 DOI: 10.1002/rcm.7483] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/07/2015] [Accepted: 12/13/2015] [Indexed: 05/19/2023]
Abstract
RATIONALE Microfaunal skeletal remains can be sensitive indicators of the contemporary ecosystem in which they are sampled and are often recovered in owl pellets in large numbers. Species identification of these remains can be obtained using a range of morphological criteria established for particular skeletal elements, but typically dominated by a reliance on cranial characters. However, this can induce biases under different environmental and taphonomic conditions. The aim of this research was to develop a high-throughput method of objectively identifying rodent remains from archaeological deposits using collagen fingerprinting, most notably the identification of rats from other myomorph rodents as a means to identify disturbances in the archaeofauna through the presence of invasive taxa not contemporary with the archaeological deposits. METHODS Collagen was extracted from complete microfaunal skeletal remains in such a manner as to leave the bones morphologically intact (i.e., weaker concentration of acid than previously used over shorter length of time). Acid-soluble collagen was then ultrafiltered into ammonium bicarbonate and digested with trypsin prior to dilution in the MALDI matrix and acquisition of peptide mass fingerprints using a matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectrometer. RESULTS Collagen fingerprinting was able to distinguish between Rattus, Mus, Apodemus and Micromys at the genus level; at the species level, R. rattus and R. norvegicus could be separated whereas A. flavicollis and A. sylvaticus could not. A total of 12,317 archaeological microvertebrate samples were screened for myomorph signatures but none were found to be invasive rats (Rattus) or mice (Mus). Of the contemporary murine fauna, no harvest mice (Micromys) were identified and only 24 field mouse (Apodemus) discovered. CONCLUSIONS As a result, no evidence of recent bioturbation could be inferred from the faunal remains of these archaeological deposits. More importantly this work presents a method for high-throughput screening of specific taxa and is the first application of collagen fingerprinting to microfaunal remains of archaeological specimens.
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Kosoy M, Khlyap L, Cosson JF, Morand S. Aboriginal and invasive rats of genus Rattus as hosts of infectious agents. Vector Borne Zoonotic Dis 2015; 15:3-12. [PMID: 25629775 DOI: 10.1089/vbz.2014.1629] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
From the perspective of ecology of zoonotic pathogens, the role of the Old World rats of the genus Rattus is exceptional. The review analyzes specific characteristics of rats that contribute to their important role in hosting pathogens, such as host-pathogen relations and rates of rat-borne infections, taxonomy, ecology, and essential factors. Specifically the review addresses recent taxonomic revisions within the genus Rattus that resulted from applications of new genetic tools in understanding relationships between the Old World rats and the infectious agents that they carry. Among the numerous species within the genus Rattus, only three species-the Norway rat (R. norvegicus), the black or roof rat (R. rattus), and the Asian black rat (R. tanezumi)-have colonized urban ecosystems globally for a historically long period of time. The fourth invasive species, R. exulans, is limited to tropical Asia-Pacific areas. One of the points highlighted in this review is the necessity to discriminate the roles played by rats as pathogen reservoirs within the land of their original diversification and in regions where only one or few rat species were introduced during the recent human history.
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Affiliation(s)
- Michael Kosoy
- 1 Centers for Disease Control and Prevention , Division of Vector-Borne Diseases, Fort Collins, Colorado
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Dobigny G, Britton-Davidian J, Robinson TJ. Chromosomal polymorphism in mammals: an evolutionary perspective. Biol Rev Camb Philos Soc 2015; 92:1-21. [PMID: 26234165 DOI: 10.1111/brv.12213] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 06/23/2015] [Accepted: 07/09/2015] [Indexed: 12/28/2022]
Abstract
Although chromosome rearrangements (CRs) are central to studies of genome evolution, our understanding of the evolutionary consequences of the early stages of karyotypic differentiation (i.e. polymorphism), especially the non-meiotic impacts, is surprisingly limited. We review the available data on chromosomal polymorphisms in mammals so as to identify taxa that hold promise for developing a more comprehensive understanding of chromosomal change. In doing so, we address several key questions: (i) to what extent are mammalian karyotypes polymorphic, and what types of rearrangements are principally involved? (ii) Are some mammalian lineages more prone to chromosomal polymorphism than others? More specifically, do (karyotypically) polymorphic mammalian species belong to lineages that are also characterized by past, extensive karyotype repatterning? (iii) How long can chromosomal polymorphisms persist in mammals? We discuss the evolutionary implications of these questions and propose several research avenues that may shed light on the role of chromosome change in the diversification of mammalian populations and species.
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Affiliation(s)
- Gauthier Dobigny
- Institut de Recherche pour le Développement, Centre de Biologie pour la Gestion des Populations (UMR IRD-INRA-Cirad-Montpellier SupAgro), Campus International de Baillarguet, CS30016, 34988, Montferrier-sur-Lez, France
| | - Janice Britton-Davidian
- Institut des Sciences de l'Evolution, Université de Montpellier, CNRS, IRD, EPHE, Cc065, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - Terence J Robinson
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7062, South Africa
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Deinum EE, Halligan DL, Ness RW, Zhang YH, Cong L, Zhang JX, Keightley PD. Recent Evolution in Rattus norvegicus Is Shaped by Declining Effective Population Size. Mol Biol Evol 2015; 32:2547-58. [PMID: 26037536 PMCID: PMC4576703 DOI: 10.1093/molbev/msv126] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The brown rat, Rattus norvegicus, is both a notorious pest and a frequently used model in biomedical research. By analyzing genome sequences of 12 wild-caught brown rats from their presumed ancestral range in NE China, along with the sequence of a black rat, Rattus rattus, we investigate the selective and demographic forces shaping variation in the genome. We estimate that the recent effective population size (Ne) of this species = 1.24×105, based on silent site diversity. We compare patterns of diversity in these genomes with patterns in multiple genome sequences of the house mouse (Mus musculus castaneus), which has a much larger Ne. This reveals an important role for variation in the strength of genetic drift in mammalian genome evolution. By a Pairwise Sequentially Markovian Coalescent analysis of demographic history, we infer that there has been a recent population size bottleneck in wild rats, which we date to approximately 20,000 years ago. Consistent with this, wild rat populations have experienced an increased flux of mildly deleterious mutations, which segregate at higher frequencies in protein-coding genes and conserved noncoding elements. This leads to negative estimates of the rate of adaptive evolution (α) in proteins and conserved noncoding elements, a result which we discuss in relation to the strongly positive estimates observed in wild house mice. As a consequence of the population bottleneck, wild rats also show a markedly slower decay of linkage disequilibrium with physical distance than wild house mice.
