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Damiani G, Sebastiano M, Dell'Omo G, Costantini D. Blood transcriptome analysis of common kestrel nestlings living in urban and non-urban environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172585. [PMID: 38641099 DOI: 10.1016/j.scitotenv.2024.172585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/21/2024]
Abstract
Urbanisation is one of the main anthropogenic forms of land cover affecting an ever-increasing number of wild animals and their habitats. Physiological plasticity represents an important process through which animals can adjust to the novel conditions of anthropogenic environments. Relying on the analysis of gene expression, it is possible to identify the molecular responses to the habitat conditions and infer possible environmental factors that affect the organismal physiology. We have quantified for the first time the blood transcriptome of common kestrel (Falco tinnunculus) nestlings living in urban sites and compared it to the transcriptome of kestrel nestlings inhabiting rural and natural environments. We found mild differences in the expression of genes among sites, indicating adaptability or acclimation of the birds to the urban habitat. We identified 58 differentially expressed genes between urban and natural kestrels, and 12 differentially expressed genes between urban and rural kestrels. The most striking differences among sites involved inflammatory-immunological, metabolic, apoptosis, DNA repair and development genes. In particular, we found that (i) urban kestrel nestlings had higher expression of genes linked to inflammation, repair of DNA damage, or apoptosis than natural kestrel nestlings, and (ii) natural and rural kestrel nestlings had higher expression of genes linked to the development and activation of immune cells, type I interferon response, or major histocompatibility complex than urban kestrel nestlings. Finally, the KEGG enrichment analysis identified the insulin signalling as the main pathway that differed between natural and urban kestrel nestlings. This is one of a limited number of studies on vertebrates that revealed habitat-associated differences in the transcriptome. It paves the way for further in-depth studies on the links between physiological variation and habitat structure at different spatial and temporal scales.
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Affiliation(s)
- Gianluca Damiani
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy; Ornis italica, Piazza Crati 15, 00199 Rome, Italy.
| | - Manrico Sebastiano
- Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | | | - David Costantini
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy; Ornis italica, Piazza Crati 15, 00199 Rome, Italy; Unité Physiologie Moléculaire et Adaptation, UMR7221-Muséum National d'Histoire Naturelle-CNRS, 75005 Paris, France.
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2
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Savage AM, Willmott MJ, Moreno‐García P, Jagiello Z, Li D, Malesis A, Miles LS, Román‐Palacios C, Salazar‐Valenzuela D, Verrelli BC, Winchell KM, Alberti M, Bonilla‐Bedoya S, Carlen E, Falvey C, Johnson L, Martin E, Kuzyo H, Marzluff J, Munshi‐South J, Phifer‐Rixey M, Stadnicki I, Szulkin M, Zhou Y, Gotanda KM. Online toolkits for collaborative and inclusive global research in urban evolutionary ecology. Ecol Evol 2024; 14:e11633. [PMID: 38919647 PMCID: PMC11197044 DOI: 10.1002/ece3.11633] [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: 02/22/2024] [Revised: 06/05/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024] Open
Abstract
Urban evolutionary ecology is inherently interdisciplinary. Moreover, it is a field with global significance. However, bringing researchers and resources together across fields and countries is challenging. Therefore, an online collaborative research hub, where common methods and best practices are shared among scientists from diverse geographic, ethnic, and career backgrounds would make research focused on urban evolutionary ecology more inclusive. Here, we describe a freely available online research hub for toolkits that facilitate global research in urban evolutionary ecology. We provide rationales and descriptions of toolkits for: (1) decolonizing urban evolutionary ecology; (2) identifying and fostering international collaborative partnerships; (3) common methods and freely-available datasets for trait mapping across cities; (4) common methods and freely-available datasets for cross-city evolutionary ecology experiments; and (5) best practices and freely available resources for public outreach and communication of research findings in urban evolutionary ecology. We outline how the toolkits can be accessed, archived, and modified over time in order to sustain long-term global research that will advance our understanding of urban evolutionary ecology.
