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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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Zhang MY, Cao RD, Chen Y, Ma JC, Shi CM, Zhang YF, Zhang JX, Zhang YH. Genomic and Phenotypic Adaptations of Rattus tanezumi to Cold Limit Its Further Northward Expansion and Range Overlap with R. norvegicus. Mol Biol Evol 2024; 41:msae106. [PMID: 38829799 PMCID: PMC11184353 DOI: 10.1093/molbev/msae106] [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: 05/23/2023] [Revised: 05/19/2024] [Accepted: 05/28/2024] [Indexed: 06/05/2024] Open
Abstract
Global climate change has led to shifts in the distribution ranges of many terrestrial species, promoting their migration from lower altitudes or latitudes to higher ones. Meanwhile, successful invaders have developed genetic adaptations enabling the colonization of new environments. Over the past 40 years, Rattus tanezumi (RT) has expanded into northern China (Northwest and North China) from its southern origins. We studied the cold adaptation of RT and its potential for northward expansion by comparing it with sympatric Rattus norvegicus (RN), which is well adapted to cold regions. Through population genomic analysis, we revealed that the invading RT rats have split into three distinct populations: the North, Northwest, and Tibetan populations. The first two populations exhibited high genetic diversity, while the latter population showed remarkably low genetic diversity. These rats have developed various genetic adaptations to cold, arid, hypoxic, and high-UV conditions. Cold acclimation tests revealed divergent thermoregulation between RT and RN. Specifically, RT exhibited higher brown adipose tissue activity and metabolic rates than did RN. Transcriptome analysis highlighted changes in genes regulating triglyceride catabolic processes in RT, including Apoa1 and Apoa4, which were upregulated, under selection and associated with local adaptation. In contrast, RN showed changes in carbohydrate metabolism genes. Despite the cold adaptation of RT, we observed genotypic and phenotypic constraints that may limit its ability to cope with severe low temperatures farther north. Consequently, it is less likely that RT rats will invade and overlap with RN rats in farther northern regions.
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Affiliation(s)
- Ming-Yu Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 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, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian-Cang Ma
- Zhangye Maize Stock Production Base, Zhangye 734024, Gansu, China
| | - Cheng-Min Shi
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Yun-Feng Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian-Xu Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 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, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, Anhui, China
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Martin E, El-Galmady S, Johnson MTJ. Urban socioeconomic variation influences the ecology and evolution of trophic interactions. Ecol Lett 2024; 27:e14407. [PMID: 38504478 DOI: 10.1111/ele.14407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/21/2024]
Abstract
As urbanization expands, it is becoming increasingly important to understand how anthropogenic activity is affecting ecological and evolutionary processes. Few studies have examined how human social patterns within cities can modify eco-evolutionary dynamics. We tested how socioeconomic variation corresponds with changes in trophic interactions and natural selection on prey phenotypes using the classic interaction between goldenrod gall flies (Eurosta solidaginis) and their natural enemies: birds, beetles, and parasitoid wasps. We sampled galls from 84 sites across neighbourhoods with varying socioeconomic levels, and quantified the frequency of predation/parasitism on flies and natural selection by each enemy. We found that bird predation was higher in the highest income neighbourhoods, increasing the strength of selection for smaller galls. Wasp and beetle attack, but not their strength of selection, increased in lower income neighbourhoods. We show that socioeconomic variation in cities can have strong unintended consequences for the ecology and evolution of trophic interactions.
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Affiliation(s)
- Ella Martin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Samer El-Galmady
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Marc T J Johnson
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
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Granjon L, Artige E, Bâ K, Brouat C, Dalecky A, Diagne C, Diallo M, Fossati‐Gaschignard O, Gauthier P, Kane M, Husse L, Niang Y, Piry S, Sarr N, Sow A, Duplantier J. Sharing space between native and invasive small mammals: Study of commensal communities in Senegal. Ecol Evol 2023; 13:e10539. [PMID: 37745790 PMCID: PMC10511302 DOI: 10.1002/ece3.10539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/18/2023] [Accepted: 09/04/2023] [Indexed: 09/26/2023] Open
Abstract
Urbanization processes are taking place at a very high rate, especially in Africa. At the same time, a number of small mammal species, be they native or invasive, take advantage of human-induced habitat modifications. They represent commensal communities of organisms that cause a number of inconveniences to humans, including potential reservoirs of zoonotic diseases. We studied via live trapping and habitat characterization such commensal small mammal communities in small villages to large cities of Senegal, to try to understand how the species share this particular space. Seven major species were recorded, with exotic invasive house mice (Mus musculus) and black rats (Rattus rattus) dominating in numbers. The shrew Crocidura olivieri appeared as the main and more widespread native species, while native rodent species (Mastomys natalensis, M. erythroleucus, Arvicanthis niloticus and Praomys daltoni) were less abundant and/or more localized. Habitat preferences, compared between species in terms of room types and characteristics, showed differences among house mice, black rats and M. natalensis especially. Niche (habitat component) breadth and overlap were measured. Among invasive species, the house mouse showed a larger niche breadth than the black rat, and overall, all species displayed high overlap values. Co-occurrence patterns were studied at the global and local scales. The latter show cases of aggregation (between the black rat and native species, for instance) and of segregation (as between the house mouse and the black rat in Tambacounda, or between the black rat and M. natalensis in Kédougou). While updating information on commensal small mammal distribution in Senegal, a country submitted to a dynamic process of invasion by the black rat and the house mouse, we bring original information on how species occupy and share the commensal space, and make predictions on the evolution of these communities in a period of ever-accelerating global changes.