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Affiliation(s)
- Eva E Deinum
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Daniel L Halligan
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Rob W Ness
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Yao-Hua Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lin Cong
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jian-Xu Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Peter D Keightley
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
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Commensalism facilitates gene flow in mountains: a comparison between two Rattus species. Heredity (Edinb) 2015; 115:253-61. [PMID: 25944468 DOI: 10.1038/hdy.2015.34] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Revised: 03/19/2015] [Accepted: 03/20/2015] [Indexed: 01/23/2023] Open
Abstract
Small mammal dispersal is strongly affected by geographical barriers. However, commensal small mammals may be passively transported over large distances and strong barriers by humans (often with agricultural products). This pattern should be especially apparent in topographically complex landscapes, such as mountain ranges, where valleys and/or peaks can limit dispersal of less vagile species. We predict that commensal species would have lower genetic differentiation and higher migration rates than related non-commensals in such landscapes. We contrasted population genetic differentiation in two sympatric Rattus species (R. satarae and R. rattus) in the Western Ghats mountains in southern India. We sampled rats from villages and adjacent forests in seven locations (20-640 km apart). Capture-based statistics confirmed that R. rattus is abundant in human settlements in this region, whereas R. satarae is non-commensal and found mostly in forests. Population structure analyses using ~970-bp mitochondrial control region and 17 microsatellite loci revealed higher differentiation for the non-commensal species (R. satarae F-statistics=0.420, 0.065, R. rattus F-statistics=0.195, 0.034; mitochondrial DNA, microsatellites, respectively). Genetic clustering analyses confirm that clusters in R. satarae are more distinct and less admixed than those in R. rattus. R. satarae shows higher slope for isolation-by-distance compared with R. rattus. Although mode of migration estimates do not strongly suggest higher rates in R. rattus than in R. satarae, they indicate that migration over long distances could still be higher in R. rattus. We suggest that association with humans could drive the observed pattern of differentiation in the commensal R. rattus, consequently impacting not only their dispersal abilities, but also their evolutionary trajectories.
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Mitochondrial phylogeography of the black rat supports a single invasion of the western Mediterranean basin. Biol Invasions 2015. [DOI: 10.1007/s10530-015-0842-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Blasdell K, Bordes F, Chaisiri K, Chaval Y, Claude J, Cosson JF, Latinne A, Michaux J, Morand S, Pagès M, Tran A. Progress on research on rodents and rodent-borne zoonoses in South-east Asia. WILDLIFE RESEARCH 2015. [DOI: 10.1071/wr14201] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This review aims to synthesise knowledge regarding the taxonomy of South-east Asian murine rodents and the challenges associated with the identification of habitat preferences and associated rodent-borne diseases. Recent studies concerning the Rattini tribe have identified unclear species boundaries that would benefit from further investigation. The development of barcoding may allow more accurate identification of rodents, specifically for complex species. However, knowledge on the distribution and habitat specialisations of many common murine rodents is still scarce, particularly regarding the specific habitat preferences of most synanthropic rodent species (Rattus tanezumi or Rattus exulans). Several studies have analysed the prevalence of major rodent-borne diseases in South-east Asia and it appears that the greatest risk of rodent zoonoses are in the lowland rain-fed and irrigated landscapes, generally in and around rice fields.
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Wells K, O'Hara RB, Morand S, Lessard JP, Ribas A. The importance of parasite geography and spillover effects for global patterns of host-parasite associations in two invasive species. DIVERS DISTRIB 2014. [DOI: 10.1111/ddi.12297] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Konstans Wells
- The Environment Institute; School of Earth and Environmental Sciences; The University of Adelaide; Adelaide SA Australia
| | - Robert B. O'Hara
- Biodiversity and Climate Research Centre (BiK-F); Frankfurt Germany
| | - Serge Morand
- Centre d'Infectiologie Christophe Mérieux du Laos; CIRAD AGIRs, CNRS ISEM; Vientiane Lao People's Democratic Republic
| | - Jean-Philippe Lessard
- Québec Centre for Biodiversity Science; McGill University; Montréal QC Canada
- Department of Biology; Concordia University; Montréal QC Canada
| | - Alexis Ribas
- Biodiversity Research Group; Faculty of Science; Udon Thani Rajabhat University; Udon Thani Thailand
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Song Y, Lan Z, Kohn MH. Mitochondrial DNA phylogeography of the Norway rat. PLoS One 2014; 9:e88425. [PMID: 24586325 PMCID: PMC3938417 DOI: 10.1371/journal.pone.0088425] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 01/08/2014] [Indexed: 11/18/2022] Open
Abstract
Central Eastern Asia, foremost the area bordering northern China and Mongolia, has been thought to be the geographic region where Norway rats (Rattus norvegicus) have originated. However recent fossil analyses pointed to their origin in southern China. Moreover, whereas analyses of fossils dated the species' origin as ∼1.2–1.6 million years ago (Mya), molecular analyses yielded ∼0.5–2.9 Mya. Here, to study the geographic origin of the Norway rat and its spread across the globe we analyzed new and all published mitochondrial DNA cytochrome-b (cyt-b; N = 156) and D-loop (N = 212) sequences representing wild rats from four continents and select inbred strains. Our results are consistent with an origin of the Norway rat in southern China ∼1.3 Mya, subsequent prehistoric differentiation and spread in China and Asia from an initially weakly structured ancestral population, followed by further spread and differentiation across the globe during historic times. The recent spreading occurred mostly from derived European populations rather than from archaic Asian populations. We trace laboratory strains to wild lineages from Europe and North America and these represent a subset of the diversity of the rat; leaving Asian lineages largely untapped as a resource for biomedical models. By studying rats from Europe we made the observation that mtDNA diversity cannot be interpreted without consideration of pest control and, possibly, the evolution of rodenticide resistance. However, demographic models explored by forward-time simulations cannot fully explain the low mtDNA diversity of European rats and lack of haplotype sharing with their source from Asia. Comprehensive nuclear marker analyses of a larger sample of Norway rats representing the world are needed to better resolve the evolutionary history of wild rats and of laboratory rats, as well as to better understand the evolution of anticoagulant resistance.
