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Stone NE, Hamond C, Clegg J, McDonough RF, Bourgeois RM, Ballard R, Thornton NB, Nuttall M, Hertzel H, Anderson T, Whealy RN, Timm S, Roberts AK, Barragán V, Phipatanakul W, Leibler JH, Benson H, Specht A, White R, LeCount K, Furstenau TN, Galloway RL, Hill NJ, Madison JD, Fofanov VY, Pearson T, Sahl JW, Busch JD, Weiner Z, Nally JE, Wagner DM, Rosenbaum MH. Host population structure and rare dispersal events drive leptospirosis transmission patterns among Rattus norvegicus in Boston, Massachusetts, US. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598639. [PMID: 38915728 PMCID: PMC11195238 DOI: 10.1101/2024.06.12.598639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Leptospirosis (caused by pathogenic bacteria in the genus Leptospira ) is prevalent worldwide but more common in tropical and subtropical regions. Transmission can occur following direct exposure to infected urine from reservoir hosts, such as rats, or a urine-contaminated environment, which then can serve as an infection source for additional rats and other mammals, including humans. The brown rat, Rattus norvegicus , is an important reservoir of leptospirosis in urban settings. We investigated leptospirosis among brown rats in Boston, Massachusetts and hypothesized that rat dispersal in this urban setting influences the movement, persistence, and diversity of Leptospira . We analyzed DNA from 328 rat kidney samples collected from 17 sites in Boston over a seven-year period (2016-2022); 59 rats representing 12 of 17 sites were positive for Leptospira . We used 21 neutral microsatellite loci to genotype 311 rats and utilized the resulting data to investigate genetic connectivity among sampling sites. We generated whole genome sequences for 28 Leptospira isolates obtained from frozen and fresh tissue from some of the 59 Leptospira -positive rat kidneys. When isolates were not obtained, we attempted Leptospira genomic DNA capture and enrichment, which yielded 14 additional Leptospira genomes from rats. We also generated an enriched Leptospira genome from a 2018 human case in Boston. We found evidence of high genetic structure and limited dispersal among rat populations that is likely influenced by major roads and/or other unknown dispersal barriers, resulting in distinct rat population groups within the city; at certain sites these groups persisted for multiple years. We identified multiple distinct phylogenetic clades of L. interrogans among rats, with specific clades tightly linked to distinct rat populations. This pattern suggests L. interrogans persists in local rat populations and movement of leptospirosis in this urban rat community is driven by rat dispersal. Finally, our genomic analyses of the 2018 human leptospirosis case in Boston suggests a link to rats as the source. These findings will be useful for guiding rat control and human leptospirosis mitigation efforts in this and other urban settings.
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Robinson SJ, Pearl DL, Himsworth CG, Weese JS, Lindsay LR, Dibernardo A, Huynh C, Hill JE, Fernando C, Jardine CM. Environmental and sociodemographic factors associated with zoonotic pathogen occurrence in Norway rats (Rattus norvegicus) from Windsor, Ontario. Zoonoses Public Health 2024; 71:416-428. [PMID: 38419369 DOI: 10.1111/zph.13120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 11/21/2023] [Accepted: 02/19/2024] [Indexed: 03/02/2024]
Abstract
AIMS Rat-associated zoonotic pathogen transmission at the human-wildlife interface is a public health concern in urban environments where Norway rats (Rattus norvegicus) thrive on abundant anthropogenic resources and live in close contact with humans and other animal species. To identify potential factors influencing zoonotic pathogen occurrence in rats, we investigated associations between environmental and sociodemographic factors and Leptospira interrogans and Bartonella spp. infections in rats from Windsor, Ontario, Canada, while controlling for the potential confounding effects of animal characteristics (i.e., sexual maturity and body condition). METHODS AND RESULTS Between November 2018 and June 2021, 252 rats were submitted by collaborating pest control professionals. Kidney and spleen samples were collected for L. interrogans and Bartonella spp. PCR and sequencing, respectively. Of the rats tested by PCR, 12.7% (32/252) were positive for L. interrogans and 16.3% (37/227) were positive for Bartonella species. Associations between infection status and environmental and sociodemographic variables of interest were assessed via mixed multivariable logistic regression models with a random intercept for social group and fixed effects to control for sexual maturity and body condition in each model. The odds of L. interrogans infection were significantly higher in rats from areas with high building density (odds ratio [OR]: 3.76; 95% CI: 1.31-10.79; p = 0.014), high human population density (OR: 3.31; 95% CI: 1.20-9.11; p = 0.021), high proportion of buildings built in 1960 or before (OR: 11.21; 95% CI: 2.06-60.89; p = 0.005), and a moderate number of reports of uncollected garbage compared to a low number of reports (OR: 4.88; 95% CI: 1.01-23.63; p = 0.049). A negative association was observed between median household income and Bartonella spp. infection in rats (OR: 0.26; 95% CI: 0.08-0.89; p = 0.031). CONCLUSIONS Due to the complexity of the ecology of rat-associated zoonoses, consideration of environmental and sociodemographic factors is of critical importance to better understand the nuances of host-pathogen systems and inform how urban rat surveillance and intervention efforts should be distributed within cities.
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Affiliation(s)
- Sarah J Robinson
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - David L Pearl
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Chelsea G Himsworth
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - J Scott Weese
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - L Robbin Lindsay
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Antonia Dibernardo
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Chris Huynh
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Janet E Hill
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Champika Fernando
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Claire M Jardine
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
- Canadian Wildlife Health Cooperative, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
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Caizergues AE, Santangelo JS, Ness RW, Angeoletto F, Anstett DN, Anstett J, Baena-Diaz F, Carlen EJ, Chaves JA, Comerford MS, Dyson K, Falahati-Anbaran M, Fellowes MDE, Hodgins KA, Hood GR, Iñiguez-Armijos C, Kooyers NJ, Lázaro-Lobo A, Moles AT, Munshi-South J, Paule J, Porth IM, Santiago-Rosario LY, Whitney KS, Tack AJM, Johnson MTJ. Does urbanisation lead to parallel demographic shifts across the world in a cosmopolitan plant? Mol Ecol 2024; 33:e17311. [PMID: 38468155 DOI: 10.1111/mec.17311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/08/2023] [Accepted: 01/30/2024] [Indexed: 03/13/2024]
Abstract
Urbanisation is occurring globally, leading to dramatic environmental changes that are altering the ecology and evolution of species. In particular, the expansion of human infrastructure and the loss and fragmentation of natural habitats in cities is predicted to increase genetic drift and reduce gene flow by reducing the size and connectivity of populations. Alternatively, the 'urban facilitation model' suggests that some species will have greater gene flow into and within cities leading to higher diversity and lower differentiation in urban populations. These alternative hypotheses have not been contrasted across multiple cities. Here, we used the genomic data from the GLobal Urban Evolution project (GLUE), to study the effects of urbanisation on non-adaptive evolutionary processes of white clover (Trifolium repens) at a global scale. We found that white clover populations presented high genetic diversity and no evidence of reduced Ne linked to urbanisation. On the contrary, we found that urban populations were less likely to experience a recent decrease in effective population size than rural ones. In addition, we found little genetic structure among populations both globally and between urban and rural populations, which showed extensive gene flow between habitats. Interestingly, white clover displayed overall higher gene flow within urban areas than within rural habitats. Our study provides the largest comprehensive test of the demographic effects of urbanisation. Our results contrast with the common perception that heavily altered and fragmented urban environments will reduce the effective population size and genetic diversity of populations and contribute to their isolation.
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Affiliation(s)
- Aude E Caizergues
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - James S Santangelo
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA
| | - Rob W Ness
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Fabio Angeoletto
- Programa de Pós-Graduação em Gestão e Tecnologia Ambiental da Universidade Federal de Rondonópolis, Rondonópolis, Brasil
| | - Daniel N Anstett
- Department of Plant Biology, Department of Entomology, Plant Resilience Institute, Michigan State University, East Lansing, Michigan, USA
| | - Julia Anstett
- Genomic Sciences and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Elizabeth J Carlen
- Living Earth Collaborative, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jaime A Chaves
- Universidad San Francisco de Quito, Ecuador, Quito
- San Francisco State University, San Francisco, California, USA
| | - Mattheau S Comerford
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, USA
| | | | | | | | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Glen Ray Hood
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Carlos Iñiguez-Armijos
- Laboratorio de Ecología Tropical y Servicios Ecosistémicos (EcoSs-Lab), Universidad Técnica Particular de Loja, Loja, Ecuador
| | | | - Adrián Lázaro-Lobo
- Biodiversity Research Institute (IMIB), CSIC-University of Oviedo-Principality of Asturias, Mieres, Spain
| | - Angela T Moles
- Evolution & Ecology Research Centre, UNSW-University of New South Wales, Sydney, New South Wales, Australia
| | - Jason Munshi-South
- Department of Biology and Louis Calder Center, Fordham University, New York City, New York, USA
| | - Juraj Paule
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Ilga M Porth
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Luis Y Santiago-Rosario
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Kaitlin Stack Whitney
- Science, Technology & Society Department, Rochester Institute of Technology, Rochester, New York, USA
| | - Ayko J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Marc T J Johnson
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
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Zhang YH, Zhao L, Zhang MY, Cao RD, Hou GM, Teng HJ, Zhang JX. Fatty acid metabolism decreased while sexual selection increased in brown rats spreading south. iScience 2023; 26:107742. [PMID: 37731619 PMCID: PMC10507208 DOI: 10.1016/j.isci.2023.107742] [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: 03/20/2023] [Revised: 06/27/2023] [Accepted: 08/24/2023] [Indexed: 09/22/2023] Open
Abstract
For mammals that originate in the cold north, adapting to warmer environments is crucial for southwards invasion. The brown rat (Rattus norvegicus) originated in Northeast China and has become a global pest. R. n. humiliatus (RNH) spread from the northeast, where R. n. caraco (RNC) lives, to North China and diverged to form a subspecies. Genomic analyses revealed that subspecies differentiation was promoted by temperature but impeded by gene flow and that genes related to fatty acid metabolism were under the strongest selection. Transcriptome analyses revealed downregulated hepatic genes related to fatty acid metabolism and upregulated those related to pheromones in RNH vs. RNC. Similar patterns were observed in relation to cold/warm acclimation. RNH preferred mates with stronger pheromone signals intra-populationally and more genetic divergence inter-populationally. We concluded that RNH experienced reduced fat utilization and increased pheromone-mediated sexual selection during its invasion from the cold north to warm south.
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Affiliation(s)
- Yao-Hua Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China
| | - Lei Zhao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming-Yu Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui-Dong Cao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guan-Mei Hou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hua-Jing Teng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jian-Xu Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
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Cole R, Holroyd N, Tracey A, Berriman M, Viney M. The parasitic nematode Strongyloides ratti exists predominantly as populations of long-lived asexual lineages. Nat Commun 2023; 14:6427. [PMID: 37833369 PMCID: PMC10575991 DOI: 10.1038/s41467-023-42250-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
Nematodes are important parasites of people and animals, and in natural ecosystems they are a major ecological force. Strongyloides ratti is a common parasitic nematode of wild rats and we have investigated its population genetics using single-worm, whole-genome sequencing. We find that S. ratti populations in the UK consist of mixtures of mainly asexual lineages that are widely dispersed across a host population. These parasite lineages are likely very old and may have originated in Asia from where rats originated. Genes that underly the parasitic phase of the parasite's life cycle are hyperdiverse compared with the rest of the genome, and this may allow the parasites to maximise their fitness in a diverse host population. These patterns of parasitic nematode population genetics have not been found before and may also apply to Strongyloides spp. that infect people, which will affect how we should approach their control.