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Affiliation(s)
- Laurent Granjon
- CBGP, IRD, INRAE, CIRAD, Montpellier SupAgro, Univ MontpellierMontpellierFrance
| | - Emanuelle Artige
- CBGP, IRD, INRAE, CIRAD, Montpellier SupAgro, Univ MontpellierMontpellierFrance
| | - Khalilou Bâ
- BIOPASS, CBGP‐IRD, ISRA, UCAD, CIRADDakarSenegal
| | - Carine Brouat
- CBGP, IRD, INRAE, CIRAD, Montpellier SupAgro, Univ MontpellierMontpellierFrance
| | | | - Christophe Diagne
- CBGP, IRD, INRAE, CIRAD, Montpellier SupAgro, Univ MontpellierMontpellierFrance
| | | | | | - Philippe Gauthier
- CBGP, IRD, INRAE, CIRAD, Montpellier SupAgro, Univ MontpellierMontpellierFrance
| | - Mamadou Kane
- BIOPASS, CBGP‐IRD, ISRA, UCAD, CIRADDakarSenegal
| | - Laëtitia Husse
- CBGP, IRD, INRAE, CIRAD, Montpellier SupAgro, Univ MontpellierMontpellierFrance
- BIOPASS, CBGP‐IRD, ISRA, UCAD, CIRADDakarSenegal
| | | | - Sylvain Piry
- CBGP, IRD, INRAE, CIRAD, Montpellier SupAgro, Univ MontpellierMontpellierFrance
| | | | - Aliou Sow
- BIOPASS, CBGP‐IRD, ISRA, UCAD, CIRADDakarSenegal
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Kiyokawa Y, Tamogami S, Ootaki M, Kahl E, Mayer D, Fendt M, Nagaoka S, Tanikawa T, Takeuchi Y. An appeasing pheromone ameliorates fear responses in the brown rat ( Rattus norvegicus). iScience 2023; 26:107081. [PMID: 37426349 PMCID: PMC10329171 DOI: 10.1016/j.isci.2023.107081] [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: 02/19/2023] [Revised: 05/23/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
The brown rat (Rattus norvegicus) is one of the major animals both in the laboratory and in urban centers. Brown rats communicate various types of information using pheromones, the chemicals that mediate intra-species communication in minute amounts. Therefore, analyses of pheromones would further our understanding of the mode of life of rats. We show that a minute amount of 2-methylbutyric acid (2-MB) released from the neck region can ameliorate fear responses both in laboratory rats and in wild brown rats. Based on these findings, we conclude that 2-MB is an appeasing pheromone in the brown rat. A better understanding of rats themselves would allow us to perform more effective ecologically based research on social skills and pest management campaigns with low animal welfare impacts, which might contribute to furthering the advancement of science and improving public health.
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Affiliation(s)
- Yasushi Kiyokawa
- Laboratory of Veterinary Ethology, the University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shigeyuki Tamogami
- Laboratory of Veterinary Ethology, the University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masato Ootaki
- Laboratory of Veterinary Ethology, the University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Evelyn Kahl
- Institute for Pharmacology and Toxicology & Center for Behavioral Brain Sciences, Otto-von-Guericke University Magdeburg, D-39120 Magdeburg, Germany
| | - Dana Mayer
- Institute for Pharmacology and Toxicology & Center for Behavioral Brain Sciences, Otto-von-Guericke University Magdeburg, D-39120 Magdeburg, Germany
| | - Markus Fendt
- Institute for Pharmacology and Toxicology & Center for Behavioral Brain Sciences, Otto-von-Guericke University Magdeburg, D-39120 Magdeburg, Germany
| | - Satoru Nagaoka
- Daimaru Compound Chemical Co., Ltd, Nagano 381-1222, Japan
| | - Tsutomu Tanikawa
- Technical Research Laboratory, Ikari Shodoku Co., Ltd, Chiba 275-0024, Japan
| | - Yukari Takeuchi
- Laboratory of Veterinary Ethology, the University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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6
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Luo Y, Wei QM, Newman C, Huang XQ, Luo XY, Zhou ZM. Variation in Pheidole nodus (Hymenoptera: Formicidae) functional morphology across urban parks. PeerJ 2023; 11:e15679. [PMID: 37483976 PMCID: PMC10361077 DOI: 10.7717/peerj.15679] [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: 03/20/2023] [Accepted: 06/13/2023] [Indexed: 07/25/2023] Open
Abstract
Background Habitat fragmentation and consequent population isolation in urban areas can impose significant selection pressures on individuals and species confined to urban islands, such as parks. Despite many comparative studies on the diversity and structure of ant community living in urban areas, studies on ants' responses to these highly variable ecosystems are often based on assemblage composition and interspecific mean trait values, which ignore the potential for high intraspecific functional trait variation among individuals. Methods Here, we examined differences in functional traits among populations of the generalist ant Pheidole nodus fragmented between urban parks. We used pitfall trapping, which is more random and objective than sampling colonies directly, despite a trade-off against sample size. We then tested whether trait-filtering could explain phenotypic differences among urban park ant populations, and whether ant populations in different parks exhibited different phenotypic optima, leading to positional shifts in anatomical morphospace through the regional ant meta-population. Results Intraspecific morphological differentiation was evident across this urban region. Populations had different convex hull volumes, positioned differently over the morphospace. Conclusions Fragmentation and habitat degradation reduced phenotypic diversity and, ultimately, changed the morphological optima of populations in this urban landscape. Considering ants' broad taxonomic and functional diversity and their important role in ecosystems, further work over a variety of ant taxa is necessary to ascertain those varied morphological response pathways operating in response to population segregation in urban environments.