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Affiliation(s)
- Ying Song
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas, United States of America,
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Weed and Rodent Biology and Management, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhenjiang Lan
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas, United States of America,
| | - Michael H. Kohn
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas, United States of America,
- * E-mail:
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Yasuda SP, Gamage CD, Koizumi N, Nishio S, Isozumi R, Shimizu K, Koma T, Amada T, Suzuki H, Yoshimatsu K, Arikawa J. Distinct genetic characteristics of Sri Lankan Rattus and Bandicota (Murinae, Rodentia) inferred from mitochondrial and nuclear markers. Genes Genet Syst 2014; 89:71-80. [DOI: 10.1266/ggs.89.71] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Shumpei P. Yasuda
- Department of Microbiology, Hokkaido University Graduate School of Medicine
| | - Chandika D. Gamage
- Department of Microbiology, Hokkaido University Graduate School of Medicine
| | - Nobuo Koizumi
- Department of Bacteriology, National Institute of Infectious Diseases
| | - Sanae Nishio
- Department of Microbiology, Hokkaido University Graduate School of Medicine
| | - Rie Isozumi
- Department of Microbiology, Hokkaido University Graduate School of Medicine
| | - Kenta Shimizu
- Department of Microbiology, Hokkaido University Graduate School of Medicine
| | - Takaaki Koma
- Department of Microbiology, Hokkaido University Graduate School of Medicine
| | - Takako Amada
- Department of Microbiology, Hokkaido University Graduate School of Medicine
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Earth Science, Hokkaido University
| | - Kumiko Yoshimatsu
- Department of Microbiology, Hokkaido University Graduate School of Medicine
| | - Jiro Arikawa
- Department of Microbiology, Hokkaido University Graduate School of Medicine
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Fabre PH, Jønsson KA, Douzery EJP. Jumping and gliding rodents: mitogenomic affinities of Pedetidae and Anomaluridae deduced from an RNA-Seq approach. Gene 2013; 531:388-97. [PMID: 23973722 DOI: 10.1016/j.gene.2013.07.059] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/10/2013] [Accepted: 07/16/2013] [Indexed: 10/26/2022]
Abstract
An RNA-Seq strategy was used to obtain the complete set of protein-coding mitochondrial genes from two rodent taxa. Thanks to the next generation sequencing (NGS) 454 approach, we determined the complete mitochondrial DNA genome from Graphiurus kelleni (Mammalia: Rodentia: Gliridae) and partial mitogenome from Pedetes capensis (Pedetidae), and compared them with published rodent and outgroup mitogenomes. We finished the mitogenome sequencing by a series of amplicons using conserved PCR primers to fill the gaps corresponding to tRNA, rRNA and control regions. Phylogenetic analyses of the mitogenomes suggest a well-supported rodent phylogeny in agreement with nuclear gene trees. Pedetes groups with Anomalurus into the clade Anomaluromorpha, while Graphiurus branches within the squirrel-related clade. Moreover, Pedetes+Anomalurus branch with Castor into the mouse-related clade. Our study demonstrates the utility of NGS for obtaining new mitochondrial genomes as well as the importance of choosing adequate models of sequence evolution to infer the phylogeny of rodents.