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Affiliation(s)
- Rebecca Cole
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Nancy Holroyd
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Alan Tracey
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Matt Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- School of Infection & Immunity, University of Glasgow, 120 University Place, Glasgow, G12 8TA, UK
| | - Mark Viney
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK.
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, L69 7ZB, UK.
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6
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Lajmi A, Glinka F, Privman E. Optimizing ddRAD sequencing for population genomic studies with ddgRADer. Mol Ecol Resour 2023. [PMID: 37732396 DOI: 10.1111/1755-0998.13870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 08/04/2023] [Accepted: 08/31/2023] [Indexed: 09/22/2023]
Abstract
Double-digest Restriction-site Associated DNA sequencing (ddRADseq) is widely used to generate genomic data for non-model organisms in evolutionary and ecological studies. Along with affordable paired-end sequencing, this method makes population genomic analyses more accessible. However, multiple factors should be considered when designing a ddRADseq experiment, which can be challenging for new users. The generated data often suffer from substantial read overlaps and adaptor contamination, severely reducing sequencing efficiency and affecting data quality. Here, we analyse diverse datasets from the literature and carry out controlled experiments to understand the effects of enzyme choice and size selection on sequencing efficiency. The empirical data reveal that size selection is imprecise and has limited efficacy. In certain scenarios, a substantial proportion of short fragments pass below the lower size-selection cut-off resulting in low sequencing efficiency. However, enzyme choice can considerably mitigate inadvertent inclusion of these shorter fragments. A simple model based on these experiments is implemented to predict the number of genomic fragments generated after digestion and size selection, number of SNPs genotyped, number of samples that can be multiplexed and the expected sequencing efficiency. We developed ddgRADer - http://ddgrader.haifa.ac.il/ - a user-friendly webtool and incorporated these calculations to aid in ddRADseq experimental design while optimizing sequencing efficiency. This tool can also be used for single enzyme protocols such as Genotyping-by-Sequencing. Given user-defined study goals, ddgRADer recommends enzyme pairs and allows users to compare and choose enzymes and size-selection criteria. ddgRADer improves the accessibility and ease of designing ddRADseq experiments and increases the probability of success of the first population genomic study conducted in labs with no prior experience in genomics.
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Affiliation(s)
- Aparna Lajmi
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Felix Glinka
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Eyal Privman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
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7
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Ramsay MS, Sgarlata GM, Barratt CD, Salmona J, Andriatsitohaina B, Kiene F, Manzi S, Ramilison ML, Rakotondravony R, Chikhi L, Lehman SM, Radespiel U. Effects of Forest Fragmentation on Connectivity and Genetic Diversity in an Endemic and an Invasive Rodent in Northwestern Madagascar. Genes (Basel) 2023; 14:1451. [PMID: 37510355 PMCID: PMC10378931 DOI: 10.3390/genes14071451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/07/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Habitat loss and fragmentation are of concern to conservation biologists worldwide. However, not all organisms are affected equally by these processes; thus, it is important to study the effects of living in fragmented habitats on species that differ in lifestyle and habitat requirements. In this study, we examined the dispersal and connectivity patterns of rodents, one endemic (Eliurus myoxinus) and one invasive (Rattus rattus), in two landscapes containing forest fragments and adjacent continuous forest patches in northwestern Madagascar. We generated genetic (RADseq) data for 66 E. myoxinus and 81 R. rattus individuals to evaluate differences in genetic diversity as well as inbreeding and connectivity in two landscapes. We found higher levels of inbreeding and lower levels of genetic diversity in E. myoxinus compared with R. rattus. We observed related dyads both within and between habitat patches and positive spatial autocorrelation at lower distance classes for both species, with a stronger pattern of spatial autocorrelation in R. rattus. Across each site, we identified contrasting migration rates for each species, but these did not correspond to habitat-matrix dichotomies. The relatively low genetic diversity in the endemic E. myoxinus suggests ecological constraints that require further investigation.
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Affiliation(s)
- Malcolm S Ramsay
- Department of Anthropology, University of Toronto, Toronto, ON M5S 2S2, Canada
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | | | - Christopher D Barratt
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Jordi Salmona
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, 31062 Toulouse, France
| | - Bertrand Andriatsitohaina
- Planet Madagascar, Antananarivo 101, Madagascar
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga 401, Madagascar
| | - Frederik Kiene
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | - Sophie Manzi
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, 31062 Toulouse, France
| | - Miarisoa L Ramilison
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga 401, Madagascar
- Department of Primate Behavior and Ecology, Central Washington University, Ellensburg, WA 98926, USA
| | - Romule Rakotondravony
- Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Mahajanga 401, Madagascar
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, 31062 Toulouse, France
| | - Shawn M Lehman
- Department of Anthropology, University of Toronto, Toronto, ON M5S 2S2, Canada
| | - Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
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8
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Sosa CC, Arenas C, García-Merchán VH. Human Population Density Influences Genetic Diversity of Two Rattus Species Worldwide: A Macrogenetic Approach. Genes (Basel) 2023; 14:1442. [PMID: 37510346 PMCID: PMC10379283 DOI: 10.3390/genes14071442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/18/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
On a planet experiencing constant human population growth, it is necessary to explore the anthropogenic effects on the genetic diversity of species, and specifically invasive species. Using an analysis that integrates comparative phylogeography, urban landscape genetics, macrogenetics and a systematic review, we explore the worldwide genetic diversity of the human commensal and anthropogenic species Rattus rattus and Rattus norvegicus. Based on metadata obtained considering 35 selected studies related to observed heterozygosity, measured by nuclear molecular markers (microsatellites, Single Nucleotide Polymorphisms-SNPs-, restrictition site-associated DNA sequencing -RAD-Seq-), socioeconomic and mobility anthropogenic factors were used as predictors of genetic diversity of R. rattus and R. norvegicus, using the Gini index, principal component analysis and Random Forest Regression as analysis methodology. Population density was on average the best predictor of genetic diversity in the Rattus species analyzed, indicating that the species respond in a particular way to the characteristics present in urban environments because of a combination of life history characteristics and human-mediated migration and colonization processes. To create better management and control strategies for these rodents and their associated diseases, it is necessary to fill the existing information gap in urban landscape genetics studies with more metadata repositories, with emphasis on tropical and subtropical regions of the world.
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Affiliation(s)
- Chrystian C Sosa
- Evolution, Ecology and Conservation Research Group-EECO, Biology Program, Faculty of Basic Sciences and Technologies, Universidad del Quindío, Armenia 630004, Colombia
- Department of Natural Sciences and Mathematics, Pontificia Universidad Javeriana, Cali 7 #40-62, Bogotá 110311, Colombia
| | - Catalina Arenas
- Evolution, Ecology and Conservation Research Group-EECO, Biology Program, Faculty of Basic Sciences and Technologies, Universidad del Quindío, Armenia 630004, Colombia
| | - Víctor Hugo García-Merchán
- Evolution, Ecology and Conservation Research Group-EECO, Biology Program, Faculty of Basic Sciences and Technologies, Universidad del Quindío, Armenia 630004, Colombia
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Urban population structure and dispersal of an Australian mosquito (Aedes notoscriptus) involved in disease transmission. Heredity (Edinb) 2023; 130:99-108. [PMID: 36539450 PMCID: PMC9905534 DOI: 10.1038/s41437-022-00584-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
Dispersal is a critical parameter for successful pest control measures as it determines the rate of movement across target control areas and influences the risk of human exposure. We used a fine-scale spatial population genomic approach to investigate the dispersal ecology and population structure of Aedes notoscriptus, an important disease transmitting mosquito at the Mornington Peninsula, Australia. We sampled and reared Ae. notoscriptus eggs at two time points from 170 traps up to 5 km apart and generated genomic data from 240 individuals. We also produced a draft genome assembly from a laboratory colony established from mosquitoes sampled near the study area. We found low genetic structure (Fst) and high coancestry throughout the study region. Using genetic data to identify close kin dyads, we found that mosquitoes had moved distances of >1 km within a generation, which is further than previously recorded. A spatial autocorrelation analysis of genetic distances indicated genetic similarity at >1 km separation, a tenfold higher distance than for a comparable population of Ae. aegypti, from Cairns, Australia. These findings point to high mobility of Ae. notoscriptus, highlighting challenges of localised intervention strategies. Further sampling within the same area 6 and 12 months after initial sampling showed that egg-counts were relatively consistent across time, and that spatial variation in egg-counts covaried with spatial variation in Wright's neighbourhood size (NS). As NS increases linearly with population density, egg-counts may be useful for estimating relative density in Ae. notoscriptus. The results highlight the importance of acquiring species-specific data when planning control measures.
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10
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Etougbétché JR, Hamidović A, Dossou HJ, Coan-Grosso M, Roques R, Plault N, Houéménou G, Badou S, Missihoun AA, Abdou Karim IY, Galal L, Diagne C, Dardé ML, Dobigny G, Mercier A. Molecular prevalence, genetic characterization and patterns of Toxoplasma gondii infection in domestic small mammals from Cotonou, Benin. Parasite 2022; 29:58. [PMID: 36562439 PMCID: PMC9879161 DOI: 10.1051/parasite/2022058] [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: 07/06/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Toxoplasmosis, one of the most prevalent parasitic infections in humans and animals, is caused by the intracellular protozoan parasite Toxoplasma gondii. Small mammals play a key role as intermediate reservoir hosts in the maintenance of the T. gondii life cycle. In this study, we estimated the molecular prevalence and provide genetic diversity data for T. gondii in 632 small mammals sampled in four areas of Cotonou city, Benin. Both the brain and heart of each individual were screened through T. gondii-targeting qPCR, and positive samples were then genotyped using a set of 15 T. gondii-specific microsatellites. Prevalence data were statistically analyzed in order to assess the relative impact of individual host characteristics, spatial distribution, composition of small mammal community, and urban landscape features. An overall T. gondii molecular prevalence of 15.2% was found and seven genotypes, all belonging to the Africa 1 lineage, could be retrieved from the invasive black rat Rattus rattus and the native African giant shrew Crocidura olivieri. Statistical analyses did not suggest any significant influence of the environmental parameters used in this study. Rather, depending on the local context, T. gondii prevalence appeared to be associated either with black rat, shrew, or mouse abundance or with the trapping period. Overall, our results highlight the intricate relationships between biotic and abiotic factors involved in T. gondii epidemiology and suggest that R. rattus and C. olivieri are two competent reservoirs for the Africa 1 lineage, a widespread lineage in tropical Africa and the predominant lineage in Benin.