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Affiliation(s)
- Amy M. Savage
- Department of Biology & Center for Computational and Integrative BiologyRutgers University – CamdenCamdenNew JerseyUSA
| | - Meredith J. Willmott
- Department of Biology & Center for Computational and Integrative BiologyRutgers University – CamdenCamdenNew JerseyUSA
| | - Pablo Moreno‐García
- Department of Biological Sciences, Center for Computation & TechnologyLouisiana State UniversityBaton RougeLouisianaUSA
| | - Zuzanna Jagiello
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research CentreUniversity of WarsawWarsawPoland
| | - Daijiang Li
- Department of Biological Sciences, Center for Computation & TechnologyLouisiana State UniversityBaton RougeLouisianaUSA
| | - Anna Malesis
- Department of Urban Design and PlanningUniversity of WashingtonSeattleWashingtonUSA
| | - Lindsay S. Miles
- Virginia Polytechnic and State UniversityEntomology DepartmentBlacksburgVirginiaUSA
| | | | - David Salazar‐Valenzuela
- Centro de Investigación de la Biodiversidad y Cambio Climático & Facultad de Ciencias de Medio AmbienteUniversidad IndoaméricaQuitoEcuador
| | - Brian C. Verrelli
- Center for Biological Data ScienceVirginia Commonwealth UniversityRichmondVirginiaUSA
| | | | - Marina Alberti
- Department of Urban Design and PlanningUniversity of WashingtonSeattleWashingtonUSA
| | | | - Elizabeth Carlen
- Department of BiologyWashington University of St. LouisSt. LouisMissouriUSA
| | - Cleo Falvey
- Department of Biology & Center for Computational and Integrative BiologyRutgers University – CamdenCamdenNew JerseyUSA
| | - Lauren Johnson
- Department of BiologyWashington University of St. LouisSt. LouisMissouriUSA
| | - Ella Martin
- Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
| | - Hanna Kuzyo
- Frankfurt Zoological SocietyFrankfurtGermany
| | - John Marzluff
- Department of Urban Design and PlanningUniversity of WashingtonSeattleWashingtonUSA
| | - Jason Munshi‐South
- Louis Calder Center & Department of Biological SciencesFordham UniversityArmonkNew YorkUSA
| | | | - Ignacy Stadnicki
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research CentreUniversity of WarsawWarsawPoland
| | - Marta Szulkin
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research CentreUniversity of WarsawWarsawPoland
| | - Yuyu Zhou
- Department of Geological and Atmospheric SciencesIowa State UniversityAmesIowaUSA
| | - Kiyoko M. Gotanda
- Department of Biological SciencesBrock UniversitySt. CatharinesOntarioCanada
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3
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Folkertsma R, Charbonnel N, Henttonen H, Heroldová M, Huitu O, Kotlík P, Manzo E, Paijmans JLA, Plantard O, Sándor AD, Hofreiter M, Eccard JA. Genomic signatures of climate adaptation in bank voles. Ecol Evol 2024; 14:e10886. [PMID: 38455148 PMCID: PMC10918726 DOI: 10.1002/ece3.10886] [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: 05/05/2023] [Revised: 11/17/2023] [Accepted: 12/18/2023] [Indexed: 03/09/2024] Open
Abstract
Evidence for divergent selection and adaptive variation across the landscape can provide insight into a species' ability to adapt to different environments. However, despite recent advances in genomics, it remains difficult to detect the footprints of climate-mediated selection in natural populations. Here, we analysed ddRAD sequencing data (21,892 SNPs) in conjunction with geographic climate variation to search for signatures of adaptive differentiation in twelve populations of the bank vole (Clethrionomys glareolus) distributed across Europe. To identify the loci subject to selection associated with climate variation, we applied multiple genotype-environment association methods, two univariate and one multivariate, and controlled for the effect of population structure. In total, we identified 213 candidate loci for adaptation, 74 of which were located within genes. In particular, we identified signatures of selection in candidate genes with functions related to lipid metabolism and the immune system. Using the results of redundancy analysis, we demonstrated that population history and climate have joint effects on the genetic variation in the pan-European metapopulation. Furthermore, by examining only candidate loci, we found that annual mean temperature is an important factor shaping adaptive genetic variation in the bank vole. By combining landscape genomic approaches, our study sheds light on genome-wide adaptive differentiation and the spatial distribution of variants underlying adaptive variation influenced by local climate in bank voles.