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Affiliation(s)
- Pierre-Henri Fabre
- Institut des Sciences de l'Evolution (ISEM, UMR 5554 UM2-CNRS-IRD), Université Montpellier II, Place Eugène Bataillon - CC 064 - 34095 Montpellier Cedex 5, France; Center for Macroecology Evolution and Climate at the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken, 15, DK-2100 Copenhagen Ø, Denmark
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Tollenaere C, Jacquet S, Ivanova S, Loiseau A, Duplantier JM, Streiff R, Brouat C. Beyond an AFLP genome scan towards the identification of immune genes involved in plague resistance inRattus rattusfrom Madagascar. Mol Ecol 2012; 22:354-67. [DOI: 10.1111/mec.12115] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 09/20/2012] [Accepted: 10/02/2012] [Indexed: 12/26/2022]
Affiliation(s)
- C. Tollenaere
- IRD UMR CBGP (INRA / IRD / Cirad / Montpellier SupAgro); Campus International Baillarguet; CS 30016 34988 Montferrier sur Lez cedex France
| | - S. Jacquet
- IRD UMR CBGP (INRA / IRD / Cirad / Montpellier SupAgro); Campus International Baillarguet; CS 30016 34988 Montferrier sur Lez cedex France
| | - S. Ivanova
- IRD UMR CBGP (INRA / IRD / Cirad / Montpellier SupAgro); Campus International Baillarguet; CS 30016 34988 Montferrier sur Lez cedex France
| | - A. Loiseau
- INRA UMR CBGP (INRA / IRD / Cirad / Montpellier SupAgro); Campus International Baillarguet; CS 30016 34988 Montferrier sur Lez cedex France
| | - J.-M. Duplantier
- IRD UMR CBGP (INRA / IRD / Cirad / Montpellier SupAgro); Campus International Baillarguet; CS 30016 34988 Montferrier sur Lez cedex France
| | - R. Streiff
- INRA UMR CBGP (INRA / IRD / Cirad / Montpellier SupAgro); Campus International Baillarguet; CS 30016 34988 Montferrier sur Lez cedex France
| | - C. Brouat
- IRD UMR CBGP (INRA / IRD / Cirad / Montpellier SupAgro); Campus International Baillarguet; CS 30016 34988 Montferrier sur Lez cedex France
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Galan M, Pagès M, Cosson JF. Next-generation sequencing for rodent barcoding: species identification from fresh, degraded and environmental samples. PLoS One 2012; 7:e48374. [PMID: 23144869 PMCID: PMC3492341 DOI: 10.1371/journal.pone.0048374] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 09/25/2012] [Indexed: 11/18/2022] Open
Abstract
Rodentia is the most diverse order among mammals, with more than 2,000 species currently described. Most of the time, species assignation is so difficult based on morphological data solely that identifying rodents at the specific level corresponds to a real challenge. In this study, we compared the applicability of 100 bp mini-barcodes from cytochrome b and cytochrome c oxidase 1 genes to enable rodent species identification. Based on GenBank sequence datasets of 115 rodent species, a 136 bp fragment of cytochrome b was selected as the most discriminatory mini-barcode, and rodent universal primers surrounding this fragment were designed. The efficacy of this new molecular tool was assessed on 946 samples including rodent tissues, feces, museum samples and feces/pellets from predators known to ingest rodents. Utilizing next-generation sequencing technologies able to sequence mixes of DNA, 1,140 amplicons were tagged, multiplexed and sequenced together in one single 454 GS-FLX run. Our method was initially validated on a reference sample set including 265 clearly identified rodent tissues, corresponding to 103 different species. Following validation, 85.6% of 555 rodent samples from Europe, Asia and Africa whose species identity was unknown were able to be identified using the BLASTN program and GenBank reference sequences. In addition, our method proved effective even on degraded rodent DNA samples: 91.8% and 75.9% of samples from feces and museum specimens respectively were correctly identified. Finally, we succeeded in determining the diet of 66.7% of the investigated carnivores from their feces and 81.8% of owls from their pellets. Non-rodent species were also identified, suggesting that our method is sensitive enough to investigate complete predator diets. This study demonstrates how this molecular identification method combined with high-throughput sequencing can open new realms of possibilities in achieving fast, accurate and inexpensive species identification.
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Affiliation(s)
- Maxime Galan
- Institut national de la recherche agronomique, Joint Research Unit Centre de Biologie pour la Gestion des Populations (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, Montferrier-sur-Lez, France.
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Complete mitochondrial genome of the Eurasian flying squirrel Pteromys volans (Sciuromorpha, Sciuridae) and revision of rodent phylogeny. Mol Biol Rep 2012; 40:1917-26. [PMID: 23114915 DOI: 10.1007/s11033-012-2248-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 10/10/2012] [Indexed: 10/27/2022]
Abstract
In this study, the complete mitochondrial genome of the Eurasian flying squirrel Pteromys volans (Rodentia, Sciuromorpha, Sciuridae) was sequenced and characterized in detail. The entire mitochondrial genome of P. volans consisted of 16,513 bp and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions. Its gene arrangement pattern was consistent with the mammalian ground pattern. The overall base composition and AT contents were similar to those of other rodent mitochondrial genomes. The light-strand origin generally identified between tRNA ( Asn ) and tRNA ( Cys ) consisted of a secondary structure with an 11-bp stem and an 11-bp loop. The large control region was constructed of three characteristic domains, ETAS, CD, and CSB without any repeat sequences. Each domain contained ETAS1, subsequences A, B, and C, and CSB1, respectively. In order to examine phylogenetic contentious issues of the monophyly of rodents and phylogenetic relationships among five rodent suborders, here, phylogenetic analyses based on nucleotide sequence data of the 35 rodent and 3 lagomorph mitochondrial genomes were performed using the Bayesian inference and maximum likelihood method. The result strongly supported the rodent monophyly with high node confidence values (BP 100 % in ML and BPP 1.00 in BI) and also monophylies of four rodent suborders (BP 85-100 % in ML and BPP 1.00 in BI), except for Anomalumorpha in which only one species was examined here. Also, phylogenetic relationships among the five rodent suborders were suggested and discussed in detail.