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Affiliation(s)
- Jonas R. Etougbétché
- Ecole Polytechnique d’Abomey-Calavi, Laboratoire de Recherche en Biologie Appliquée, Unité de Recherche sur les Invasions Biologiques, Université d’Abomey-Calavi 01 BP 2009 Cotonou Benin,Laboratoire de Génétique Moléculaire et d’Analyse des Génomes, Faculté des Sciences et Techniques, Université d’Abomey-Calavi 01BP 526 Cotonou Bénin,Corresponding authors: ;
| | - Azra Hamidović
- Inserm U1094, IRD U270, Univ. Limoges, CHU Limoges, EpiMaCT - Epidémiologie des maladies chroniques en zone tropicale, Institut d’Epidémiologie et de Neurologie Tropicale, Omega Health 87000 Limoges France
| | - Henri-Joël Dossou
- Ecole Polytechnique d’Abomey-Calavi, Laboratoire de Recherche en Biologie Appliquée, Unité de Recherche sur les Invasions Biologiques, Université d’Abomey-Calavi 01 BP 2009 Cotonou Benin,Institut du Cadre de Vie (ICaV), Université d’Abomey-Calavi BP 2899 Abomey-Calavi Benin
| | - Maeva Coan-Grosso
- Inserm U1094, IRD U270, Univ. Limoges, CHU Limoges, EpiMaCT - Epidémiologie des maladies chroniques en zone tropicale, Institut d’Epidémiologie et de Neurologie Tropicale, Omega Health 87000 Limoges France
| | - Roxane Roques
- Inserm U1094, IRD U270, Univ. Limoges, CHU Limoges, EpiMaCT - Epidémiologie des maladies chroniques en zone tropicale, Institut d’Epidémiologie et de Neurologie Tropicale, Omega Health 87000 Limoges France
| | - Nicolas Plault
- Inserm U1094, IRD U270, Univ. Limoges, CHU Limoges, EpiMaCT - Epidémiologie des maladies chroniques en zone tropicale, Institut d’Epidémiologie et de Neurologie Tropicale, Omega Health 87000 Limoges France
| | - Gualbert Houéménou
- Ecole Polytechnique d’Abomey-Calavi, Laboratoire de Recherche en Biologie Appliquée, Unité de Recherche sur les Invasions Biologiques, Université d’Abomey-Calavi 01 BP 2009 Cotonou Benin
| | - Sylvestre Badou
- Ecole Polytechnique d’Abomey-Calavi, Laboratoire de Recherche en Biologie Appliquée, Unité de Recherche sur les Invasions Biologiques, Université d’Abomey-Calavi 01 BP 2009 Cotonou Benin
| | - Antoine A. Missihoun
- Laboratoire de Génétique Moléculaire et d’Analyse des Génomes, Faculté des Sciences et Techniques, Université d’Abomey-Calavi 01BP 526 Cotonou Bénin
| | - Issaka Youssao Abdou Karim
- Ecole Polytechnique d’Abomey-Calavi, Laboratoire de Biotechnologie Animale et de Technologie des Viandes, Université d’Abomey-Calavi 01 BP 2009 Cotonou Benin
| | - Lokman Galal
- Inserm U1094, IRD U270, Univ. Limoges, CHU Limoges, EpiMaCT - Epidémiologie des maladies chroniques en zone tropicale, Institut d’Epidémiologie et de Neurologie Tropicale, Omega Health 87000 Limoges France
| | - Christophe Diagne
- Institut de Recherche pour le Développement, UMR CBGP (IRD, INRA, Cirad, Montpellier SupAgro), Montpellier Université d’Excellence 755 avenue du campus Agropolis 34988 Montferrier-sur-Lez Cedex France
| | - Marie-Laure Dardé
- Inserm U1094, IRD U270, Univ. Limoges, CHU Limoges, EpiMaCT - Epidémiologie des maladies chroniques en zone tropicale, Institut d’Epidémiologie et de Neurologie Tropicale, Omega Health 87000 Limoges France,Centre National de Référence (CNR) Toxoplasmose/Toxoplasma Biological Center (BRC), Centre Hospitalier-Universitaire Dupuytren 87000 Limoges France
| | - Gauthier Dobigny
- Institut de Recherche pour le Développement, UMR CBGP (IRD, INRA, Cirad, Montpellier SupAgro), Montpellier Université d’Excellence 755 avenue du campus Agropolis 34988 Montferrier-sur-Lez Cedex France,Unité Peste, Institut Pasteur de Madagascar BP 1274 Ambatofotsikely Avaradoha 101 Antananarivo Madagascar
| | - Aurélien Mercier
- Inserm U1094, IRD U270, Univ. Limoges, CHU Limoges, EpiMaCT - Epidémiologie des maladies chroniques en zone tropicale, Institut d’Epidémiologie et de Neurologie Tropicale, Omega Health 87000 Limoges France,Centre National de Référence (CNR) Toxoplasmose/Toxoplasma Biological Center (BRC), Centre Hospitalier-Universitaire Dupuytren 87000 Limoges France
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11
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Dunn RR, Burger JR, Carlen EJ, Koltz AM, Light JE, Martin RA, Munshi-South J, Nichols LM, Vargo EL, Yitbarek S, Zhao Y, Cibrián-Jaramillo A. A Theory of City Biogeography and the Origin of Urban Species. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.761449] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many of the choices humans make with regard to infrastructure, urban planning and other phenomena have impacts that will last thousands of years. This can readily be seen in modern cities in which contemporary streets run along street grids that were laid out thousands of years prior or even in which ancient viaducts still play a role. However, rarely do evolutionary biologists explicitly consider the future of life likely to be associated with the decisions we are making today. Here, we consider the evolutionary future of species in cities with a focus on the origin of lineages and species. We do so by adjusting evolutionary predictions from the theory of island biogeography so as to correspond to the unique features of cities as islands. Specifically, the species endemic to cities tend to be associated with the gray habitats in cities. Those habitats tend to be dominated by human bodies, pet bodies and stored food. It is among such species where the origin of new lineages is most likely, although most research on evolution in cities has focused on green habitats. We conclude by considering a range of scenarios for the far future and their implications for the origin of lineages and species.
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12
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The introduction and diversity of commensal rodents in 19th century Australasia. Biol Invasions 2022. [DOI: 10.1007/s10530-021-02717-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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13
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Awoniyi AM, Souza FN, Zeppelini CG, Xavier BIA, Barreto AM, Santiago DCC, Santana JO, da Silva EM, Costa F, Begon M, Khalil H. Using Rhodamine B to assess the movement of small mammals in an urban slum. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | - Juliet Oliveira Santana
- Instituto de Pesquisas Gonçalo Moniz Fundação Oswaldo CruzMinistério da Saúde Salvador Bahia Brasil
| | - Eduardo Mendes da Silva
- Instituto de Biologia Universidade Federal da Bahia Salvador Brasil
- Instituto de Biologia Universidade Federal da Bahia and National Institute of Science and Technology on Interdisciplinary Studies of Ecology and Evolution (INCT IN‐TREE) Salvador Brazil
| | - Federico Costa
- Instituto de Biologia Universidade Federal da Bahia Salvador Brasil
- Instituto de Pesquisas Gonçalo Moniz Fundação Oswaldo CruzMinistério da Saúde Salvador Bahia Brasil
- Instituto de Saúde Coletiva Universidade Federal da Bahia Salvador Brasil
- Department of Epidemiology of Microbial Diseases Yale School of Public Health New Haven CT USA
- Lancaster Medical School Lancaster University Lancaster UK
| | - Michael Begon
- Department of Evolution, Ecology and Behaviour University of Liverpool Liverpool UK
| | - Hussein Khalil
- Department of Wildlife Fish and Environmental Studies (VFM) Swedish University of Agricultural Sciences (SLU) Uppsala Sweden
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14
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Managing the Health of Captive Herds of Exotic Companion Mammals. Vet Clin North Am Exot Anim Pract 2021; 24:547-566. [PMID: 34366010 DOI: 10.1016/j.cvex.2021.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Common medical problems diagnosed and treated in individual companion exotic mammals are relevant in a herd-health setting. Many of these problems are often associated with poor husbandry and/or inappropriate nutrition. Rabbits, ferrets, chinchillas, and rodents have been domesticated alongside humans and an understanding of their ethology gives veterinarians a base knowledge in making recommendations for animals in their care. This article briefly reviews the ethology and husbandry in such species, but detailed needs are beyond the scope of this article.
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15
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Chafin TK, Zbinden ZD, Douglas MR, Martin BT, Middaugh CR, Gray MC, Ballard JR, Douglas ME. Spatial population genetics in heavily managed species: Separating patterns of historical translocation from contemporary gene flow in white-tailed deer. Evol Appl 2021; 14:1673-1689. [PMID: 34178112 PMCID: PMC8210790 DOI: 10.1111/eva.13233] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 03/10/2021] [Indexed: 01/16/2023] Open
Abstract
Approximately 100 years ago, unregulated harvest nearly eliminated white-tailed deer (Odocoileus virginianus) from eastern North America, which subsequently served to catalyze wildlife management as a national priority. An extensive stock-replenishment effort soon followed, with deer broadly translocated among states as a means of re-establishment. However, an unintended consequence was that natural patterns of gene flow became obscured and pretranslocation signatures of population structure were replaced. We applied cutting-edge molecular and biogeographic tools to disentangle genetic signatures of historical management from those reflecting spatially heterogeneous dispersal by evaluating 35,099 single nucleotide polymorphisms (SNPs) derived via reduced-representation genomic sequencing from 1143 deer sampled statewide in Arkansas. We then employed Simpson's diversity index to summarize ancestry assignments and visualize spatial genetic transitions. Using sub-sampled transects across these transitions, we tested clinal patterns across loci against theoretical expectations of their response under scenarios of re-colonization and restricted dispersal. Two salient results emerged: (A) Genetic signatures from historic translocations are demonstrably apparent; and (B) Geographic filters (major rivers; urban centers; highways) now act as inflection points for the distribution of this contemporary ancestry. These results yielded a statewide assessment of contemporary population structure in deer as driven by historic translocations as well as ongoing processes. In addition, the analytical framework employed herein to effectively decipher extant/historic drivers of deer distribution in Arkansas is also applicable for other biodiversity elements with similarly complex demographic histories.
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Affiliation(s)
- Tyler K. Chafin
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
- Present address:
Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderCOUSA
| | - Zachery D. Zbinden
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Marlis R. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Bradley T. Martin
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | | | - M. Cory Gray
- Research DivisionArkansas Game and Fish CommissionLittle RockARUSA
| | | | - Michael E. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
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16
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VanWallendael A, Alvarez M, Franks SJ. Patterns of population genomic diversity in the invasive Japanese knotweed species complex. AMERICAN JOURNAL OF BOTANY 2021; 108:857-868. [PMID: 33942283 DOI: 10.1002/ajb2.1653] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Invasive species are expected to undergo a reduction in genetic diversity due to founder effects, which should limit their ability to adapt to new habitats. Still, many invasive species achieve widespread distributions and dense populations. This paradox of invasions could potentially be overcome through multiple introductions or hybridization, both of which increase genetic diversity. We conducted a population genomics study of Japanese knotweed (Reynoutria japonica), which is a polyploid, clonally reproducing invasive species that has been notoriously successful worldwide despite supposedly low genetic diversity. METHODS We used genotyping by sequencing to collect 12,912 SNP markers from 88 samples collected at 38 locations across North America for the species complex. We used alignment-free k-mer hashing analysis in addition to traditional population genetic analyses to account for the challenges of genotyping polyploids. RESULTS Genotypes conformed to three genetic clusters, likely representing Japanese knotweed, giant knotweed, and hybrid bohemian knotweed. We found that, contrary to previous findings, the Japanese knotweed cluster had substantial genetic diversity, though it had no apparent genetic structure across the landscape. In contrast, giant knotweed and hybrids showed distinct population groups. We did not find evidence of isolation by distance in the species complex, likely reflecting the stochastic introduction history of this species complex. CONCLUSIONS The results indicate that clonal invasive species can show substantial genetic diversity and can be successful at colonizing a variety of habitats without showing evidence of local adaptation or genetic structure.