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Affiliation(s)
- Yi Luo
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Qing-Ming Wei
- Nanchong Vocational and Technical College, Nanchong, China
| | - Chris Newman
- Wildlife Conservation Research Unit, Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Xiang-Qin Huang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Xin-Yu Luo
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Zhao-Min Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
- Key Laboratory of Environmental Science and Biodiversity Conservation (Sichuan Province), China West Normal University, Nanchong, China
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7
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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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8
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The importance of habitat in the tumor-associated Pten, Mtor, and Akt gene expressions and chromosomal aberrations for wild rats. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01272-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Verrelli BC, Alberti M, Des Roches S, Harris NC, Hendry AP, Johnson MTJ, Savage AM, Charmantier A, Gotanda KM, Govaert L, Miles LS, Rivkin LR, Winchell KM, Brans KI, Correa C, Diamond SE, Fitzhugh B, Grimm NB, Hughes S, Marzluff JM, Munshi-South J, Rojas C, Santangelo JS, Schell CJ, Schweitzer JA, Szulkin M, Urban MC, Zhou Y, Ziter C. A global horizon scan for urban evolutionary ecology. Trends Ecol Evol 2022; 37:1006-1019. [PMID: 35995606 DOI: 10.1016/j.tree.2022.07.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 10/31/2022]
Abstract
Research on the evolutionary ecology of urban areas reveals how human-induced evolutionary changes affect biodiversity and essential ecosystem services. In a rapidly urbanizing world imposing many selective pressures, a time-sensitive goal is to identify the emergent issues and research priorities that affect the ecology and evolution of species within cities. Here, we report the results of a horizon scan of research questions in urban evolutionary ecology submitted by 100 interdisciplinary scholars. We identified 30 top questions organized into six themes that highlight priorities for future research. These research questions will require methodological advances and interdisciplinary collaborations, with continued revision as the field of urban evolutionary ecology expands with the rapid growth of cities.
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Affiliation(s)
- Brian C Verrelli
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA 23284, USA.
| | - Marina Alberti
- Department of Urban Design and Planning, University of Washington, Seattle, WA 98195, USA
| | - Simone Des Roches
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195, USA
| | - Nyeema C Harris
- Applied Wildlife Ecology Lab, Yale School of the Environment, Yale University, New Haven, CT 06511, USA
| | - Andrew P Hendry
- Department of Biology, Redpath Museum, McGill University, Montreal, QC H3A 0C4, Canada
| | - Marc T J Johnson
- Department of Biology, Centre for Urban Environments, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Amy M Savage
- Department of Biology and Center for Computational & Integrative Biology, Rutgers University-Camden, Camden, NJ 08103, USA
| | | | - Kiyoko M Gotanda
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada; Département de Biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Lynn Govaert
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, 12587 Berlin, Germany
| | - Lindsay S Miles
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - L Ruth Rivkin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON L5L 1C6, Canada; Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Kristin M Winchell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Kristien I Brans
- Department of Biology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Cristian Correa
- Instituto de Conservación Biodiversidad y Territorio, Centro de Humedales Río Cruces, Universidad Austral de Chile, Valdivia, 5090000, Chile
| | - Sarah E Diamond
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ben Fitzhugh
- Department of Anthropology, University of Washington, Seattle, WA 98195, USA
| | - Nancy B Grimm
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Sara Hughes
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI 48109, USA
| | - John M Marzluff
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jason Munshi-South
- Louis Calder Center & Department of Biological Sciences, Fordham University, Armonk, NY 10504, USA
| | - Carolina Rojas
- Instituto de Estudios Urbanos y Territoriales, Centro de Desarrollo Sustentable CEDEUS, Pontificia Universidad Católica de Chile, El Comendador 1916, Providencia, 7500000, Santiago, Chile
| | - James S Santangelo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON L5L 1C6, Canada
| | - Christopher J Schell
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Schweitzer
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37917, USA
| | - Marta Szulkin
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Mark C Urban
- Department of Ecology and Evolutionary Biology & Center of Biological Risk, University of Connecticut, Storrs, CT 06269, USA
| | - Yuyu Zhou
- Department of Geological and Atmospheric Sciences, Iowa State University, Ames, IA 50011, USA
| | - Carly Ziter
- Department of Biology, Concordia University, Montreal, QC H4B 1R6, Canada
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10
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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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11
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Pettengill JB, Kase JA, Murray MH. The Population Genetics, Virulence, and Public Health Concerns of Escherichia coli Collected From Rats Within an Urban Environment. Front Microbiol 2021; 12:631761. [PMID: 34777266 PMCID: PMC8585510 DOI: 10.3389/fmicb.2021.631761] [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: 11/20/2020] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
The co-existence of rats and humans in urban environments has long been a cause for concern regarding human health because of the potential for rats to harbor and transmit disease-causing pathogens. Here, we analyze whole-genome sequence (WGS) data from 41 Escherichia coli isolates collected from rat feces from 12 locations within the city of Chicago, IL, United States to determine the potential for rats to serve as a reservoir for pathogenic E. coli and describe its population structure. We identified 25 different serotypes, none of which were isolated from strains containing significant virulence markers indicating the presence of Shiga toxin-producing and other disease-causing E. coli. Nor did the E. coli isolates harbor any particularly rare stress tolerant or antimicrobial resistance genes. We then compared the isolates against a public database of approximately 100,000 E. coli and Shigella isolates of primarily food, food facility, or clinical origin. We found that only one isolate was genetically similar to genome sequences in the database. Phylogenetic analyses showed that isolates cluster by serotype, and there was little geographic structure (e.g., isolation by distance) among isolates. However, a greater signal of isolation by distance was observed when we compared genetic and geographic distances among isolates of the same serotype. This suggests that E. coli serotypes are independent lineages and recombination between serotypes is rare.