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Lack JB, Greene DU, Conroy CJ, Hamilton MJ, Braun JK, Mares MA, Van Den Bussche RA. Invasion facilitates hybridization with introgression in the Rattus rattus species complex. Mol Ecol 2012; 21:3545-61. [PMID: 22607228 DOI: 10.1111/j.1365-294x.2012.05620.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biological invasions result in novel species interactions, which can have significant evolutionary impacts on both native and invading taxa. One evolutionary concern with invasions is hybridization among lineages that were previously isolated, but make secondary contact in their invaded range(s). Black rats, consisting of several morphologically very similar but genetically distinct taxa that collectively have invaded six continents, are arguably the most successful mammalian invaders on the planet. We used mitochondrial cytochrome b sequences, two nuclear gene sequences (Atp5a1 and DHFR) and nine microsatellite loci to examine the distribution of three invasive black rat lineages (Rattus tanezumi, Rattus rattus I and R. rattus IV) in the United States and Asia and to determine the extent of hybridization among these taxa. Our analyses revealed two mitochondrial lineages that have spread to multiple continents, including a previously undiscovered population of R. tanezumi in the south-eastern United States, whereas the third lineage (R. rattus IV) appears to be confined to Southeast Asia. Analyses of nuclear DNA (both sequences and microsatellites) suggested significant hybridization is occurring among R. tanezumi and R. rattus I in the United States and also suggest hybridization between R. tanezumi and R. rattus IV in Asia, although further sampling of the latter species pair in Asia is required. Furthermore, microsatellite analyses suggest unidirectional introgression from both R. rattus I and R. rattus IV into R. tanezumi. Within the United States, introgression appears to be occurring to such a pronounced extent that we were unable to detect any nuclear genetic signal for R. tanezumi, and a similar pattern was detected in Asia.
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Affiliation(s)
- Justin B Lack
- Department of Zoology, 501 Life Sciences West, Oklahoma State University, Stillwater, OK 74078, USA.
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Badenhorst D, Tatard C, Suputtamongkol Y, Robinson TJ, Dobigny G. Host cell/Orientia tsutsugamushi interactions: evolution and expression of syndecan-4 in Asian rodents (Rodentia, Muridae). INFECTION GENETICS AND EVOLUTION 2012; 12:1136-46. [PMID: 22484764 DOI: 10.1016/j.meegid.2012.03.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 03/21/2012] [Accepted: 03/22/2012] [Indexed: 11/18/2022]
Abstract
Scrub typhus is an acute febrile zoonotic disease and worldwide more than a billion people may be at risk for infection. Orientia tsutsugamushi, the causative agent of scrub typhus, is an obligate intracellular bacterium. Rodents are reported to be the primary reservoir hosts of the disease and according to the most recent surveys, all species within the Rattus sensu lato complex of the tribe Rattini are carriers of scrub typhus. There is no evidence that any of mouse (Mus) species serves as the primary reservoir of the bacterium even when occurring in sympatry with wild infected rats. This contrast in the host/syndecan-4 interactions between Rattini and Asian Murini may be due to intrinsic (i.e., genetic) differences. Herein we compare the sequence and expression levels of syndecan-4 (the putative cell receptor of O. tsutsugamushi) between Rattini species that are known to be natural reservoirs for the typhus agents, and Murini species that are not. Although it was not possible to conclusively link the structural variations detected in syndecan-4 with carrier status in either Rattini and Murini, our findings indicate the absence of a strong Orientia-mediated selective regime acting on gene structure. In contrast, variable spleen-specific syndecan-4 expression levels show a strong correlation between under-expression of syndecan-4 in Murini and seropositive Rattini, compared to seronegative Rattini rodents. We postulate that two divergent responses may be at work in Murini and Rattini, both linked with differential expression of syndecan-4: (i) reduced syndecan-4 transcription in Murini decreases the likelihood that the host cells will become infected by the Orientia bacterium, while (ii) reduced syndecan-4 expression in seropositive Rattini limits the pathogenicity of Orientia and consequently improves the longevity of the rat hosts. These patterns may underpin the poor carrier status of wild mice on the one hand, and the effective role of wild rats as reservoir hosts on the other.
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Affiliation(s)
- Daleen Badenhorst
- Evolutionary Genomics Group, University of Stellenbosch, Botany and Zoology Department, Private Bag X1, 7604 Matieland, South Africa
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Tollenaere C, Ivanova S, Duplantier JM, Loiseau A, Rahalison L, Rahelinirina S, Brouat C. Contrasted patterns of selection on MHC-linked microsatellites in natural populations of the Malagasy plague reservoir. PLoS One 2012; 7:e32814. [PMID: 22403713 PMCID: PMC3293896 DOI: 10.1371/journal.pone.0032814] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Accepted: 02/06/2012] [Indexed: 01/14/2023] Open
Abstract
Plague (Yersinia pestis infection) is a highly virulent rodent disease that persists in many natural ecosystems. The black rat (Rattus rattus) is the main host involved in the plague focus of the central highlands of Madagascar. Black rat populations from this area are highly resistant to plague, whereas those from areas in which the disease is absent (low altitude zones of Madagascar) are susceptible. Various lines of evidence suggest a role for the Major Histocompatibility Complex (MHC) in plague resistance. We therefore used the MHC region as a candidate for detecting signatures of plague-mediated selection in Malagasy black rats, by comparing population genetic structures for five MHC-linked microsatellites and neutral markers in two sampling designs. We first compared four pairs of populations, each pair including one population from the plague focus and one from the disease-free zone. Plague-mediated selection was expected to result in greater genetic differentiation between the two zones than expected under neutrality and this was observed for one MHC-class I-linked locus (D20Img2). For this marker as well as for four other MHC-linked loci, a geographic pattern of genetic structure was found at local scale within the plague focus. This pattern would be expected if plague selection pressures were spatially variable. Finally, another MHC-class I-linked locus (D20Rat21) showed evidences of balancing selection, but it seems more likely that this selection would be related to unknown pathogens more widely distributed in Madagascar than plague.