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Affiliation(s)
- Acer VanWallendael
- Biology Department, Fordham University, 441 E. Fordham Road, Bronx, NY, 10458, USA
- Biology Department, Duke University, 130 Science Drive, Durham, NC, 27708, USA
| | - Mariano Alvarez
- Biology Department, Duke University, 130 Science Drive, Durham, NC, 27708, USA
| | - Steven J Franks
- Biology Department, Fordham University, 441 E. Fordham Road, Bronx, NY, 10458, USA
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17
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Reese AT, Chadaideh KS, Diggins CE, Schell LD, Beckel M, Callahan P, Ryan R, Emery Thompson M, Carmody RN. Effects of domestication on the gut microbiota parallel those of human industrialization. eLife 2021; 10:60197. [PMID: 33755015 PMCID: PMC7987347 DOI: 10.7554/elife.60197] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 02/12/2021] [Indexed: 12/21/2022] Open
Abstract
Domesticated animals experienced profound changes in diet, environment, and social interactions that likely shaped their gut microbiota and were potentially analogous to ecological changes experienced by humans during industrialization. Comparing the gut microbiota of wild and domesticated mammals plus chimpanzees and humans, we found a strong signal of domestication in overall gut microbial community composition and similar changes in composition with domestication and industrialization. Reciprocal diet switches within mouse and canid dyads demonstrated the critical role of diet in shaping the domesticated gut microbiota. Notably, we succeeded in recovering wild-like microbiota in domesticated mice through experimental colonization. Although fundamentally different processes, we conclude that domestication and industrialization have impacted the gut microbiota in related ways, likely through shared ecological change. Our findings highlight the utility, and limitations, of domesticated animal models for human research and the importance of studying wild animals and non-industrialized humans for interrogating signals of host-microbial coevolution.
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Affiliation(s)
- Aspen T Reese
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States.,Society of Fellows, Harvard University, Cambridge, MA, United States
| | - Katia S Chadaideh
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Caroline E Diggins
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Laura D Schell
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Mark Beckel
- Wildlife Science Center, Stacy, MN, United States
| | | | - Roberta Ryan
- Wildlife Science Center, Stacy, MN, United States
| | | | - Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States
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18
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19
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Dennis EJ, El Hady A, Michaiel A, Clemens A, Tervo DRG, Voigts J, Datta SR. Systems Neuroscience of Natural Behaviors in Rodents. J Neurosci 2021; 41:911-919. [PMID: 33443081 PMCID: PMC7880287 DOI: 10.1523/jneurosci.1877-20.2020] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 11/21/2022] Open
Abstract
Animals evolved in complex environments, producing a wide range of behaviors, including navigation, foraging, prey capture, and conspecific interactions, which vary over timescales ranging from milliseconds to days. Historically, these behaviors have been the focus of study for ecology and ethology, while systems neuroscience has largely focused on short timescale behaviors that can be repeated thousands of times and occur in highly artificial environments. Thanks to recent advances in machine learning, miniaturization, and computation, it is newly possible to study freely moving animals in more natural conditions while applying systems techniques: performing temporally specific perturbations, modeling behavioral strategies, and recording from large numbers of neurons while animals are freely moving. The authors of this review are a group of scientists with deep appreciation for the common aims of systems neuroscience, ecology, and ethology. We believe it is an extremely exciting time to be a neuroscientist, as we have an opportunity to grow as a field, to embrace interdisciplinary, open, collaborative research to provide new insights and allow researchers to link knowledge across disciplines, species, and scales. Here we discuss the origins of ethology, ecology, and systems neuroscience in the context of our own work and highlight how combining approaches across these fields has provided fresh insights into our research. We hope this review facilitates some of these interactions and alliances and helps us all do even better science, together.
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Affiliation(s)
- Emily Jane Dennis
- Princeton University and Howard Hughes Medical Institute, Princeton, New Jersey, 08540
| | - Ahmed El Hady
- Princeton University and Howard Hughes Medical Institute, Princeton, New Jersey, 08540
| | | | - Ann Clemens
- University of Edinburgh, Edinburgh, Scotland, EH8 9JZ
| | | | - Jakob Voigts
- Massachusetts Institute of Technology, Cambridge, Massachusets, 02139
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20
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Schmidt TL, Swan T, Chung J, Karl S, Demok S, Yang Q, Field MA, Muzari MO, Ehlers G, Brugh M, Bellwood R, Horne P, Burkot TR, Ritchie S, Hoffmann AA. Spatial population genomics of a recent mosquito invasion. Mol Ecol 2021; 30:1174-1189. [PMID: 33421231 DOI: 10.1111/mec.15792] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/20/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023]
Abstract
Population genomic approaches can characterize dispersal across a single generation through to many generations in the past, bridging the gap between individual movement and intergenerational gene flow. These approaches are particularly useful when investigating dispersal in recently altered systems, where they provide a way of inferring long-distance dispersal between newly established populations and their interactions with existing populations. Human-mediated biological invasions represent such altered systems which can be investigated with appropriate study designs and analyses. Here we apply temporally restricted sampling and a range of population genomic approaches to investigate dispersal in a 2004 invasion of Aedes albopictus (the Asian tiger mosquito) in the Torres Strait Islands (TSI) of Australia. We sampled mosquitoes from 13 TSI villages simultaneously and genotyped 373 mosquitoes at genome-wide single nucleotide polymorphisms (SNPs): 331 from the TSI, 36 from Papua New Guinea (PNG) and four incursive mosquitoes detected in uninvaded regions. Within villages, spatial genetic structure varied substantially but overall displayed isolation by distance and a neighbourhood size of 232-577. Close kin dyads revealed recent movement between islands 31-203 km apart, and deep learning inferences showed incursive Ae. albopictus had travelled to uninvaded regions from both adjacent and nonadjacent islands. Private alleles and a co-ancestry matrix indicated direct gene flow from PNG into nearby islands. Outlier analyses also detected four linked alleles introgressed from PNG, with the alleles surrounding 12 resistance-associated cytochrome P450 genes. By treating dispersal as both an intergenerational process and a set of discrete events, we describe a highly interconnected invasive system.
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Affiliation(s)
- Thomas L Schmidt
- Pest and Environmental Adaptation Research Group, School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Tom Swan
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, Cairns, QLD, Australia
| | - Jessica Chung
- Pest and Environmental Adaptation Research Group, School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia.,Melbourne Bioinformatics, University of Melbourne, Parkville, VIC, Australia
| | - Stephan Karl
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Samuel Demok
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Qiong Yang
- Pest and Environmental Adaptation Research Group, School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Matt A Field
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Mutizwa Odwell Muzari
- Medical Entomology, Tropical Public Health Services Cairns, Cairns and Hinterland Hospital & Health Services, Cairns, QLD, Australia
| | - Gerhard Ehlers
- Medical Entomology, Tropical Public Health Services Cairns, Cairns and Hinterland Hospital & Health Services, Cairns, QLD, Australia
| | - Mathew Brugh
- Medical Entomology, Tropical Public Health Services Cairns, Cairns and Hinterland Hospital & Health Services, Cairns, QLD, Australia
| | - Rodney Bellwood
- Medical Entomology, Tropical Public Health Services Cairns, Cairns and Hinterland Hospital & Health Services, Cairns, QLD, Australia
| | - Peter Horne
- Medical Entomology, Tropical Public Health Services Cairns, Cairns and Hinterland Hospital & Health Services, Cairns, QLD, Australia
| | - Thomas R Burkot
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Scott Ritchie
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Cairns, QLD, Australia.,Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia
| | - Ary A Hoffmann
- Pest and Environmental Adaptation Research Group, School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
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21
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Fusco NA, Pehek E, Munshi‐South J. Urbanization reduces gene flow but not genetic diversity of stream salamander populations in the New York City metropolitan area. Evol Appl 2021; 14:99-116. [PMID: 33519959 PMCID: PMC7819553 DOI: 10.1111/eva.13025] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022] Open
Abstract
Natural landscape heterogeneity and barriers resulting from urbanization can reduce genetic connectivity between populations. The evolutionary, demographic, and ecological effects of reduced connectivity may lead to population isolation and ultimately extinction. Alteration to the terrestrial and aquatic environment caused by urban influence can affect gene flow, specifically for stream salamanders who depend on both landscapes for survival and reproduction. To examine how urbanization affects a relatively common stream salamander species, we compared genetic connectivity of Eurycea bislineata (northern two-lined salamander) populations within and between streams in an urban, suburban, and rural habitat around the New York City (NYC) metropolitan area. We report reduced genetic connectivity between streams within the urban landscape found to correspond with potential barriers to gene flow, that is, areas with more dense urbanization (roadways, industrial buildings, and residential housing). The suburban populations also exhibited areas of reduced connectivity correlated with areas of greater human land use and greater connectivity within a preserve protected from development. Connectivity was relatively high among neighboring rural streams, but a major roadway corresponded with genetic breaks even though the habitat contained more connected green space overall. Despite greater human disturbance across the landscape, urban and suburban salamander populations maintained comparable levels of genetic diversity to their rural counterparts. Yet small effective population size in the urban habitats yielded a high probability of loss of heterozygosity due to genetic drift in the future. In conclusion, urbanization impacted connectivity among stream salamander populations where its continual influence may eventually hinder population persistence for this native species in urban habitats.
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Affiliation(s)
| | - Ellen Pehek
- Natural Resources GroupNew York City Department of Parks & RecreationNew YorkNYUSA
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22
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Carlen E, Munshi‐South J. Widespread genetic connectivity of feral pigeons across the Northeastern megacity. Evol Appl 2021; 14:150-162. [PMID: 33519962 PMCID: PMC7819573 DOI: 10.1111/eva.12972] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/31/2022] Open
Abstract
Urbanization may restrict, facilitate, or have no effect on gene flow, depending on the organism and extent of urbanization. In human commensals, with high dispersal ability, urbanization can facilitate gene flow by providing continuous suitable habitat across a wide range. Additionally, suburban or rural areas with lower human population density may act as a barrier to gene flow for these human commensals. Spatial population genetic approaches provide a means to understand genetic connectivity across geographically expansive areas that encompass multiple metropolitan areas. Here, we examined the spatial genetic patterns of feral pigeons (Columba livia) living in cities in the eastern United States. We focused our sampling on the Northeastern megacity, which is a region covering six large cities (Boston, Providence, New York City, Philadelphia, Baltimore, and Washington, DC). We performed ddRAD-Seqon 473 samples, recovered 35,200 SNPs, and then used multiple evolutionary clustering analyses to investigate population structuring. These analyses revealed that pigeons formed two genetic clusters-a northern cluster containing samples from Boston and Providence and a southern cluster containing all other samples. This substructuring is possibly due to reduced urbanization across coastal Connecticut that separates Boston and Providence from New York and mid-Atlantic cities. We found that pairs of pigeons within 25 km are highly related (Mantel r = 0.217, p = .001) and that beyond 50 km, pigeons are no more related than they would be at random. Our analysis detected higher-than-expected gene flow under an isolation by distance model within each city. We conclude that the extreme urbanization characteristic of the Northeastern megacity is likely facilitating gene flow in feral pigeons.
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Des Roches S, Brans KI, Lambert MR, Rivkin LR, Savage AM, Schell CJ, Correa C, De Meester L, Diamond SE, Grimm NB, Harris NC, Govaert L, Hendry AP, Johnson MTJ, Munshi‐South J, Palkovacs EP, Szulkin M, Urban MC, Verrelli BC, Alberti M. Socio-eco-evolutionary dynamics in cities. Evol Appl 2021; 14:248-267. [PMID: 33519968 PMCID: PMC7819562 DOI: 10.1111/eva.13065] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/22/2020] [Accepted: 06/29/2020] [Indexed: 12/31/2022] Open
Abstract
Cities are uniquely complex systems regulated by interactions and feedbacks between nature and human society. Characteristics of human society-including culture, economics, technology and politics-underlie social patterns and activity, creating a heterogeneous environment that can influence and be influenced by both ecological and evolutionary processes. Increasing research on urban ecology and evolutionary biology has coincided with growing interest in eco-evolutionary dynamics, which encompasses the interactions and reciprocal feedbacks between evolution and ecology. Research on both urban evolutionary biology and eco-evolutionary dynamics frequently focuses on contemporary evolution of species that have potentially substantial ecological-and even social-significance. Still, little work fully integrates urban evolutionary biology and eco-evolutionary dynamics, and rarely do researchers in either of these fields fully consider the role of human social patterns and processes. Because cities are fundamentally regulated by human activities, are inherently interconnected and are frequently undergoing social and economic transformation, they represent an opportunity for ecologists and evolutionary biologists to study urban "socio-eco-evolutionary dynamics." Through this new framework, we encourage researchers of urban ecology and evolution to fully integrate human social drivers and feedbacks to increase understanding and conservation of ecosystems, their functions and their contributions to people within and outside cities.