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Affiliation(s)
- J B Pettengill
- Division of Biostatistics and Bioinformatics, Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, MD, United States
| | - J A Kase
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, MD, United States
| | - M H Murray
- Davee Center for Epidemiology and Endocrinology, Urban Wildlife Institute, Lincoln Park Zoo, Chicago, IL, United States
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12
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Zeppelini CG, Carvalho-Pereira T, Alves RS, Santiago DCC, Santo VFE, Begon M, Costa F, Khalil H. Demographic drivers of Norway rat populations from urban slums in Brazil. Urban Ecosyst 2021; 24:801-809. [PMID: 34720572 PMCID: PMC8550123 DOI: 10.1007/s11252-020-01075-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2020] [Indexed: 11/27/2022]
Abstract
The Norway rat is a globally distributed pest, known for its resilience to eradication and control programs. Efficient population control, especially in urban settings, is dependent on knowledge of rat demography and population ecology. We analyzed the relationship between four demographic outcomes, estimated by live-trapping data, and fine-scale environmental features measured at the capture site. Wounds, a proxy for agonistic interactions, were associated with mature individuals. Areas with environmental features favorable to rats, such as open sewers and unpaved earth, were associated with more mature individuals with a better body condition index. The control measures (environmental stressors) are likely to be disrupting the social structure of rat colonies, increasing the frequency and distribution of agonistic interactions, which were common in both sexes and maturity states. The relationship between the favorable environmental conditions and the demographic markers analyzed indicate possible targets for infestation control through environmental manipulation, and could be incorporated into current pest management programs to achieve long-term success. Our study indicate that urban interventions focused on removal of potential resources for rats could be potential long-term solutions by reducing the carrying capacity of the environment. Supplementary Information The online version contains supplementary material available at 10.1007/s11252-020-01075-2.
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Affiliation(s)
- C G Zeppelini
- Laboratório de Mamíferos, Universidade Federal da Paraíba, Cidade Universitária, João Pessoa, Brazil.,Programa de Pós-Graduação em Ecologia: Teoria, Aplicações e Valores, Universidade Federal da Bahia, R. Barão do Geremoabo, Salvador, 147 Brazil
| | - T Carvalho-Pereira
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, R. Basílio da Gama, S/N, Salvador, Brazil
| | - R Sady Alves
- Programa de Pós-Graduação em Ciência Animal nos Trópicos, Universidade federal da Bahia, R. Barão do Geremoabo, Salvador, 147 Brazil
| | - D C C Santiago
- Instituto de Biologia, Universidade Federal da Bahia, R. Barão do Geremoabo, Salvador, 147 Brazil
| | - V F Espirito Santo
- Faculdade de Farmácia, Universidade Federal da Bahia, R. Barão do Geremoabo, Salvador, 147 Brazil
| | - M Begon
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, L69 7ZB UK
| | - F Costa
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, R. Basílio da Gama, S/N, Salvador, Brazil
| | - Hussein Khalil
- Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
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13
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Assessment of dispersal and population structure of Norway rats (Rattus norvegicus) in a seaport setting. Urban Ecosyst 2021. [DOI: 10.1007/s11252-021-01171-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractSeaports are introduction hotspots for invasive alien species (IAS). This is especially true for rodents, which have accompanied humans around the globe since the earliest days of ocean-going voyages. The rapid spread of IAS soon after arrival in a new environment is facilitated by further human-mediated transport or landscape features, like roads. By measuring genetic diversity and structure to investigate dispersal pathways, we gained insight into the transport, spread and establishment stages of a biological invasion, leveraging the most common rodent species (R. norvegicus) in this setting. We characterized the genetic structure of three Norway rat populations along a busy industrial road used by trucks to access the Port area in Paranaguá city (Brazil). A total of 71 rats were genotyped using 11 microsatellite markers. The results revealed a pattern of gene flow contrary to the expected stepping-stone model along the linear transect, with the two furthest apart populations being clustered together. We hypothesize that the observed outcome is explained by natural dispersal along the corridor being lower than human-mediated transport. The sampled area furthest from the port is a gas station frequented by trucks which are considered the most likely mode of transportation. In terms of management strategies, we suggest more emphasis should be put on cargo surveillance to lower the risk of Norway rat dispersal, not only for biosecurity, but also for sanitary reasons, as this port is a major grain trading point.
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14
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Chen Y, Hou G, Jing M, Teng H, Liu Q, Yang X, Wang Y, Qu J, Shi C, Lu L, Zhang J, Zhang Y. Genomic analysis unveils mechanisms of northward invasion and signatures of plateau adaptation in the Asian house rat. Mol Ecol 2021; 30:6596-6610. [PMID: 34564921 DOI: 10.1111/mec.16194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 07/21/2021] [Accepted: 09/20/2021] [Indexed: 12/20/2022]
Abstract
The Asian house rat (AHR), Rattus tanezumi, has recently invaded the northern half of China. The AHR is a highly adaptive rat species that has also successfully conquered the Qinghai-Tibet Plateau (QTP) and replaced the brown rat (BR), R. norvegicus, at the edge of the QTP. Here, we assembled a draft genome of the AHR and explored the mechanisms of its northward invasion and the genetic basis underlying plateau adaptation in this species. Population genomic analyses revealed that the northwardly invasive AHRs consisted of two independent and genetically distinct populations which might result from multiple independent primary invasion events. One invasive population exhibited reduced genetic diversity and distinct population structure compared with its source population, while the other displayed preserved genetic polymorphisms and little genetic differentiation from its source population. Genes involved in G-protein coupled receptors and carbohydrate metabolism may contribute to the local adaptation of northern AHRs. In particular, RTN4 was identified as a key gene for AHRs in the QTP that favours adaptation to high-altitude hypoxia. Coincidently, the physiological performance and transcriptome profiles of hypoxia-exposed rats both showed better hypoxia adaptation in AHRs than in BRs that failed to colonize the heart of the QTP, which may have facilitated the replacement of the BR population by the invading AHRs at the edge of the QTP. This study provides profound insights into the multiple origins of the northwardly invasive AHR and the great tolerance to hypoxia in this species.