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Affiliation(s)
- Charlotte Tollenaere
- Institut de Recherche pour le Développement, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Montferrier sur Lez, France
| | - Svilena Ivanova
- Institut de Recherche pour le Développement, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Montferrier sur Lez, France
| | - Jean-Marc Duplantier
- Institut de Recherche pour le Développement, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Montferrier sur Lez, France
| | - Anne Loiseau
- Institut National de la Recherche Agronomique, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Montferrier sur Lez, France
| | - Lila Rahalison
- Institut Pasteur de Madagascar, Unité Peste, Antananarivo, Madagascar
| | | | - Carine Brouat
- Institut de Recherche pour le Développement, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Montferrier sur Lez, France
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Pagès M, Chevret P, Gros-Balthazard M, Hughes S, Alcover JA, Hutterer R, Rando JC, Michaux J, Hänni C. Paleogenetic analyses reveal unsuspected phylogenetic affinities between mice and the extinct Malpaisomys insularis, an endemic rodent of the Canaries. PLoS One 2012; 7:e31123. [PMID: 22363563 PMCID: PMC3283599 DOI: 10.1371/journal.pone.0031123] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 01/03/2012] [Indexed: 12/22/2022] Open
Abstract
Background The lava mouse, Malpaisomys insularis, was endemic to the Eastern Canary islands and became extinct at the beginning of the 14th century when the Europeans reached the archipelago. Studies to determine Malpaisomys' phylogenetic affinities, based on morphological characters, remained inconclusive because morphological changes experienced by this insular rodent make phylogenetic investigations a real challenge. Over 20 years since its first description, Malpaisomys' phylogenetic position remains enigmatic. Methodology/Principal Findings In this study, we resolved this issue using molecular characters. Mitochondrial and nuclear markers were successfully amplified from subfossils of three lava mouse samples. Molecular phylogenetic reconstructions revealed, without any ambiguity, unsuspected relationships between Malpaisomys and extant mice (genus Mus, Murinae). Moreover, through molecular dating we estimated the origin of the Malpaisomys/mouse clade at 6.9 Ma, corresponding to the maximal age at which the archipelago was colonised by the Malpaisomys ancestor via natural rafting. Conclusion/Significance This study reconsiders the derived morphological characters of Malpaisomys in light of this unexpected molecular finding. To reconcile molecular and morphological data, we propose to consider Malpaisomys insularis as an insular lineage of mouse.
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Affiliation(s)
- Marie Pagès
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Pascale Chevret
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Lyon, France
- * E-mail:
| | - Muriel Gros-Balthazard
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Sandrine Hughes
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Josep Antoni Alcover
- Institut Mediterrani d'Estudis Avançats, Esporles, Mallorca, Spain
- Department of Mammalogy, American Museum of Natural History, New York, New York, United States of America
| | - Rainer Hutterer
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Juan Carlos Rando
- Departamento de Biología Animal (UDI Zoología), Universidad de La Laguna La Laguna, Tenerife, Canary Islands, Spain
- Island Ecology and Evolution Research Group (IPNA-CSIC), La Laguna, Tenerife, Canary Islands, Spain
| | - Jacques Michaux
- EPHE–ISEM, UMR 5554 CNRS Université Montpellier II, Université de Montpellier, Montpellier, France
| | - Catherine Hänni
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Lyon, France
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Aplin KP, Suzuki H, Chinen AA, Chesser RT, Ten Have J, Donnellan SC, Austin J, Frost A, Gonzalez JP, Herbreteau V, Catzeflis F, Soubrier J, Fang YP, Robins J, Matisoo-Smith E, Bastos ADS, Maryanto I, Sinaga MH, Denys C, Van Den Bussche RA, Conroy C, Rowe K, Cooper A. Multiple geographic origins of commensalism and complex dispersal history of Black Rats. PLoS One 2011; 6:e26357. [PMID: 22073158 PMCID: PMC3206810 DOI: 10.1371/journal.pone.0026357] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Accepted: 09/25/2011] [Indexed: 01/22/2023] Open
Abstract
The Black Rat (Rattus rattus) spread out of Asia to become one of the world's worst agricultural and urban pests, and a reservoir or vector of numerous zoonotic diseases, including the devastating plague. Despite the global scale and inestimable cost of their impacts on both human livelihoods and natural ecosystems, little is known of the global genetic diversity of Black Rats, the timing and directions of their historical dispersals, and the risks associated with contemporary movements. We surveyed mitochondrial DNA of Black Rats collected across their global range as a first step towards obtaining an historical genetic perspective on this socioeconomically important group of rodents. We found a strong phylogeographic pattern with well-differentiated lineages of Black Rats native to South Asia, the Himalayan region, southern Indochina, and northern Indochina to East Asia, and a diversification that probably commenced in the early Middle Pleistocene. We also identified two other currently recognised species of Rattus as potential derivatives of a paraphyletic R. rattus. Three of the four phylogenetic lineage units within R. rattus show clear genetic signatures of major population expansion in prehistoric times, and the distribution of particular haplogroups mirrors archaeologically and historically documented patterns of human dispersal and trade. Commensalism clearly arose multiple times in R. rattus and in widely separated geographic regions, and this may account for apparent regionalism in their associated pathogens. Our findings represent an important step towards deeper understanding the complex and influential relationship that has developed between Black Rats and humans, and invite a thorough re-examination of host-pathogen associations among Black Rats.
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Affiliation(s)
- Ken P Aplin
- Australian National Wildlife Collection, CSIRO Ecosystem Sciences, Canberra, Australia.