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Affiliation(s)
- Simone Des Roches
- Department of Urban Design and PlanningUniversity of WashingtonSeattleWAUSA
| | - Kristien I. Brans
- Department of BiologyLaboratory of Aquatic Ecology, Evolution and ConservationKU LeuvenLeuvenBelgium
| | - Max R. Lambert
- Department of Environmental Science, Policy, and ManagementUniversity of CaliforniaBerkeleyCAUSA
| | - L. Ruth Rivkin
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
- Department of BiologyUniversity of Toronto MississaugaMississaugaONCanada
- Centre for Urban EnvironmentsUniversity of Toronto MississaugaMississaugaONCanada
| | - Amy Marie Savage
- Department of BiologyCenter for Computational and Integrative BiologyRutgers UniversityCamdenNJUSA
| | - Christopher J. Schell
- School of Interdisciplinary Arts and SciencesUniversity of Washington TacomaTacomaWAUSA
| | - Cristian Correa
- Facultad de Ciencias Forestales y Recursos NaturalesInstituto de Conservación Biodiversidad y TerritorioUniversidad Austral de ChileValdiviaChile
- Centro de Humedales Río CrucesUniversidad Austral de ChileValdiviaChile
| | - Luc De Meester
- Department of BiologyLaboratory of Aquatic Ecology, Evolution and ConservationKU LeuvenLeuvenBelgium
- Institute of BiologyFreie UniversitätBerlinGermany
- Leibniz Institut für Gewasserökologie und BinnenfischereiBerlinGermany
| | - Sarah E. Diamond
- Department of BiologyCase Western Reserve UniversityClevelandOHUSA
| | - Nancy B. Grimm
- School of Life SciencesArizona State UniversityTempeAZUSA
| | - Nyeema C. Harris
- Applied Wildlife Ecology Lab, Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
| | - Lynn Govaert
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
- Department of Aquatic EcologySwiss Federal Institute of Aquatic Science and TechnologyDuebendorfSwitzerland
| | - Andrew P. Hendry
- Department of BiologyRedpath MuseumMcGill UniversityMontrealQCCanada
| | - Marc T. J. Johnson
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
- Department of BiologyUniversity of Toronto MississaugaMississaugaONCanada
- Centre for Urban EnvironmentsUniversity of Toronto MississaugaMississaugaONCanada
| | - Jason Munshi‐South
- Department of Biological Sciences and Louis Calder CenterFordham UniversityArmonkNYUSA
| | - Eric P. Palkovacs
- Department of Ecology & Evolutionary BiologyUniversity of CaliforniaSanta CruzCAUSA
| | - Marta Szulkin
- Centre of New TechnologiesUniversity of WarsawWarsawPoland
| | - Mark C. Urban
- Center of Biological Risk and Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsCTUSA
| | - Brian C. Verrelli
- Center for Life Sciences EducationVirginia Commonwealth UniversityRichmondVAUSA
| | - Marina Alberti
- Department of Urban Design and PlanningUniversity of WashingtonSeattleWAUSA
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24
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Byers KA, Booker TR, Combs M, Himsworth CG, Munshi‐South J, Patrick DM, Whitlock MC. Using genetic relatedness to understand heterogeneous distributions of urban rat-associated pathogens. Evol Appl 2021; 14:198-209. [PMID: 33519965 PMCID: PMC7819557 DOI: 10.1111/eva.13049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/12/2020] [Accepted: 06/14/2020] [Indexed: 11/28/2022] Open
Abstract
Urban Norway rats (Rattus norvegicus) carry several pathogens transmissible to people. However, pathogen prevalence can vary across fine spatial scales (i.e., by city block). Using a population genomics approach, we sought to describe rat movement patterns across an urban landscape and to evaluate whether these patterns align with pathogen distributions. We genotyped 605 rats from a single neighborhood in Vancouver, Canada, and used 1,495 genome-wide single nucleotide polymorphisms to identify parent-offspring and sibling relationships using pedigree analysis. We resolved 1,246 pairs of relatives, of which only 1% of pairs were captured in different city blocks. Relatives were primarily caught within 33 meters of each other leading to a highly leptokurtic distribution of dispersal distances. Using binomial generalized linear mixed models, we evaluated whether family relationships influenced rat pathogen status with the bacterial pathogens Leptospira interrogans, Bartonella tribocorum, and Clostridium difficile, and found that an individual's pathogen status was not predicted any better by including disease status of related rats. The spatial clustering of related rats and their pathogens lends support to the hypothesis that spatially restricted movement promotes the heterogeneous patterns of pathogen prevalence evidenced in this population. Our findings also highlight the utility of evolutionary tools to understand movement and rat-associated health risks in urban landscapes.
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Affiliation(s)
- Kaylee A. Byers
- Department of Interdisciplinary StudiesUniversity of British ColumbiaVancouverBCCanada
- Biodiversity Research CentreUniversity of British ColumbiaVancouverBCCanada
- Canadian Wildlife Health CooperativeAnimal Health CentreBritish Columbia Ministry of AgricultureAbbotsfordBCCanada
| | - Tom R. Booker
- Biodiversity Research CentreUniversity of British ColumbiaVancouverBCCanada
| | - Matthew Combs
- Department of Ecology, Evolution and Environmental BiologyColumbia UniversityNew YorkNYUSA
| | - Chelsea G. Himsworth
- Canadian Wildlife Health CooperativeAnimal Health CentreBritish Columbia Ministry of AgricultureAbbotsfordBCCanada
- School of Population and Public HealthUniversity of British ColumbiaVancouverBCCanada
- Animal Health CentreBritish Columbia Ministry of AgricultureAbbotsfordBCCanada
| | - Jason Munshi‐South
- Louis Calder Center‐Biological Field Station and Department of Biological ScienceFordham UniversityArmonkNYUSA
| | - David M. Patrick
- School of Population and Public HealthUniversity of British ColumbiaVancouverBCCanada
- British Columbia Centre for Disease ControlVancouverBCCanada
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25
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Gender Inequality and Symbolic Violence in Women’s Access to Family Land in the Southern Highlands of Tanzania. LAND 2020. [DOI: 10.3390/land9110468] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We set out to unveil gender inequality with respect to women’s access to family land following the surge in tree-planting in selected villages in the Southern Highlands of Tanzania. Specifically, the study describes land-transaction procedures at the household level and shows how the lack of women’s involvement in such land transactions affect their access to and control over family lands. Gender inequality is portrayed in a variety of social and economic activities, with women being deprived of access to, control over, and ownership of land. Although the current land laws address gender inequalities pertaining to women’s access to, ownership of, and control over land, the impact of such reforms has been minimal. Drawing on Bourdieu’s concept of symbolic violence, we reveal how women suffer symbolic violence through traditional practices of land management and administration. Societies in the studied villages are strongly patriarchal, with men being dominant and women subordinate. In such a patriarchal system, women’s empowerment is urgent. Women require knowledge and awareness of the laws and regulations that affirm their rights not only to family lands, but also to participation in decision-making processes regarding family assets. We recommend non-oppressive approaches to natural-resource management. As such, we call for existing authorities at the village and district levels, Non Governmental Organisations (NGOs) and legal bodies to promote gender equality in land-management practices. We also advocate dialectical communication between women and men in order to reveal and heal practices of symbolic violence, and enhance gender equality in respect of access to land and its control and ownership in villages in the Southern Highlands of Tanzania. Effective implementation of existing land laws and regulations that address gender inequality and associated violence is unavoidable.
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26
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Harpak A, Garud N, Rosenberg NA, Petrov DA, Combs M, Pennings PS, Munshi-South J. Genetic Adaptation in New York City Rats. Genome Biol Evol 2020; 13:5991490. [PMID: 33211096 PMCID: PMC7851592 DOI: 10.1093/gbe/evaa247] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2020] [Indexed: 02/06/2023] Open
Abstract
Brown rats (Rattus norvegicus) thrive in urban environments by navigating the anthropocentric environment and taking advantage of human resources and by-products. From the human perspective, rats are a chronic problem that causes billions of dollars in damage to agriculture, health, and infrastructure. Did genetic adaptation play a role in the spread of rats in cities? To approach this question, we collected whole-genome sequences from 29 brown rats from New York City (NYC) and scanned for genetic signatures of adaptation. We tested for 1) high-frequency, extended haplotypes that could indicate selective sweeps and 2) loci of extreme genetic differentiation between the NYC sample and a sample from the presumed ancestral range of brown rats in northeast China. We found candidate selective sweeps near or inside genes associated with metabolism, diet, the nervous system, and locomotory behavior. Patterns of differentiation between NYC and Chinese rats at putative sweep loci suggest that many sweeps began after the split from the ancestral population. Together, our results suggest several hypotheses on adaptation in rats living in proximity to humans.
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Affiliation(s)
- Arbel Harpak
- Department of Biological Sciences, Columbia University
| | - Nandita Garud
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles
| | | | | | - Matthew Combs
- Department of Biological Sciences, Fordham University.,Department of Ecology, Evolution and Environmental Biology, Columbia University
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27
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Parker LD, Hawkins MTR, Camacho-Sanchez M, Campana MG, West-Roberts JA, Wilbert TR, Lim HC, Rockwood LL, Leonard JA, Maldonado JE. Little genetic structure in a Bornean endemic small mammal across a steep ecological gradient. Mol Ecol 2020; 29:4074-4090. [PMID: 32911576 DOI: 10.1111/mec.15626] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/14/2020] [Accepted: 08/20/2020] [Indexed: 01/02/2023]
Abstract
Janzen's influential "mountain passes are higher in the tropics" hypothesis predicts restricted gene flow and genetic isolation among populations spanning elevational gradients in the tropics. Few studies have tested this prediction, and studies that focus on population genetic structure in Southeast Asia are particularly underrepresented in the literature. Here, we test the hypothesis that mountain treeshrews (Tupaia montana) exhibit limited dispersal across their broad elevational range which spans ~2,300 m on two peaks in Kinabalu National Park (KNP) in Borneo: Mt Tambuyukon (MT) and Mt Kinabalu (MK). We sampled 83 individuals across elevations on both peaks and performed population genomics analyses on mitogenomes and single nucleotide polymorphisms from 4,106 ultraconserved element loci. We detected weak genetic structure and infer gene flow both across elevations and between peaks. We found higher genetic differentiation on MT than MK despite its lower elevation and associated environmental variation. This implies that, contrary to our hypothesis, genetic structure in this system is not primarily shaped by elevation. We propose that this pattern may instead be the result of historical processes and limited upslope gene flow on MT. Importantly, our results serve as a foundational estimate of genetic diversity and population structure from which to track potential future effects of climate change on mountain treeshrews in KNP, an important conservation stronghold for the mountain treeshrew and other montane species.