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Affiliation(s)
- Remco Folkertsma
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
- Comparative Cognition Unit, Messerli Research InstituteUniversity of Veterinary Medicine ViennaViennaAustria
| | | | | | - Marta Heroldová
- Department of Forest Ecology, FFWTMendel University in BrnoBrnoCzech Republic
| | - Otso Huitu
- Natural Resources Institute FinlandHelsinkiFinland
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and GeneticsCzech Academy of SciencesLiběchovCzech Republic
| | - Emiliano Manzo
- Fondazione Ethoikos, Convento dell'OsservanzaRadicondoliItaly
| | - Johanna L. A. Paijmans
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
- Present address:
Evolutionary Ecology Group, Department of ZoologyUniversity of CambridgeCambridgeUK
| | | | - Attila D. Sándor
- HUN‐RENClimate Change: New Blood‐Sucking Parasites and Vector‐Borne Pathogens Research GroupBudapestHungary
- Department of Parasitology and ZoologyUniversity of Veterinary MedicineBudapestHungary
- Department of Parasitology and Parasitic DiseasesUniversity of Agricultural Sciences and Veterinary MedicineCluj‐NapocaRomania
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
| | - Jana A. Eccard
- Animal Ecology, Institute for Biochemistry and Biology, Faculty of ScienceBerlin‐Brandenburg Institute for Biodiversity ResearchUniversity of PotsdamPotsdamGermany
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4
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Moran PA, Bosse M, Mariën J, Halfwerk W. Genomic footprints of (pre) colonialism: Population declines in urban and forest túngara frogs coincident with historical human activity. Mol Ecol 2024; 33:e17258. [PMID: 38153193 DOI: 10.1111/mec.17258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 11/21/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023]
Abstract
Urbanisation is rapidly altering ecosystems, leading to profound biodiversity loss. To mitigate these effects, we need a better understanding of how urbanisation impacts dispersal and reproduction. Two contrasting population demographic models have been proposed that predict that urbanisation either promotes (facilitation model) or constrains (fragmentation model) gene flow and genetic diversity. Which of these models prevails likely depends on the strength of selection on specific phenotypic traits that influence dispersal, survival, or reproduction. Here, we a priori examined the genomic impact of urbanisation on the Neotropical túngara frog (Engystomops pustulosus), a species known to adapt its reproductive traits to urban selective pressures. Using whole-genome resequencing for multiple urban and forest populations we examined genomic diversity, population connectivity and demographic history. Contrary to both the fragmentation and facilitation models, urban populations did not exhibit substantial changes in genomic diversity or differentiation compared with forest populations, and genomic variation was best explained by geographic distance rather than environmental factors. Adopting an a posteriori approach, we additionally found both urban and forest populations to have undergone population declines. The timing of these declines appears to coincide with extensive human activity around the Panama Canal during the last few centuries rather than recent urbanisation. Our study highlights the long-lasting legacy of past anthropogenic disturbances in the genome and the importance of considering the historical context in urban evolution studies as anthropogenic effects may be extensive and impact nonurban areas on both recent and older timescales.