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Buzan EV, Pagès M, Michaux J, Krystufek B. Phylogenetic position of the Ohiya rat (Srilankamys ohiensis) based on mitochondrial and nuclear gene sequence analysis. ZOOL SCR 2011. [DOI: 10.1111/j.1463-6409.2011.00494.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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45
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Chromosomal evolution in Rattini (Muridae, Rodentia). Chromosome Res 2011; 19:709-27. [PMID: 21850459 DOI: 10.1007/s10577-011-9227-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 07/28/2011] [Accepted: 07/29/2011] [Indexed: 10/17/2022]
Abstract
The Rattini (Muridae, Murinae) includes the biologically important model species Rattus norvegicus (RNO) and represents a group of rodents that are of clinical, agricultural and epidemiological importance. We present a comparative molecular cytogenetic investigation of ten Rattini species representative of the genera Maxomys, Leopoldamys, Niviventer, Berylmys, Bandicota and Rattus using chromosome banding, cross-species painting (Zoo-fluorescent in situ hybridization or FISH) and BAC-FISH mapping. Our results show that these taxa are characterised by slow to moderate rates of chromosome evolution that contrasts with the extensive chromosome restructuring identified in most other murid rodents, particularly the mouse lineage. This extends to genomic features such as NOR location (for example, NORs on RNO 3 are present on the corresponding chromosomes in all species except Bandicota savilei and Niviventer fulvescens, and the NORs on RNO 10 are conserved in all Rattini with the exception of Rattus). The satellite I DNA family detected and characterised herein appears to be taxon (Rattus) specific, and of recent origin (consistent with a feedback model of satellite evolution). BAC-mapping using clones that span regions responsible for the morphological variability exhibited by RNO 1, 12 and 13 (acrocentric/submetacentric) and their orthologues in Rattus species, demonstrated that the differences are most likely due to pericentric inversions as exemplified by data on Rattus tanezumi. Chromosomal characters detected using R. norvegicus and Maxomys surifer whole chromosome painting probes were mapped to a consensus sequence-based phylogenetic tree thus allowing an objective assessment of ancestral states for the reconstruction of the putative Rattini ancestral karyotype. This is thought to have comprised 46 chromosomes that, with the exception of a single pair of metacentric autosomes, were acrocentric in morphology.
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46
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Kaewmongkol G, Kaewmongkol S, McInnes LM, Burmej H, Bennett MD, Adams PJ, Ryan U, Irwin PJ, Fenwick SG. Genetic characterization of flea-derived Bartonella species from native animals in Australia suggests host-parasite co-evolution. INFECTION GENETICS AND EVOLUTION 2011; 11:1868-72. [PMID: 21856444 DOI: 10.1016/j.meegid.2011.07.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 07/26/2011] [Accepted: 07/28/2011] [Indexed: 11/28/2022]
Abstract
Fleas are important arthropod vectors for a variety of diseases in veterinary and human medicine, and bacteria belonging to the genus Bartonella are among the organisms most commonly transmitted by these ectoparasites. Recently, a number of novel Bartonella species and novel species candidates have been reported in marsupial fleas in Australia. In the present study the genetic diversity of marsupial fleas was investigated; 10 species of fleas were collected from seven different marsupial and placental mammal hosts in Western Australia including woylies (Bettongia penicillata), western barred bandicoots (Perameles bougainville), mardos (Antechinus flavipes), bush rats (Rattus fuscipes), red foxes (Vulpes vulpes), feral cats (Felis catus) and rabbits (Oryctolagus cuniculus). PCR and sequence analysis of the cytochrome oxidase subunit I (COI) and the 18S rRNA genes from these fleas was performed. Concatenated phylogenetic analysis of the COI and 18S rRNA genes revealed a close genetic relationship between marsupial fleas, with Pygiopsylla hilli from woylies, Pygiopsylla tunneyi from western barred bandicoots and Acanthopsylla jordani from mardos, forming a separate cluster from fleas collected from the placental mammals in the same geographical area. The clustering of Bartonella species with their marsupial flea hosts suggests co-evolution of marsupial hosts, marsupial fleas and Bartonella species in Australia.
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Affiliation(s)
- Gunn Kaewmongkol
- School of Veterinary and Biomedical Sciences, Murdoch University, South Street, Murdoch 6150, Western Australia, Australia.
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Rowe KC, Singhal S, Macmanes MD, Ayroles JF, Morelli TL, Rubidge EM, Bi K, Moritz CC. Museum genomics: low-cost and high-accuracy genetic data from historical specimens. Mol Ecol Resour 2011; 11:1082-92. [PMID: 21791033 DOI: 10.1111/j.1755-0998.2011.03052.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Natural history collections are unparalleled repositories of geographical and temporal variation in faunal conditions. Molecular studies offer an opportunity to uncover much of this variation; however, genetic studies of historical museum specimens typically rely on extracting highly degraded and chemically modified DNA samples from skins, skulls or other dried samples. Despite this limitation, obtaining short fragments of DNA sequences using traditional PCR amplification of DNA has been the primary method for genetic study of historical specimens. Few laboratories have succeeded in obtaining genome-scale sequences from historical specimens and then only with considerable effort and cost. Here, we describe a low-cost approach using high-throughput next-generation sequencing to obtain reliable genome-scale sequence data from a traditionally preserved mammal skin and skull using a simple extraction protocol. We show that single-nucleotide polymorphisms (SNPs) from the genome sequences obtained independently from the skin and from the skull are highly repeatable compared to a reference genome.
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Affiliation(s)
- Kevin C Rowe
- Sciences Department, Museum Victoria, GPO Box 666, Melbourne, Vic. 3001, Australia.