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Affiliation(s)
- Lillian D Parker
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, DC, USA.,School of Systems Biology, George Mason University, Fairfax, VA, USA
| | - Melissa T R Hawkins
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, DC, USA.,Division of Mammals, Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
| | - Miguel Camacho-Sanchez
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, DC, USA.,School of Systems Biology, George Mason University, Fairfax, VA, USA.,Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
| | - Jacob A West-Roberts
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, DC, USA.,Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Tammy R Wilbert
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, DC, USA
| | - Haw Chuan Lim
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, DC, USA.,School of Systems Biology, George Mason University, Fairfax, VA, USA
| | - Larry L Rockwood
- School of Systems Biology, George Mason University, Fairfax, VA, USA
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, DC, USA.,School of Systems Biology, George Mason University, Fairfax, VA, USA.,Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
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28
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Murray MH, Fidino M, Fyffe R, Byers KA, Pettengill JB, Sondgeroth KS, Killion H, Magle SB, Rios MJ, Ortinau N, Santymire RM. City sanitation and socioeconomics predict rat zoonotic infection across diverse neighbourhoods. Zoonoses Public Health 2020; 67:673-683. [PMID: 32583624 DOI: 10.1111/zph.12748] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/11/2020] [Accepted: 05/25/2020] [Indexed: 01/06/2023]
Abstract
Rat-associated zoonoses transmitted through faeces or urine are of particular concern for public health because environmental exposure in homes and businesses may be frequent and undetected. To identify times and locations with greater public health risks from rats, we investigated whether rat characteristics, environmental features, socioeconomic factors, or season could predict rat infection risk across diverse urban neighbourhoods. In partnership with a pest management company, we sampled rats in 13 community areas along an income gradient in Chicago, a large city where concern about rats has increased in recent years. We collected kidneys for Leptospira spp. testing and colon contents for aerobic bacteria such as Salmonella spp. and Escherichia coli. Of 202 sampled rats, 5% carried Leptospira spp. and 22% carried E. coli. Rats were significantly more likely to carry Leptospira spp. on blocks with more standing water complaints in higher-income neighbourhoods (OR = 6.74, 95% CI: 1.54-29.39). Rats were significantly more likely to carry E. coli on blocks with more food vendors (OR = 9.94, 2.27-43.50) particularly in low-income neighbourhoods (OR = 0.26, 0.09-0.82) and in the spring (OR = 15.96, 2.90-88.62). We detected a high diversity of E. coli serovars but none contained major virulence factors. These associations between environmental features related to sanitation and infection risk in rats support transmission through water for Leptospira spp. and faecal-oral transmission for E. coli. We also found opposing relationships between zoonotic infection risk and income for these two pathogens. Thus, our results highlight the importance of sanitation for predicting zoonotic disease risks and including diverse urban areas in pathogen surveillance to mitigate public health risks from rats.
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Affiliation(s)
- Maureen H Murray
- Department of Conservation and Science, Lincoln Park Zoo, Chicago, IL, USA
| | - Mason Fidino
- Department of Conservation and Science, Lincoln Park Zoo, Chicago, IL, USA
| | | | - Kaylee A Byers
- Department of Interdisciplinary Studies, University of British Columbia, Vancouver, BC, Canada.,Canadian Wildlife Health Cooperative, Animal Health Centre, Abbotsford, BC, Canada
| | - James B Pettengill
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, MD, USA
| | | | | | - Seth B Magle
- Department of Conservation and Science, Lincoln Park Zoo, Chicago, IL, USA
| | - Maria Jazmin Rios
- Department of Conservation and Science, Lincoln Park Zoo, Chicago, IL, USA
| | - Nora Ortinau
- School of Public Health, University of Illinois at Chicago, Chicago, IL, USA
| | - Rachel M Santymire
- Department of Conservation and Science, Lincoln Park Zoo, Chicago, IL, USA
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29
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Brewer VN, Lane SJ, Sewall KB, Mabry KE. Effects of low-density urbanization on genetic structure in the Song Sparrow. PLoS One 2020; 15:e0234008. [PMID: 32530950 PMCID: PMC7292390 DOI: 10.1371/journal.pone.0234008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 05/15/2020] [Indexed: 11/19/2022] Open
Abstract
Urbanization fragments landscapes and can impede the movement of organisms through their environment, which can decrease population connectivity. Reduction in connectivity influences gene flow and allele frequencies, and can lead to a reduction in genetic diversity and the fixation of certain alleles, with potential negative effects for populations. Previous studies have detected effects of urbanization on genetic diversity and structure in terrestrial animals living in landscapes that vary in their degree of urbanization, even over very short distances. We investigated the effects of low-intensity urbanization on genetic diversity and genetic structure in Song Sparrows (Melospiza melodia). We captured 208 Song Sparrows at seven sites along a gradient of urbanization in and around Blacksburg, VA, USA, then genotyped them using a panel of fifteen polymorphic microsatellite loci. We found that genetic diversity was comparable among the seven study sites, and there was no evidence of genetic structuring among sites. These findings suggest that over a gradient of urbanization characterized by low density urban development, Song Sparrows likely exist in a single panmictic population.
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Affiliation(s)
- Valerie N. Brewer
- Department of Biology, New Mexico State University, Las Cruces, NM, United States of America
| | - Samuel J. Lane
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States of America
| | - Kendra B. Sewall
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States of America
| | - Karen E. Mabry
- Department of Biology, New Mexico State University, Las Cruces, NM, United States of America
- * E-mail:
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30
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Zhao L, Zhang JX, Zhang YH. Genetic boundary and gene flow between 2 parapatric subspecies of brown rats. Curr Zool 2020; 66:677-688. [PMID: 33391367 PMCID: PMC7769575 DOI: 10.1093/cz/zoaa027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/30/2020] [Indexed: 12/30/2022] Open
Abstract
Two parapatric Rattus norvegicus subspecies, R. n. humiliatus (RNH) and R. n. caraco (RNC), are classified according to morphological divergence and are mainly distributed in North and Northeast China. Here, we aimed to explore the population genetic structure, genetic boundary, and gene flow in these rats using 16 microsatellite loci. Structure analysis and principal component analysis revealed 3 ancestral clusters. We found that the intermediate cluster exhibited higher genetic diversity and a lower inbreeding coefficient than the other 2 clusters. The genetic differentiation between the 3 clusters was significant but weak, with a higher FST value being observed between the clusters on both sides. The subspecies boundary inferred from microsatellite markers may indicate the existence of an admixture or hybridization area covering Liaoning, Inner Mongolia, and Jilin Provinces, rather than corresponding to the administrative provincial boundaries between Liaoning and Jilin. The RNH and RNC subspecies presented moderate gene exchange and an asymmetric bidirectional gene flow pattern, with higher gene flow from the RNH subspecies to the RNC subspecies, constraining speciation. Such genetic characteristics might be explained by biological processes such as dispersal ability, mate choice, and dynamic lineage boundaries.
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Affiliation(s)
- Lei Zhao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian-Xu Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yao-Hua Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China
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31
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Puckett EE, Sherratt E, Combs M, Carlen EJ, Harcourt‐Smith W, Munshi‐South J. Variation in brown rat cranial shape shows directional selection over 120 years in New York City. Ecol Evol 2020; 10:4739-4748. [PMID: 32551057 PMCID: PMC7297766 DOI: 10.1002/ece3.6228] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/02/2020] [Accepted: 03/06/2020] [Indexed: 01/22/2023] Open
Abstract
Urbanization exposes species to novel environments and selection pressures that may change morphological traits within a population. We investigated how the shape and size of crania and mandibles changed over time within a population of brown rats (Rattus norvegicus) living in Manhattan, New York, USA, a highly urbanized environment. We measured 3D landmarks on the cranium and mandible of 62 adult individuals sampled in the 1890s and 2010s. Static allometry explained approximately 22% of shape variation in crania and mandible datasets, while time accounted for approximately 14% of variation. We did not observe significant changes in skull size through time or between the sexes. Estimating the P-matrix revealed that directional selection explained temporal change of the crania but not the mandible. Specifically, rats from the 2010s had longer noses and shorter upper molar tooth rows, traits identified as adaptive to colder environments and higher quality or softer diets, respectively. Our results highlight the continual evolution to selection pressures. We acknowledge that urban selection pressures impacting cranial shape likely began in Europe prior to the introduction of rats to Manhattan. Yet, our study period spanned changes in intensity of artificial lighting, human population density, and human diet, thereby altering various aspects of rat ecology and hence pressures on the skull.
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Affiliation(s)
- Emily E. Puckett
- Department of Biological SciencesUniversity of MemphisMemphisTNUSA
- Department of Biological SciencesLouis Calder Center‐Biological Field StationFordham UniversityArmonkNYUSA
| | - Emma Sherratt
- Department of Ecology and Evolutionary BiologySchool of Biological SciencesThe University of AdelaideAdelaideSAAustralia
| | - Matthew Combs
- Department of Biological SciencesLouis Calder Center‐Biological Field StationFordham UniversityArmonkNYUSA
- Present address:
Department of Ecology, Evolution and Environmental BiologyColumbia UniversityNew YorkNYUSA
| | - Elizabeth J. Carlen
- Department of Biological SciencesLouis Calder Center‐Biological Field StationFordham UniversityArmonkNYUSA
| | - William Harcourt‐Smith
- Division of PaleontologyAmerican Museum of Natural HistoryNew YorkNYUSA
- Department of AnthropologyThe Graduate CenterCity University of New YorkNew YorkNYUSA
- Lehman CollegeCity University of New YorkBronxNYUSA
| | - Jason Munshi‐South
- Department of Biological SciencesLouis Calder Center‐Biological Field StationFordham UniversityArmonkNYUSA
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32
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Lambert MR, Donihue CM. Urban biodiversity management using evolutionary tools. Nat Ecol Evol 2020; 4:903-910. [PMID: 32393868 DOI: 10.1038/s41559-020-1193-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 03/20/2020] [Indexed: 01/06/2023]
Abstract
Cities are fully functioning ecosystems and are home to no-analogue communities of species that interact with each other and which are subject to novel urban stressors. As such, biodiversity can evolve in response to these new urban conditions, making urban species a moving target for conservation and management efforts. An evolving urban biodiversity necessitates integrating evolutionary insights into management for these efforts to be successful in a dynamic urban milieu. Here we present a framework for categorizing urban biodiversity from a management perspective. We then discuss a suite of example management tools and their potential evolutionary implications-both their opportunities for and potential consequence to management. Urban ecosystems are proliferating but, far from being ecological lost causes, they may provide unique insights and opportunities for biodiversity conservation. Determining how to achieve urban biodiversity priorities while managing pest species requires evolutionary thinking.
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Affiliation(s)
- Max R Lambert
- Department of Environmental Science, Policy and Management, UC Berkeley, Berkeley, CA, USA.
| | - Colin M Donihue
- Department of Biology, Washington University, St Louis, MO, USA
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33
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Adducci A, Jasperse J, Riley S, Brown J, Honeycutt R, Monzón J. Urban coyotes are genetically distinct from coyotes in natural habitats. JOURNAL OF URBAN ECOLOGY 2020. [DOI: 10.1093/jue/juaa010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
AbstractUrbanization is increasing throughout the world, transforming natural habitats. Coyotes (Canis latrans) are found in highly urban, suburban, rural and undeveloped mountainous habitats, making them an exemplary model organism to investigate the effects of urbanization on animals. We hypothesized that coyotes in natural habitats are more genetically related to distant coyotes in similar natural habitats and less related to coyotes in urban areas due to natal habitat-biased dispersal. We also hypothesized that increasing urbanization would result in decreased genetic diversity due to habitat fragmentation, dispersal barriers and genetic drift. We analyzed 10 microsatellite genetic markers from 125 individual coyotes sampled across a spectrum of highly urban to highly natural areas in southern California. Most coyotes clustered into four distinct genetic populations, whereas others appeared to have admixed ancestry. Three genetic populations were associated primarily with urban habitats in Los Angeles and Orange Counties. In contrast, the remaining population was associated with more naturally vegetated land near the surrounding mountains. Coyotes living in natural areas formed a genetically distinct cluster despite long geographic distances separating them. Genetic diversity was negatively associated with urban/suburban land cover and local road density, and positively associated with the relative amount of natural vegetation. These results indicate that genetic differentiation and loss of genetic diversity coincided with the extremely rapid expansion of Greater Los Angeles throughout the 1900s. Thus, urbanization reduces gene flow and erodes genetic diversity even in a habitat generalist thought to be minimally impacted by land development.