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Affiliation(s)
- Peter A Moran
- A-LIFE, Section Ecology & Evolution, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mirte Bosse
- A-LIFE, Section Ecology & Evolution, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Janine Mariën
- A-LIFE, Section Ecology & Evolution, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Wouter Halfwerk
- A-LIFE, Section Ecology & Evolution, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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5
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Ramírez-Sánchez D, Gibelin-Viala C, Roux F, Vailleau F. Genetic architecture of the response of Arabidopsis thaliana to a native plant-growth-promoting bacterial strain. FRONTIERS IN PLANT SCIENCE 2023; 14:1266032. [PMID: 38023938 PMCID: PMC10665851 DOI: 10.3389/fpls.2023.1266032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
By improving plant nutrition and alleviating abiotic and biotic stresses, plant growth-promoting bacteria (PGPB) can help to develop eco-friendly and sustainable agricultural practices. Besides climatic conditions, soil conditions, and microbe-microbe interactions, the host genotype influences the effectiveness of PGPB. Yet, most GWAS conducted to characterize the genetic architecture of response to PGPB are based on non-native interactions between a host plant and PGPB strains isolated from the belowground compartment of other plants. In this study, a GWAS was set up under in vitro conditions to describe the genetic architecture of the response of Arabidopsis thaliana to the PGPB Pseudomonas siliginis, by inoculating seeds of 162 natural accessions from the southwest of France with one strain isolated from the leaf compartment in the same geographical region. Strong genetic variation of plant growth response to this native PGPB was observed at a regional scale, with the strain having a positive effect on the vegetative growth of small plants and a negative effect on the vegetative growth of large plants. The polygenic genetic architecture underlying this negative trade-off showed suggestive signatures of local adaptation. The main eco-evolutionary relevant candidate genes are involved in seed and root development.
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Babik W, Dudek K, Marszałek M, Palomar G, Antunes B, Sniegula S. The genomic response to urbanization in the damselfly Ischnura elegans. Evol Appl 2023; 16:1805-1818. [PMID: 38029064 PMCID: PMC10681423 DOI: 10.1111/eva.13603] [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: 03/03/2023] [Accepted: 09/19/2023] [Indexed: 12/01/2023] Open
Abstract
The complex and rapid environmental changes brought about by urbanization pose significant challenges to organisms. The multifaceted effects of urbanization often make it difficult to define and pinpoint the very nature of adaptive urban phenotypes. In such situations, scanning genomes for regions differentiated between urban and non-urban populations may be an attractive approach. Here, we investigated the genomic signatures of adaptation to urbanization in the damselfly Ischnura elegans sampled from 31 rural and urban localities in three geographic regions: southern and northern Poland, and southern Sweden. Genome-wide variation was assessed using more than 370,000 single nucleotide polymorphisms (SNPs) genotyped by ddRADseq. Associations between SNPs and the level of urbanization were tested using two genetic environment association methods: Latent Factors Mixed Models and BayPass. While we found numerous candidate SNPs and a highly significant overlap between candidates identified by the two methods within the geographic regions, there was a distinctive lack of repeatability between the geographic regions both at the level of individual SNPs and of genomic regions. However, we found "synapse organization" at the top of the functional categories enriched among the genes located in the proximity of the candidate urbanization SNPs. Interestingly, the overall significance of "synapse organization" was built up by the accretion of different genes associated with candidate SNPs in different geographic regions. This finding is consistent with the highly polygenic nature of adaptation, where the response may be achieved through a subtle adjustment of allele frequencies in different genes that contribute to adaptive phenotypes. Taken together, our results point to a polygenic adaptive response in the nervous system, specifically implicating genes involved in synapse organization, which mirrors the findings from several genomic and behavioral studies of adaptation to urbanization in other taxa.