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Cazaux B, Catalan J, Veyrunes F, Douzery EJ, Britton-Davidian J. Are ribosomal DNA clusters rearrangement hotspots?: a case study in the genus Mus (Rodentia, Muridae). BMC Evol Biol 2011; 11:124. [PMID: 21569527 PMCID: PMC3112088 DOI: 10.1186/1471-2148-11-124] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 05/13/2011] [Indexed: 11/10/2022] Open
Abstract
Background Recent advances in comparative genomics have considerably improved our knowledge of the evolution of mammalian karyotype architecture. One of the breakthroughs was the preferential localization of evolutionary breakpoints in regions enriched in repetitive sequences (segmental duplications, telomeres and centromeres). In this context, we investigated the contribution of ribosomal genes to genome reshuffling since they are generally located in pericentromeric or subtelomeric regions, and form repeat clusters on different chromosomes. The target model was the genus Mus which exhibits a high rate of karyotypic change, a large fraction of which involves centromeres. Results The chromosomal distribution of rDNA clusters was determined by in situ hybridization of mouse probes in 19 species. Using a molecular-based reference tree, the phylogenetic distribution of clusters within the genus was reconstructed, and the temporal association between rDNA clusters, breakpoints and centromeres was tested by maximum likelihood analyses. Our results highlighted the following features of rDNA cluster dynamics in the genus Mus: i) rDNA clusters showed extensive diversity in number between species and an almost exclusive pericentromeric location, ii) a strong association between rDNA sites and centromeres was retrieved which may be related to their shared constraint of concerted evolution, iii) 24% of the observed breakpoints mapped near an rDNA cluster, and iv) a substantial rate of rDNA cluster change (insertion, deletion) also occurred in the absence of chromosomal rearrangements. Conclusions This study on the dynamics of rDNA clusters within the genus Mus has revealed a strong evolutionary relationship between rDNA clusters and centromeres. Both of these genomic structures coincide with breakpoints in the genus Mus, suggesting that the accumulation of a large number of repeats in the centromeric region may contribute to the high level of chromosome repatterning observed in this group. However, the elevated rate of rDNA change observed in the chromosomally invariant clade indicates that the presence of these sequences is insufficient to lead to genome instability. In agreement with recent studies, these results suggest that additional factors such as modifications of the epigenetic state of DNA may be required to trigger evolutionary plasticity.
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Affiliation(s)
- Benoîte Cazaux
- Institut des Sciences de l'Evolution, UMR5554 CNRS/Université Montpellier II, France.
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Bastos AD, Nair D, Taylor PJ, Brettschneider H, Kirsten F, Mostert E, von Maltitz E, Lamb JM, van Hooft P, Belmain SR, Contrafatto G, Downs S, Chimimba CT. Genetic monitoring detects an overlooked cryptic species and reveals the diversity and distribution of three invasive Rattus congeners in South Africa. BMC Genet 2011; 12:26. [PMID: 21324204 PMCID: PMC3055845 DOI: 10.1186/1471-2156-12-26] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 02/16/2011] [Indexed: 11/30/2022] Open
Abstract
Background South Africa's long and extensive trade activity has ensured ample opportunities for exotic species introduction. Whereas the rich biodiversity of endemic southern African fauna has been the focus of many studies, invasive vertebrates are generally overlooked despite potential impacts on biodiversity, health and agriculture. Genetic monitoring of commensal rodents in South Africa which uncovered the presence of Rattus tanezumi, a South-East Asian endemic not previously known to occur in Africa, provided the impetus for expanded studies on all invasive Rattus species present. Results To this end, intensified sampling at 28 South African localities and at one site in Swaziland, identified 149 Rattus specimens. Cytochrome b gene sequencing revealed the presence of two R. tanezumi, seven Rattus rattus and five Rattus norvegicus haplotypes in south Africa. Phylogenetic results were consistent with a single, recent R. tanezumi introduction and indicated that R. norvegicus and R. rattus probably became established following at least two and three independent introductions, respectively. Intra- and inter-specific diversity was highest in informal human settlements, with all three species occurring at a single metropolitan township site. Rattus norvegicus and R. rattus each occurred sympatrically with Rattus tanezumi at one and five sites, respectively. Karyotyping of selected R. rattus and R. tanezumi individuals identified diploid numbers consistent with those reported previously for these cryptic species. Ordination of bioclimatic variables and MaxEnt ecological niche modelling confirmed that the bioclimatic niche occupied by R. tanezumi in south Africa was distinct from that occupied in its naturalised range in south-east Asia suggesting that factors other than climate may influence the distribution of this species. Conclusions This study has highlighted the value of genetic typing for detecting cryptic invasive species, providing historical insights into introductions and for directing future sampling. The apparent ease with which a cryptic species can become established signals the need for broader implementation of genetic monitoring programmes. In addition to providing baseline data and potentially identifying high-risk introduction routes, the predictive power of ecological niche modelling is enhanced when species records are genetically verified.
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Affiliation(s)
- Armanda D Bastos
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Private Bag 20, Hatfield 0028, Pretoria, South Africa.
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50
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Rowe KC, Aplin KP, Baverstock PR, Moritz C. Recent and Rapid Speciation with Limited Morphological Disparity in the Genus Rattus. Syst Biol 2011; 60:188-203. [PMID: 21239388 DOI: 10.1093/sysbio/syq092] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Kevin C. Rowe
- Museum of Vertebrate Zoology
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3160, USA
- Centre for Animal Conservation Genetics, School of Environmental Science and Management, Southern Cross University, PO Box 157, Lismore, NSW 2480, Australia
| | - Ken P. Aplin
- Australian National Wildlife Collection, CSIRO Division of Sustainable Ecosystems, GPO Box 284, Canberra, ACT 2601, Australia
| | - Peter R. Baverstock
- Centre for Animal Conservation Genetics, School of Environmental Science and Management, Southern Cross University, PO Box 157, Lismore, NSW 2480, Australia
| | - Craig Moritz
- Museum of Vertebrate Zoology
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3160, USA
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