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Affiliation(s)
- Yi Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Guanmei Hou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Meidong Jing
- School of Life Sciences, Nantong University, Nantong, China
| | - Huajing Teng
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Quansheng Liu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xingen Yang
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Institute of Plant Protection, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Yong Wang
- Dongting Lake Station for Wetland Ecosystem Research, Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Jiapeng Qu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai, China
| | - Chengmin Shi
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Liang Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jianxu Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Yaohua Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
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15
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Kiyokawa Y, Tanikawa T, Ootaki M, Parsons MH. Social distancing measures differentially affected rats in North America and Tokyo. JOURNAL OF PEST SCIENCE 2021; 95:79-86. [PMID: 34248453 PMCID: PMC8259536 DOI: 10.1007/s10340-021-01405-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/19/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Because rats are commensal organisms that depend on human activities for food, shifts in human behavior will have pronounced effects on local rat populations. In the spring of 2020, social distancing measures were implemented globally to curtail the spread of SARS-CoV-2. This presented a unique opportunity to obtain information regarding the immediate effects of shifts in human behavior on rat populations in a variety of countries. In response to increased sightings of rats in the USA that were reported in American media, we analyzed the changes in the number of public service calls in Tokyo, Japan. We found that the number of calls increased after the implementation of social distancing measures, suggesting that rat sightings had also increased in Tokyo. We then surveyed the changes in the business activities of pest management professionals in the USA, Canada, and Tokyo. We found that the activities were increased in 50 to 60% of the respondents from the USA and Canada. In contrast, 60 to 70% of the respondents from Tokyo answered that their activities were not changed. These results implied that, following the implementation of social distancing measures, rat infestations increased in North America, but not in Tokyo. The survey also suggested that roof rats were considered to be the predominant rodent species in Tokyo. This may account for the limited infestations in Tokyo because roof rats are more sedentary than brown rats. Taken together, our findings suggest that social distancing measures differentially affected rat populations in North America and Tokyo. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10340-021-01405-z.
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Affiliation(s)
- Yasushi Kiyokawa
- Laboratory of Veterinary Ethology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Tsutomu Tanikawa
- Tokyo Pest Control Association, 2-9-8 Kajicho, Chiyoda-ku, Tokyo, 101-0044 Japan
| | - Masato Ootaki
- Laboratory of Veterinary Ethology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Michael H. Parsons
- Department of Biological Sciences, Fordham University, 441 East Fordham Road, Bronx, NY 10458 USA
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16
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Sánchez CA, Rios MJ, Murray MH. Social and environmental correlates of rat complaints in Chicago. JOURNAL OF URBAN ECOLOGY 2021. [DOI: 10.1093/jue/juab006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Urban rats are widely distributed pests that have negative effects on public health and property. It is crucial to understand their distribution to inform control efforts and address drivers of rat presence. Analysing public rat complaints can help assess urban rat distribution and identify factors supporting rat populations. Both social and environmental factors could promote rat complaints and must be integrated to understand rat distributions. We analysed rat complaints made between 2011 and 2017 in Chicago, a city with growing rat problems and stark wealth inequality. We examined whether rat complaints at the census tract level are associated with factors that could influence rat abundance, rats’ visibility to humans, and the likelihood of people making a complaint. Complaints were significantly positively correlated with anthropogenic factors hypothesized to promote rat abundance (restaurants, older buildings, garbage complaints, and dog waste complaints) or rat visibility (building construction/demolition activity), and factors hypothesized to increase the likelihood of complaining (human population density, more owner-occupied homes); we also found that complaints were highest in the summer. Our results suggest that conflicts between residents and rats are mainly driven by seasonal variation in rat abundance and human activity and could be mitigated with strategies such as securing food waste from residential and commercial sources. Accounting for social factors such as population density, construction and demolition activity, and home ownership versus rental can also help cities more accurately predict blocks at higher risk of rat conflicts.
