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Parsons MH, Banks PB, Deutsch MA, Munshi-South J. Temporal and Space-Use Changes by Rats in Response to Predation by Feral Cats in an Urban Ecosystem. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00146] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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Ravinet M, Elgvin TO, Trier C, Aliabadian M, Gavrilov A, Sætre GP. Signatures of human-commensalism in the house sparrow genome. Proc Biol Sci 2018; 285:rspb.2018.1246. [PMID: 30089626 DOI: 10.1098/rspb.2018.1246] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/11/2018] [Indexed: 02/07/2023] Open
Abstract
House sparrows (Passer domesticus) are a hugely successful anthrodependent species; occurring on nearly every continent. Yet, despite their ubiquity and familiarity to humans, surprisingly little is known about their origins. We sought to investigate the evolutionary history of the house sparrow and identify the processes involved in its transition to a human-commensal niche. We used a whole genome resequencing dataset of 120 individuals from three Eurasian species, including three populations of Bactrianus sparrows, a non-commensal, divergent house sparrow lineage occurring in the Near East. Coalescent modelling supports a split between house and Bactrianus sparrow 11 Kya and an expansion in the house sparrow at 6 Kya, consistent with the spread of agriculture following the Neolithic revolution. Commensal house sparrows therefore likely moved into Europe with the spread of agriculture following this period. Using the Bactrianus sparrow as a proxy for a pre-commensal, ancestral house population, we performed a comparative genome scan to identify genes potentially involved with adaptation to an anthropogenic niche. We identified potential signatures of recent, positive selection in the genome of the commensal house sparrow that are absent in Bactrianus populations. The strongest selected region encompasses two major candidate genes; COL11A-which regulates craniofacial and skull development and AMY2A, part of the amylase gene family which has previously been linked to adaptation to high-starch diets in humans and dogs. Our work examines human-commensalism in an evolutionary framework, identifies genomic regions likely involved in rapid adaptation to this new niche and ties the evolution of this species to the development of modern human civilization.
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Affiliation(s)
- Mark Ravinet
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Tore Oldeide Elgvin
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway.,Natural History Museum, University of Oslo, Oslo, Norway
| | - Cassandra Trier
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | | | - Andrey Gavrilov
- Institute of Zoology, Ministry of Education and Science of the Republic of Kazakhstan, Astana, Kazakhstan
| | - Glenn-Peter Sætre
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
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Johnson MTJ, Prashad CM, Lavoignat M, Saini HS. Contrasting the effects of natural selection, genetic drift and gene flow on urban evolution in white clover ( Trifolium repens). Proc Biol Sci 2018; 285:20181019. [PMID: 30051843 PMCID: PMC6083247 DOI: 10.1098/rspb.2018.1019] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 06/21/2018] [Indexed: 02/06/2023] Open
Abstract
Urbanization is a global phenomenon with profound effects on the ecology and evolution of organisms. We examined the relative roles of natural selection, genetic drift and gene flow in influencing the evolution of white clover (Trifolium repens), which thrives in urban and rural areas. Trifolium repens exhibits a Mendelian polymorphism for the production of hydrogen cyanide (HCN), a potent antiherbivore defence. We quantified the relative frequency of HCN in 490 populations sampled along urban-rural transects in 20 cities. We also characterized genetic variation within 120 populations in eight cities using 16 microsatellite loci. HCN frequency increased by 0.6% for every kilometre from an urban centre, and the strength of this relationship did not significantly vary between cities. Populations did not exhibit changes in genetic diversity with increasing urbanization, indicating that genetic drift is unlikely to explain urban-rural clines in HCN frequency. Populations frequently exhibited isolation-by-distance and extensive gene flow along most urban-rural transects, with the exception of a single city that exhibited genetic differentiation between urban and rural populations. Our results show that urbanization repeatedly drives parallel evolution of an ecologically important trait across many cities that vary in size, and this evolution is best explained by urban-rural gradients in natural selection.
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Affiliation(s)
- 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
| | - Cindy M Prashad
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6
| | | | - Hargurdeep S Saini
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6
- University of Canberra, Bruce, Australian Territory 2617, Australia
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Desvars-Larrive A, Baldi M, Walter T, Zink R, Walzer C. Brown rats (Rattus norvegicus) in urban ecosystems: are the constraints related to fieldwork a limit to their study? Urban Ecosyst 2018. [DOI: 10.1007/s11252-018-0772-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Combs M, Byers KA, Ghersi BM, Blum MJ, Caccone A, Costa F, Himsworth CG, Richardson JL, Munshi-South J. Urban rat races: spatial population genomics of brown rats ( Rattus norvegicus) compared across multiple cities. Proc Biol Sci 2018; 285:20180245. [PMID: 29875297 PMCID: PMC6015871 DOI: 10.1098/rspb.2018.0245] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/15/2018] [Indexed: 01/30/2023] Open
Abstract
Urbanization often substantially influences animal movement and gene flow. However, few studies to date have examined gene flow of the same species across multiple cities. In this study, we examine brown rats (Rattus norvegicus) to test hypotheses about the repeatability of neutral evolution across four cities: Salvador, Brazil; New Orleans, USA; Vancouver, Canada; and New York City, USA. At least 150 rats were sampled from each city and genotyped for a minimum of 15 000 genome-wide single nucleotide polymorphisms. Levels of genome-wide diversity were similar across cities, but varied across neighbourhoods within cities. All four populations exhibited high spatial autocorrelation at the shortest distance classes (less than 500 m) owing to limited dispersal. Coancestry and evolutionary clustering analyses identified genetic discontinuities within each city that coincided with a resource desert in New York City, major waterways in New Orleans, and roads in Salvador and Vancouver. Such replicated studies are crucial to assessing the generality of predictions from urban evolution, and have practical applications for pest management and public health. Future studies should include a range of global cities in different biomes, incorporate multiple species, and examine the impact of specific characteristics of the built environment and human socioeconomics on gene flow.
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Affiliation(s)
- Matthew Combs
- Louis Calder Center-Biological Field Station, Fordham University, 31 Whippoorwill Road, Armonk, NY 10504, USA
| | - Kaylee A Byers
- Department of Interdisciplinary Studies, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Canadian Wildlife Health Cooperative, The Animal Health Centre, Abbotsford, British Columbia, Canada
| | - Bruno M Ghersi
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA
| | - Michael J Blum
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Federico Costa
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, BA, 40296-710, Brazil
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, BA, Brazil
| | - Chelsea G Himsworth
- Canadian Wildlife Health Cooperative, The Animal Health Centre, Abbotsford, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | | | - Jason Munshi-South
- Louis Calder Center-Biological Field Station, Fordham University, 31 Whippoorwill Road, Armonk, NY 10504, USA
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