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Affiliation(s)
- Anthony Adducci
- Natural Science Division, Pepperdine University, 24255 Pacific Coast Highway, Malibu, CA 90263, USA
| | - Jeremy Jasperse
- Natural Science Division, Pepperdine University, 24255 Pacific Coast Highway, Malibu, CA 90263, USA
| | - Seth Riley
- Santa Monica Mountains National Recreation Area, National Park Service, 401 West Hillcrest Drive, Thousand Oaks, CA 91360, USA
| | - Justin Brown
- Santa Monica Mountains National Recreation Area, National Park Service, 401 West Hillcrest Drive, Thousand Oaks, CA 91360, USA
| | - Rodney Honeycutt
- Natural Science Division, Pepperdine University, 24255 Pacific Coast Highway, Malibu, CA 90263, USA
| | - Javier Monzón
- Natural Science Division, Pepperdine University, 24255 Pacific Coast Highway, Malibu, CA 90263, USA
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34
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Browett SS, O'Meara DB, McDevitt AD. Genetic tools in the management of invasive mammals: recent trends and future perspectives. Mamm Rev 2020. [DOI: 10.1111/mam.12189] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Samuel S. Browett
- Ecosystems and Environment Research Centre School of Science, Engineering and Environment University of Salford Salford M5 4WTUK
| | - Denise B. O'Meara
- Molecular Ecology Research Group Eco‐Innovation Research Centre School of Science and Computing Waterford Institute of Technology Waterford Ireland
| | - Allan D. McDevitt
- Ecosystems and Environment Research Centre School of Science, Engineering and Environment University of Salford Salford M5 4WTUK
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Reed EMX, Serr ME, Maurer AS, Burford Reiskind MO. Gridlock and beltways: the genetic context of urban invasions. Oecologia 2020; 192:615-628. [PMID: 32056021 DOI: 10.1007/s00442-020-04614-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 01/30/2020] [Indexed: 01/16/2023]
Abstract
The rapid expansion of urban land across the globe presents new and numerous opportunities for invasive species to spread and flourish. Ecologists historically rejected urban ecosystems as important environments for ecology and evolution research but are beginning to recognize the importance of these systems in shaping the biology of invasion. Urbanization can aid the introduction, establishment, and spread of invaders, and these processes have substantial consequences on native species and ecosystems. Therefore, it is valuable to understand how urban areas influence populations at all stages in the invasion process. Population genetic tools are essential to explore the driving forces of invasive species dispersal, connectivity, and adaptation within cities. In this review, we synthesize current research about the influence of urban landscapes on invasion genetics dynamics. We conclude that urban areas are not only points of entry for many invasive species, they also facilitate population establishment, are pools for genetic diversity, and provide corridors for further spread both within and out of cities. We recommend the continued use of genetic studies to inform invasive species management and to understand the underlying ecological and evolutionary processes governing successful invasion.
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Affiliation(s)
- E M X Reed
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
| | - M E Serr
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - A S Maurer
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - M O Burford Reiskind
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
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36
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Maigret TA, Cox JJ, Weisrock DW. A spatial genomic approach identifies time lags and historical barriers to gene flow in a rapidly fragmenting Appalachian landscape. Mol Ecol 2020; 29:673-685. [PMID: 31981245 DOI: 10.1111/mec.15362] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/03/2020] [Accepted: 01/13/2020] [Indexed: 12/15/2022]
Abstract
The resolution offered by genomic data sets coupled with recently developed spatially informed analyses are allowing researchers to quantify population structure at increasingly fine temporal and spatial scales. However, both empirical research and conservation measures have been limited by questions regarding the impacts of data set size, data quality thresholds and the timescale at which barriers to gene flow become detectable. Here, we used restriction site associated DNA sequencing to generate a 2,140 single nucleotide polymorphism (SNP) data set for the copperhead snake (Agkistrodon contortrix) and address the population genomic impacts of recent and widespread landscape modification across an ~1,000-km2 region of eastern Kentucky, USA. Nonspatial population-based assignment and clustering methods supported little to no population structure. However, using individual-based spatial autocorrelation approaches we found evidence for genetic structuring which closely follows the path of a historically important highway which experienced high traffic volumes from c. 1920 to 1970 before losing most traffic to a newly constructed alternative route. We found no similar spatial genomic signatures associated with more recently constructed highways or surface mining activity, although a time lag effect may be responsible for the lack of any emergent spatial genetic patterns. Subsampling of our SNP data set suggested that similar results could be obtained with as few as 250 SNPs, and a range of thresholds for missing data exhibited limited impacts on the spatial patterns we detected. While we were not able to estimate relative effects of land uses or precise time lags, our findings highlight the importance of temporal factors in landscape genetics approaches, and suggest the potential advantages of genomic data sets and fine-scale, spatially informed approaches for quantifying subtle genetic patterns in temporally complex landscapes.
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Affiliation(s)
- Thomas A Maigret
- Department of Biology, University of Kentucky, Lexington, KY, USA.,Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY, USA
| | - John J Cox
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY, USA
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37
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Kimmig SE, Beninde J, Brandt M, Schleimer A, Kramer-Schadt S, Hofer H, Börner K, Schulze C, Wittstatt U, Heddergott M, Halczok T, Staubach C, Frantz AC. Beyond the landscape: Resistance modelling infers physical and behavioural gene flow barriers to a mobile carnivore across a metropolitan area. Mol Ecol 2020; 29:466-484. [PMID: 31880844 DOI: 10.1111/mec.15345] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 12/13/2019] [Accepted: 12/16/2019] [Indexed: 01/02/2023]
Abstract
Urbanization affects key aspects of wildlife ecology. Dispersal in urban wildlife species may be impacted by geographical barriers but also by a species' inherent behavioural variability. There are no functional connectivity analyses using continuous individual-based sampling across an urban-rural continuum that would allow a thorough assessment of the relative importance of physical and behavioural dispersal barriers. We used 16 microsatellite loci to genotype 374 red foxes (Vulpes vulpes) from the city of Berlin and surrounding rural regions in Brandenburg in order to study genetic structure and dispersal behaviour of a mobile carnivore across the urban-rural landscape. We assessed functional connectivity by applying an individual-based landscape genetic optimization procedure. Three commonly used genetic distance measures yielded different model selection results, with only the results of an eigenvector-based multivariate analysis reasonably explaining genetic differentiation patterns. Genetic clustering methods and landscape resistance modelling supported the presence of an urban population with reduced dispersal across the city border. Artificial structures (railways, motorways) served as main dispersal corridors within the cityscape, yet urban foxes avoided densely built-up areas. We show that despite their ubiquitous presence in urban areas, their mobility and behavioural plasticity, foxes were affected in their dispersal by anthropogenic presence. Distinguishing between man-made structures and sites of human activity, rather than between natural and artificial structures, is thus essential for better understanding urban fox dispersal. This differentiation may also help to understand dispersal of other urban wildlife and to predict how behaviour can shape population genetic structure beyond physical barriers.
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Affiliation(s)
- Sophia E Kimmig
- Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Joscha Beninde
- Department of Biogeography, Trier University, Trier, Germany.,LA Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Miriam Brandt
- Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Anna Schleimer
- Musée National d'Histoire Naturelle, Luxembourg, Luxembourg
| | - Stephanie Kramer-Schadt
- Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany.,Department of Ecology, Technische Universität Berlin, Berlin, Germany
| | - Heribert Hofer
- Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany.,Freie Universität Berlin (FU), Berlin, Germany
| | - Konstantin Börner
- Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | | | | | | | - Tanja Halczok
- Universität Greifswald, Zoologisches Institut und Museum, Greifswald, Germany
| | - Christoph Staubach
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
| | - Alain C Frantz
- Musée National d'Histoire Naturelle, Luxembourg, Luxembourg
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Abstract
Mice (Mus musculus) and rats (Rattus norvegicus) have long served as model systems for biomedical research. However, they are also excellent models for studying the evolution of populations, subspecies, and species. Within the past million years, they have spread in various waves across large parts of the globe, with the most recent spread in the wake of human civilization. They have developed into commensal species, but have also been able to colonize extreme environments on islands free of human civilization. Given that ample genomic and genetic resources are available for these species, they have thus also become ideal mammalian systems for evolutionary studies on adaptation and speciation, particularly in the combination with the rapid developments in population genomics. The chapter provides an overview of the systems and their history, as well as of available resources.
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Affiliation(s)
- Kristian K Ullrich
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany.
| | - Diethard Tautz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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Ecological analysis of gamasid mites on the body surface of Norway rats (Rattus norvegicus) in Yunnan Province, Southwest China. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00383-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Parsons MH, Deutsch MA, Dumitriu D, Munshi-South J. Differential responses by urban brown rats (Rattus norvegicus) toward male or female-produced scents in sheltered and high-risk presentations. JOURNAL OF URBAN ECOLOGY 2019. [DOI: 10.1093/jue/juz009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Wild rats (Rattus norvegicus) are among the most ubiquitous and consequential organisms in the urban environment. However, collecting data from city rats is difficult, and there has been little research to determine the influence, or valence, of rat scents on urban conspecifics. Using a mark-release-monitor protocol, we previously learned rats can be attracted to remote-sensing points when baited with mixed-bedding from male and female laboratory rats. It was thus essential that we disambiguate which scents were eliciting attraction (+ valence), inspection, a conditioned response whereby attraction may be followed by avoidance (–valence), or null-response (0 valence). We used radio-frequency identification tagging and scent-baited antennas to assess extended (>40 days) responses to either male or female scents against two risk presentations (near-shelter and exposed to predators). In response to male scents, rats (n = 8) visited both treatments (shelter, exposed) more than controls (0.2 visits/day treatment vs. 0.1/day; P < 0.05) indicating scents accounted for response more so than risk. Dwell-times, however, did not differ (1.2 s/visit treatment vs. 0.9 s/visit; P > 0.5). These outcomes are consistent with inspection (–valence). In response to female scents, rats (n = 7) increased visitation (5.02 visits/day vs. 0.1/day controls; P < 0.05), while dwell-times also increased 6.8 s/visit vs. 0.2 s/visit in both risk-settings. The latter is consistent with persistent attraction (+valence), but was also influenced by shelter, as runway visits (1.1 visits/day) were a magnitude more common than predator-exposed (0.1 visits/day). Further understanding and exploiting the mobility of city rats is necessary for improvements in basic and applied research, including city pathogen-surveillance and urban wildlife management.
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Affiliation(s)
- Michael H Parsons
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Michael A Deutsch
- Medical and Applied Entomology, Arrow Exterminating Company, Inc., Lynbrook, NY, USA
| | - Dani Dumitriu
- Departments of Pediatrics and Psychiatry, the Zuckerman Institute, and the Columbia Population Research Center, Columbia University, New York, NY, USA
| | - Jason Munshi-South
- Department of Biological Sciences and the Louis Calder Center—Biological Field Station, Fordham University, Armonk, NY, USA
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Puckett EE, Magnussen E, Khlyap LA, Strand TM, Lundkvist Å, Munshi-South J. Genomic analyses reveal three independent introductions of the invasive brown rat (Rattus norvegicus) to the Faroe Islands. Heredity (Edinb) 2019; 124:15-27. [PMID: 31399718 DOI: 10.1038/s41437-019-0255-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 07/10/2019] [Accepted: 07/20/2019] [Indexed: 11/09/2022] Open
Abstract
Population genomics offers innovative approaches to test hypotheses related to the source and timing of introduction of invasive species. These approaches are particularly appropriate to study colonization of island ecosystems. The brown rat is a cold-hardy global invasive that has reached most of the world's island ecosystems, including even highly isolated archipelagoes such as the Faroe Islands in the North Atlantic Ocean. Historic records tell of rats rafting to the southern island of Suðuroy in 1768 following a shipwreck off the coast of Scotland, then expanding across the archipelago. We investigated the demographic history of brown rats in the Faroes using 50,174 SNPs. We inferred three independent introductions of rats, including to Suðuroy, the islands of Borðoy and Viðoy, and onto Streymoy from which they expanded to Eysturoy and Vágar. All Faroese populations showed signs of strong bottlenecks and declining effective population size. We inferred that these founder events removed low frequency alleles, the exact data needed to estimate recent demographic histories. Therefore, we were unable to accurately estimate the timing of each invasion. The difficulties with demographic inference may be applicable to other invasive species, particularly those with extreme and recent bottlenecks. We identified three invasions of brown rats to the Faroe Islands that resulted in highly differentiated populations that will be useful for future studies of life history variation and genomic adaptation.