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Affiliation(s)
- Cecilia A Sánchez
- Odum School of Ecology, University of Georgia, 140 E. Green St., Athens, GA 30602, USA
- Center for the Ecology of Infectious Diseases, University of Georgia, 140 E. Green St., Athens, GA 30602, USA
| | - María Jazmín Rios
- DePaul University, 1 E. Jackson Blvd., Chicago, IL 60604, USA
- Urban Wildlife Institute, Lincoln Park Zoo, 2001 N. Clark Street, Chicago, IL 60614, USA
| | - Maureen H Murray
- Urban Wildlife Institute, Lincoln Park Zoo, 2001 N. Clark Street, Chicago, IL 60614, USA
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17
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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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18
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Schell CJ, Stanton LA, Young JK, Angeloni LM, Lambert JE, Breck SW, Murray MH. The evolutionary consequences of human-wildlife conflict in cities. Evol Appl 2021; 14:178-197. [PMID: 33519964 PMCID: PMC7819564 DOI: 10.1111/eva.13131] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 07/03/2020] [Accepted: 08/13/2020] [Indexed: 12/25/2022] Open
Abstract
Human-wildlife interactions, including human-wildlife conflict, are increasingly common as expanding urbanization worldwide creates more opportunities for people to encounter wildlife. Wildlife-vehicle collisions, zoonotic disease transmission, property damage, and physical attacks to people or their pets have negative consequences for both people and wildlife, underscoring the need for comprehensive strategies that mitigate and prevent conflict altogether. Management techniques often aim to deter, relocate, or remove individual organisms, all of which may present a significant selective force in both urban and nonurban systems. Management-induced selection may significantly affect the adaptive or nonadaptive evolutionary processes of urban populations, yet few studies explicate the links among conflict, wildlife management, and urban evolution. Moreover, the intensity of conflict management can vary considerably by taxon, public perception, policy, religious and cultural beliefs, and geographic region, which underscores the complexity of developing flexible tools to reduce conflict. Here, we present a cross-disciplinary perspective that integrates human-wildlife conflict, wildlife management, and urban evolution to address how social-ecological processes drive wildlife adaptation in cities. We emphasize that variance in implemented management actions shapes the strength and rate of phenotypic and evolutionary change. We also consider how specific management strategies either promote genetic or plastic changes, and how leveraging those biological inferences could help optimize management actions while minimizing conflict. Investigating human-wildlife conflict as an evolutionary phenomenon may provide insights into how conflict arises and how management plays a critical role in shaping urban wildlife phenotypes.
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Affiliation(s)
- Christopher J. Schell
- School of Interdisciplinary Arts and SciencesUniversity of Washington TacomaTacomaWAUSA
| | - Lauren A. Stanton
- Department of Zoology and PhysiologyUniversity of WyomingLaramieWYUSA
- Program in EcologyUniversity of WyomingLaramieWYUSA
| | - Julie K. Young
- USDA‐WS‐National Wildlife Research Center‐Predator Research FacilityMillvilleUTUSA
| | | | - Joanna E. Lambert
- Program in Environmental Studies and Department of Ecology and Evolutionary BiologyUniversity of Colorado‐BoulderBoulderCOUSA
| | - Stewart W. Breck
- USDA‐WS‐National Wildlife Research CenterFort CollinsCOUSA
- Department of Fish, Wildlife, and Conservation BiologyFort CollinsCOUSA
| | - Maureen H. Murray
- Urban Wildlife Institute and Davee Center for Epidemiology and EndocrinologyChicagoILUSA
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19
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Richardson JL, Michaelides S, Combs M, Djan M, Bisch L, Barrett K, Silveira G, Butler J, Aye TT, Munshi‐South J, DiMatteo M, Brown C, McGreevy TJ. Dispersal ability predicts spatial genetic structure in native mammals persisting across an urbanization gradient. Evol Appl 2021; 14:163-177. [PMID: 33519963 PMCID: PMC7819555 DOI: 10.1111/eva.13133] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/17/2020] [Indexed: 01/31/2023] Open
Abstract
As the rate of urbanization continues to increase globally, a growing body of research is emerging that investigates how urbanization shapes the movement-and consequent gene flow-of species in cities. Of particular interest are native species that persist in cities, either as small relict populations or as larger populations of synanthropic species that thrive alongside humans in new urban environments. In this study, we used genomic sequence data (SNPs) and spatially explicit individual-based analyses to directly compare the genetic structure and patterns of gene flow in two small mammals with different dispersal abilities that occupy the same urbanized landscape to evaluate how mobility impacts genetic connectivity. We collected 215 white-footed mice (Peromyscus leucopus) and 380 big brown bats (Eptesicus fuscus) across an urban-to-rural gradient within the Providence, Rhode Island (U.S.A.) metropolitan area (population =1,600,000 people). We found that mice and bats exhibit clear differences in their spatial genetic structure that are consistent with their dispersal abilities, with urbanization having a stronger effect on Peromyscus mice. There were sharp breaks in the genetic structure of mice within the Providence urban core, as well as reduced rates of migration and an increase in inbreeding with more urbanization. In contrast, bats showed very weak genetic structuring across the entire study area, suggesting a near-panmictic gene pool likely due to the ability to disperse by flight. Genetic diversity remained stable for both species across the study region. Mice also exhibited a stronger reduction in gene flow between island and mainland populations than bats. This study represents one of the first to directly compare multiple species within the same urban-to-rural landscape gradient, an important gap to fill for urban ecology and evolution. Moreover, here we document the impacts of dispersal capacity on connectivity for native species that have persisted as the urban landscape matrix expands.
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Affiliation(s)
| | - Sozos Michaelides
- Department of Natural Resources ScienceUniversity of Rhode IslandKingstonRIUSA
| | - Matthew Combs
- Ecology, Evolution and Environmental Biology DepartmentColumbia UniversityNew YorkNYUSA
| | - Mihajla Djan
- Department of Natural Resources ScienceUniversity of Rhode IslandKingstonRIUSA
- Department of Biology and EcologyFaculty of SciencesUniversity of Novi SadNovi SadSerbia
| | - Lianne Bisch
- Department of BiologyProvidence CollegeProvidenceRIUSA
| | - Kerry Barrett
- Department of BiologyProvidence CollegeProvidenceRIUSA
| | | | - Justin Butler
- Department of BiologyUniversity of RichmondRichmondVAUSA
| | - Than Thar Aye
- Department of BiologyUniversity of RichmondRichmondVAUSA
| | | | - Michael DiMatteo
- State Health LaboratoryRhode Island Department of HealthProvidenceRIUSA
| | - Charles Brown
- Division of Fish & WildlifeRhode Island Department of Environmental ManagementWest KingstonRIUSA
| | - Thomas J. McGreevy
- Department of Natural Resources ScienceUniversity of Rhode IslandKingstonRIUSA
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20
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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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21
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Koizumi R, Kiyokawa Y, Tanaka KD, Kimura G, Tanikawa T, Takeuchi Y. Existence of wild brown rats (Rattus norvegicus) that are indifferent to novel objects. J Vet Med Sci 2020; 83:78-83. [PMID: 33239479 PMCID: PMC7870414 DOI: 10.1292/jvms.20-0568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Exposure to novel objects typically evokes avoidance behavior in wild animals, which is called neophobia. We previously found that wild brown rats (Rattus norvegicus) that were trapped in a park in downtown Tokyo, Japan, exhibited neophobia. We also found that this behavior was accompanied by the activation of the basolateral complex of the amygdala (BLA). Previous studies have suggested that genetic factors are the primary determinants of neophobia. Since rats in cities form populations with distinct genetic characteristics, it is reasonable to assume that wild rats caught at different locations in urban centers will exhibit different levels of neophobia. Here we assessed the intensity of neophobia in wild rats trapped at a wholesale market in Tokyo. Although we performed exactly the same experiment in which neophobia was observed in wild rats trapped at the park, the presence of novel objects did not affect the behaviors of wild rats trapped at the market. Conversely, laboratory rats showed approach and exploratory behaviors as seen in the previous study, suggesting that the experiment was performed appropriately. Compared to the laboratory rats, the lack of behavioral changes in the wild rats was accompanied by fewer Fos immunoreactive cells in the BLA. In addition, the numbers of Fos immunoreactive cells in the bed nucleus of the stria terminalis and ventromedial hypothalamus were similar between the two types of rats. The results demonstrated the existence of wild rats that were indifferent to novel objects.
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Affiliation(s)
- Ryoko Koizumi
- Laboratory of Veterinary Ethology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Present address: Wildlife Damage Management Group, Central Region Agricultural Research Center, National Agricultural Food Research Organization, 2-1-18 Kannondaira, Tsukuba, Ibaraki 305-8666, Japan
| | - Yasushi Kiyokawa
- Laboratory of Veterinary Ethology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kazuyuki D Tanaka
- Technical Research Laboratory, Ikari Shodoku Corporation, 1-12-3 Akanehama, Narashino-shi, Chiba 275-0024, Japan
| | - Goro Kimura
- Technical Research Laboratory, Ikari Shodoku Corporation, 1-12-3 Akanehama, Narashino-shi, Chiba 275-0024, Japan
| | - Tsutomu Tanikawa
- Technical Research Laboratory, Ikari Shodoku Corporation, 1-12-3 Akanehama, Narashino-shi, Chiba 275-0024, Japan
| | - Yukari Takeuchi
- Laboratory of Veterinary Ethology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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22
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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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Ghersi BM, Peterson AC, Gibson NL, Dash A, Elmayan A, Schwartzenburg H, Tu W, Riegel C, Herrera C, Blum MJ. In the heart of the city: Trypanosoma cruzi infection prevalence in rodents across New Orleans. Parasit Vectors 2020; 13:577. [PMID: 33189151 PMCID: PMC7666460 DOI: 10.1186/s13071-020-04446-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/30/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Trypanosoma cruzi - the causative agent of Chagas disease - is known to circulate in commensal pests, but its occurrence in urban environments is not well understood. We addressed this deficit by determining the distribution and prevalence of T. cruzi infection in urban populations of commensal and wild rodents across New Orleans (Louisiana, USA). We assessed whether T. cruzi prevalence varies according to host species identity and species co-occurrences, and whether T. cruzi prevalence varies across mosaics of abandonment that shape urban rodent demography and assemblage structure in the city. METHODS Leveraging city-wide population and assemblage surveys, we tested 1428 rodents comprising 5 species (cotton rats, house mice, Norway rats, rice rats and roof rats) captured at 98 trapping sites in 11 study areas across New Orleans including nine residential neighborhoods and a natural area in Orleans Parish and a neighborhood in St. Bernard Parish. We also assayed Norway rats at one site in Baton Rouge (Louisiana, USA). We used chi-square tests to determine whether infection prevalence differed among host species, among study areas, and among trapping sites according to the number of host species present. We used generalized linear mixed models to identify predictors of T. cruzi infection for all rodents and each host species, respectively. RESULTS We detected T. cruzi in all host species in all study areas in New Orleans, but not in Baton Rouge. Though overall infection prevalence was 11%, it varied by study area and trapping site. There was no difference in prevalence by species, but roof rats exhibited the broadest geographical distribution of infection across the city. Infected rodents were trapped in densely populated neighborhoods like the French Quarter. Infection prevalence seasonally varied with abandonment, increasing with greater abandonment during the summer and declining with greater abandonment during the winter. CONCLUSIONS Our findings illustrate that T. cruzi can be widespread in urban landscapes, suggesting that transmission and disease risk is greater than is currently recognized. Our findings also suggest that there is disproportionate risk of transmission in historically underserved communities, which could reinforce long-standing socioecological disparities in New Orleans and elsewhere.