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Affiliation(s)
- Emily E Puckett
- Department of Biological Sciences, University of Memphis, Memphis, TN, USA. .,Louis Calder Center- Biological Field Station, Fordham University, Armonk, NY, USA.
| | - Eyðfinn Magnussen
- Faculty of Science and Technology, University of the Faroe Islands, Tórshavn, Faroe Islands
| | - Liudmila A Khlyap
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Tanja M Strand
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden.,National Veterinary Institute (SVA), Department of Microbiology, Uppsala, Sweden
| | - Åke Lundkvist
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Jason Munshi-South
- Louis Calder Center- Biological Field Station, Fordham University, Armonk, NY, USA
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Pichler V, Kotsakiozi P, Caputo B, Serini P, Caccone A, della Torre A. Complex interplay of evolutionary forces shaping population genomic structure of invasive Aedes albopictus in southern Europe. PLoS Negl Trop Dis 2019; 13:e0007554. [PMID: 31437154 PMCID: PMC6705758 DOI: 10.1371/journal.pntd.0007554] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/17/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In the last four decades, the Asian tiger mosquito, Aedes albopictus, vector of several human arboviruses, has spread from its native range in South-East Asia to all over the world, largely through the transportation of its eggs via the international trade in used tires. Albania was the first country invaded in Europe in 1979, followed by Italy in 1990 and other Mediterranean countries after 2000. METHODS/PRINCIPAL FINDINGS We here inferred the invasion history and migration patterns of Ae. albopictus in Italy (today the most heavily-infested country in Europe), Greece and Albania, by analyzing a panel of >100,000 single nucleotide polymorphisms (SNPs) obtained by sequencing of double-digest Restriction site-Associated DNA (ddRADseq). The obtained dataset was combined with samples previously analyzed from both the native and invasive range worldwide to interpret the results using a broader spatial and historical context. The emerging evolutionary scenario complements the results of other studies in showing that the extraordinary worldwide expansion of Ae. albopictus has occurred thanks to multiple independent invasions by large numbers of colonists from multiple geographic locations in both native and previously invaded areas, consistently with the role of used tires shipments to move large numbers of eggs worldwide. By analyzing mosquitoes from nine sites across ~1,000-km transect in Italy, we were able to detect a complex interplay of drift, isolation by distance mediated divergence, and gene flow in shaping the species very recent invasion and range expansion, suggesting overall high connectivity, likely due to passive transportation of adults via ground transportation, as well as specific adaptations to local conditions. CONCLUSIONS/SIGNIFICANCE Results contribute to characterize one of the most successful histories of animal invasion, and could be used as a baseline for future studies to track epidemiologically relevant characters (e.g. insecticide resistance).
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Affiliation(s)
- Verena Pichler
- Dipartimento di Sanità Pubblica e Malattie Infettive, Laboratorio affiliato Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Università di Roma ‘Sapienza’, Roma, Italia
| | - Panayiota Kotsakiozi
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Beniamino Caputo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Laboratorio affiliato Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Università di Roma ‘Sapienza’, Roma, Italia
| | - Paola Serini
- Dipartimento di Sanità Pubblica e Malattie Infettive, Laboratorio affiliato Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Università di Roma ‘Sapienza’, Roma, Italia
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Alessandra della Torre
- Dipartimento di Sanità Pubblica e Malattie Infettive, Laboratorio affiliato Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Università di Roma ‘Sapienza’, Roma, Italia
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43
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Larsen PA, Matocq MD. Emerging genomic applications in mammalian ecology, evolution, and conservation. J Mammal 2019. [DOI: 10.1093/jmammal/gyy184] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Peter A Larsen
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science; Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, USA
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44
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Puckett EE, Munshi-South J. Brown rat demography reveals pre-commensal structure in eastern Asia before expansion into Southeast Asia. Genome Res 2019; 29:762-770. [PMID: 30910795 PMCID: PMC6499317 DOI: 10.1101/gr.235754.118] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/21/2019] [Indexed: 01/26/2023]
Abstract
Fossil evidence indicates that the globally distributed brown rat (Rattus norvegicus) originated in northern China and Mongolia. Historical records report the human-mediated invasion of rats into Europe in the 1500s, followed by global spread because of European imperialist activity during the 1600s–1800s. We analyzed 14 genomes representing seven previously identified evolutionary clusters, and tested alternative demographic models to infer patterns of range expansion, divergence times, and changes in effective population (Ne) size for this globally important pest species. We observed three range expansions from the ancestral population that produced the Pacific (diverged ∼16.1 kya), eastern China (∼17.5 kya), and Southeast (SE) Asia (∼0.86 kya) lineages. Our model shows a rapid range expansion from SE Asia into the Middle East and then continued expansion into central Europe 788 yr ago (1227 AD). We observed declining Ne within all brown rat lineages from 150–1 kya, reflecting population contractions during glacial cycles. Ne increased since 1 kya in Asian and European, but not in Pacific, evolutionary clusters. Our results support the hypothesis that northern Asia was the ancestral range for brown rats. We suggest that southward human migration across China between the 800s–1550s AD resulted in the introduction of rats to SE Asia, from which they rapidly expanded via existing maritime trade routes. Finally, we discovered that North America was colonized separately on both the Atlantic and Pacific seaboards, by evolutionary clusters of vastly different ages and genomic diversity levels. Our results should stimulate discussions among historians and zooarcheologists regarding the relationship between humans and rats.
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Affiliation(s)
- Emily E Puckett
- Louis Calder Center, Fordham University, Armonk, New York 10504, USA.,Department of Biological Sciences, University of Memphis, Memphis, Tennessee 38152, USA
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45
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Childs JE, Klein SL, Glass GE. A Case Study of Two Rodent-Borne Viruses: Not Always the Same Old Suspects. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00035] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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Rivkin LR, Santangelo JS, Alberti M, Aronson MFJ, de Keyzer CW, Diamond SE, Fortin M, Frazee LJ, Gorton AJ, Hendry AP, Liu Y, Losos JB, MacIvor JS, Martin RA, McDonnell MJ, Miles LS, Munshi‐South J, Ness RW, Newman AEM, Stothart MR, Theodorou P, Thompson KA, Verrelli BC, Whitehead A, Winchell KM, Johnson MTJ. A roadmap for urban evolutionary ecology. Evol Appl 2019; 12:384-398. [PMID: 30828362 PMCID: PMC6383741 DOI: 10.1111/eva.12734] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/29/2018] [Accepted: 11/05/2018] [Indexed: 12/13/2022] Open
Abstract
Urban ecosystems are rapidly expanding throughout the world, but how urban growth affects the evolutionary ecology of species living in urban areas remains largely unknown. Urban ecology has advanced our understanding of how the development of cities and towns change environmental conditions and alter ecological processes and patterns. However, despite decades of research in urban ecology, the extent to which urbanization influences evolutionary and eco-evolutionary change has received little attention. The nascent field of urban evolutionary ecology seeks to understand how urbanization affects the evolution of populations, and how those evolutionary changes in turn influence the ecological dynamics of populations, communities, and ecosystems. Following a brief history of this emerging field, this Perspective article provides a research agenda and roadmap for future research aimed at advancing our understanding of the interplay between ecology and evolution of urban-dwelling organisms. We identify six key questions that, if addressed, would significantly increase our understanding of how urbanization influences evolutionary processes. These questions consider how urbanization affects nonadaptive evolution, natural selection, and convergent evolution, in addition to the role of urban environmental heterogeneity on species evolution, and the roles of phenotypic plasticity versus adaptation on species' abundance in cities. Our final question examines the impact of urbanization on evolutionary diversification. For each of these six questions, we suggest avenues for future research that will help advance the field of urban evolutionary ecology. Lastly, we highlight the importance of integrating urban evolutionary ecology into urban planning, conservation practice, pest management, and public engagement.
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News Feature: Cities serve as testbeds for evolutionary change. Proc Natl Acad Sci U S A 2019; 116:2787-2790. [PMID: 30783018 DOI: 10.1073/pnas.1820852116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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DeCandia AL, Brzeski KE, Heppenheimer E, Caro CV, Camenisch G, Wandeler P, Driscoll C, vonHoldt BM. Urban colonization through multiple genetic lenses: The city-fox phenomenon revisited. Ecol Evol 2019; 9:2046-2060. [PMID: 30847091 PMCID: PMC6392345 DOI: 10.1002/ece3.4898] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/11/2018] [Accepted: 12/13/2018] [Indexed: 12/31/2022] Open
Abstract
Urbanization is driving environmental change on a global scale, creating novel environments for wildlife to colonize. Through a combination of stochastic and selective processes, urbanization is also driving evolutionary change. For instance, difficulty in traversing human-modified landscapes may isolate newly established populations from rural sources, while novel selective pressures, such as altered disease risk, toxicant exposure, and light pollution, may further diverge populations through local adaptation. Assessing the evolutionary consequences of urban colonization and the processes underlying them is a principle aim of urban evolutionary ecology. In the present study, we revisited the genetic effects of urbanization on red foxes (Vulpes vulpes) that colonized Zurich, Switzerland. Through use of genome-wide single nucleotide polymorphisms and microsatellite markers linked to the major histocompatibility complex (MHC), we expanded upon a previous neutral microsatellite study to assess population structure, characterize patterns of genetic diversity, and detect outliers associated with urbanization. Our results indicated the presence of one large evolutionary cluster, with substructure evident between geographic sampling areas. In urban foxes, we observed patterns of neutral and functional diversity consistent with founder events and reported increased differentiation between populations separated by natural and anthropogenic barriers. We additionally reported evidence of selection acting on MHC-linked markers and identified outlier loci with putative gene functions related to energy metabolism, behavior, and immunity. We concluded that demographic processes primarily drove patterns of diversity, with outlier tests providing preliminary evidence of possible urban adaptation. This study contributes to our overall understanding of urban colonization ecology and emphasizes the value of combining datasets when examining evolutionary change in an increasingly urban world.
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Affiliation(s)
- Alexandra L. DeCandia
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
| | - Kristin E. Brzeski
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
- School of Forest Resources and Environmental ScienceMichigan Technological UniversityHoughtonMichigan
| | | | - Catherine V. Caro
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
| | - Glauco Camenisch
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | | | - Carlos Driscoll
- Laboratory of Comparative Behavioral GenomicsNational Institute on Alcohol Abuse and Alcoholism, National Institutes of HealthRockvilleMaryland
| | - Bridgett M. vonHoldt
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
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Byers KA, Lee MJ, Patrick DM, Himsworth CG. Rats About Town: A Systematic Review of Rat Movement in Urban Ecosystems. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00013] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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50
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Murray MH, Fyffe R, Fidino M, Byers KA, Ríos MJ, Mulligan MP, Magle SB. Public Complaints Reflect Rat Relative Abundance Across Diverse Urban Neighborhoods. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00189] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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