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Affiliation(s)
- Bruno M. Ghersi
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN USA
| | - Anna C. Peterson
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN USA
| | - Nathaniel L. Gibson
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN USA
| | - Asha Dash
- Department of Tropical Medicine, Vector-Borne Infectious Disease Research Center, Tulane University, School of Public Health and Tropical Medicine, New Orleans, LA USA
| | - Ardem Elmayan
- Department of Tropical Medicine, Vector-Borne Infectious Disease Research Center, Tulane University, School of Public Health and Tropical Medicine, New Orleans, LA USA
| | - Hannah Schwartzenburg
- Department of Tropical Medicine, Vector-Borne Infectious Disease Research Center, Tulane University, School of Public Health and Tropical Medicine, New Orleans, LA USA
| | - Weihong Tu
- Department of Tropical Medicine, Vector-Borne Infectious Disease Research Center, Tulane University, School of Public Health and Tropical Medicine, New Orleans, LA USA
| | - Claudia Riegel
- City of New Orleans Mosquito, Termite, Rodent Control Board, New Orleans, LA USA
| | - Claudia Herrera
- Department of Tropical Medicine, Vector-Borne Infectious Disease Research Center, Tulane University, School of Public Health and Tropical Medicine, New Orleans, LA USA
| | - Michael J. Blum
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN USA
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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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Puckett EE, Orton D, Munshi‐South J. Commensal Rats and Humans: Integrating Rodent Phylogeography and Zooarchaeology to Highlight Connections between Human Societies. Bioessays 2020; 42:e1900160. [DOI: 10.1002/bies.201900160] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/09/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Emily E. Puckett
- Department of Biological SciencesUniversity of Memphis Memphis TN 38152 USA
| | - David Orton
- BioArChDepartment of ArchaeologyUniversity of York York YO10 5DD UK
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26
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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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27
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Su Q, Chen Y, Li M, Ma J, Wang B, Luo J, He H. Genetic Characterization and Molecular Evolution of Urban Seoul Virus in Southern China. Viruses 2019; 11:v11121137. [PMID: 31835357 PMCID: PMC6950471 DOI: 10.3390/v11121137] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/06/2019] [Accepted: 12/07/2019] [Indexed: 01/03/2023] Open
Abstract
Seoul virus (SEOV), which causes hemorrhagic fever with renal syndrome (HFRS) in humans, has spread all over the world, especially in mainland China. Understanding basic mechanisms of SEOV evolution is essential to better combat and prevent viral diseases. Here, we examined SEOV prevalence and evolution in the residential area of four districts in Guangzhou city, China. The carriage of SEOV was observed in 33.33% of the sampled rodents, with 35.96% of the sampled Rattus norvegicus and 13.33% of R. tanezumi. Based on the comprehensive analyses of large (L), medium (M), and small (S) segments, our study first demonstrated that the genetic characterization of urban SEOV was shaped by high nucleotide substitution rates, purifying selection, and recombination. Additionally, we detected mutational saturation in the S segment of SEOV, which may lead to the biases of genetic divergence and substitution rates in our study. Importantly, we have filled the gap of SEOV evolution in the urban area. The genetic variation of SEOV may highlight the risk of HFRS, which merits further investigation.
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Affiliation(s)
- Qianqian Su
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Q.S.); (M.L.); (J.M.); (B.W.); (J.L.)
- University of Chinese Academy of Sciences, Beijing 100101, China;
| | - Yi Chen
- University of Chinese Academy of Sciences, Beijing 100101, China;
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meng Li
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Q.S.); (M.L.); (J.M.); (B.W.); (J.L.)
| | - Jiajun Ma
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Q.S.); (M.L.); (J.M.); (B.W.); (J.L.)
| | - Bo Wang
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Q.S.); (M.L.); (J.M.); (B.W.); (J.L.)
- University of Chinese Academy of Sciences, Beijing 100101, China;
| | - Jing Luo
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Q.S.); (M.L.); (J.M.); (B.W.); (J.L.)
| | - Hongxuan He
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Q.S.); (M.L.); (J.M.); (B.W.); (J.L.)
- Correspondence:
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Richardson JL, Silveira G, Soto Medrano I, Arietta AZ, Mariani C, Pertile AC, Carvalho Pereira T, Childs JE, Ko AI, Costa F, Caccone A. Significant Genetic Impacts Accompany an Urban Rat Control Campaign in Salvador, Brazil. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] 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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30
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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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31
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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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Minter A, Himsworth CG, Byers KA, Childs JE, Ko AI, Costa F. Tails of Two Cities: Age and Wounding Are Associated With Carriage of Leptospira interrogans by Norway Rats (Rattus norvegicus) in Ecologically Distinct Urban Environments. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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34
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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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35
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Santangelo JS, Rivkin LR, Johnson MTJ. The evolution of city life. Proc Biol Sci 2018; 285:rspb.2018.1529. [PMID: 30111603 DOI: 10.1098/rspb.2018.1529] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 07/26/2018] [Indexed: 12/21/2022] Open
Abstract
Urbanization represents a dominant and growing form of disturbance to Earth's natural ecosystems, affecting biodiversity and ecosystem services on a global scale. While decades of research have illuminated the effects of urban environmental change on the structure and function of ecological communities in cities, only recently have researchers begun exploring the effects of urbanization on the evolution of urban populations. The 15 articles in this special feature represent the leading edge of urban evolutionary biology and address existing gaps in our knowledge. These gaps include: (i) the absence of theoretical models examining how multiple evolutionary mechanisms interact to affect evolution in urban environments; (ii) a lack of data on how urbanization affects natural selection and local adaptation; (iii) poor understanding of whether urban areas consistently affect non-adaptive and adaptive evolution in similar ways across multiple cities; (iv) insufficient data on the genetic and especially genomic signatures of urban evolutionary change; and (v) limited understanding of the evolutionary processes underlying the origin of new human commensals. Using theory, observations from natural populations, common gardens, genomic data and cutting-edge population genomic and landscape genetic tools, the papers in this special feature address these gaps and highlight the power of urban evolutionary biology as a globally replicated 'experiment' that provides a powerful approach for understanding how human altered environments affect evolution.
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Affiliation(s)
- James S Santangelo
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6 .,Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
| | - L Ruth Rivkin
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6 .,Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
| | - Marc T J Johnson
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6 .,Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
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