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Affiliation(s)
- W. Babik
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - K. Dudek
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - M. Marszałek
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - G. Palomar
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
- Department of Genetics, Physiology and Microbiology, Faculty of Biological SciencesComplutense University of MadridMadridSpain
| | - B. Antunes
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - S. Sniegula
- Department of Ecosystem Conservation, Institute of Nature ConservationPolish Academy of SciencesKrakówPoland
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7
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Minias P. The effects of urban life on animal immunity: Adaptations and constraints. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:165085. [PMID: 37379938 DOI: 10.1016/j.scitotenv.2023.165085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/21/2023] [Accepted: 06/21/2023] [Indexed: 06/30/2023]
Abstract
Land transformation, including urbanization, is a dominant form of anthropogenic change to the global environment at the dawn of the Anthropocene epoch. More and more species are brought into direct contact with humans, being either required to develop broad-scale adaptations to urban environment or filtered out from urbanized areas. While behavioural or physiological adaptations are at the forefront of urban biology research, there is accumulating evidence for divergent pathogen pressure across urbanization gradients, requiring adjustments in host immune function. At the same time, host immunity may be constrained by unfavourable components of an urban environment, such as poor-quality food resources, disturbance, or pollution. Here, I reviewed existing evidence for adaptations and constrains in the immune system of urban animals, focusing on the recent implementation of metabarcoding, genomic, transcriptomic, and epigenomic approaches in urban biology research. I show that spatial variation in pathogen pressure across urban and non-urban landscapes is highly complex and may be context-dependent, but there is solid evidence for pathogen-driven immunostimulation in urban-dwelling animals. I also show that genes coding for molecules directly involved in interactions with pathogens are the prime candidates for immunogenetic adaptations to urban life. Evidence emerging from landscape genomics and transcriptomics show that immune adaptations to urban life may have a polygenic nature, but immune traits may not be among the key biological functions experiencing broad-scale microevolutionary changes in response to urbanization. Finally, I provided recommendations for future research, including i) a better integration of different 'omic' approaches to obtain a more complete picture of immune adaptations to urban life in non-model animal taxa, ii) quantification of fitness landscapes for immune phenotypes and genotypes across urbanization gradient, and iii) much broader taxonomic coverage (including invertebrates) necessary to draw more robust conclusions on how general (or taxa-specific) are immune responses of animals to urbanization.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237 Łódź, Poland.
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8
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Mascarenhas R, Meirelles PM, Batalha-Filho H. Urbanization drives adaptive evolution in a Neotropical bird. Curr Zool 2023; 69:607-619. [PMID: 37637315 PMCID: PMC10449428 DOI: 10.1093/cz/zoac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/16/2022] [Indexed: 08/29/2023] Open
Abstract
Urbanization has dramatic impacts on natural habitats and such changes may potentially drive local adaptation of urban populations. Behavioral change has been specifically shown to facilitate the fast adaptation of birds to changing environments, but few studies have investigated the genetic mechanisms of this process. Such investigations could provide insights into questions about both evolutionary theory and management of urban populations. In this study, we investigated whether local adaptation has occurred in urban populations of a Neotropical bird species, Coereba flaveola, specifically addressing whether observed behavioral adaptations are correlated to genetic signatures of natural selection. To answer this question, we sampled 24 individuals in urban and rural environments, and searched for selected loci through a genome-scan approach based on RADseq genomic data, generated and assembled using a reference genome for the species. We recovered 46 loci as putative selection outliers, and 30 of them were identified as associated with biological processes possibly related to urban adaptation, such as the regulation of energetic metabolism, regulation of genetic expression, and changes in the immunological system. Moreover, genes involved in the development of the nervous system showed signatures of selection, suggesting a link between behavioral and genetic adaptations. Our findings, in conjunction with similar results in previous studies, support the idea that cities provide a similar selective pressure on urban populations and that behavioral plasticity may be enhanced through genetic changes in urban populations.
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Affiliation(s)
- Rilquer Mascarenhas
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, 40170-115 Salvador, Bahia, Brazil
| | - Pedro Milet Meirelles
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, 40170-115 Salvador, Bahia, Brazil
| | - Henrique Batalha-Filho
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, 40170-115 Salvador, Bahia, Brazil
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9
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Corkey BE. Reactive oxygen species: role in obesity and mitochondrial energy efficiency. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220210. [PMID: 37482778 PMCID: PMC10363708 DOI: 10.1098/rstb.2022.0210] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/29/2023] [Indexed: 07/25/2023] Open
Abstract
Changes correlating with increasing obesity include insulin resistance, hyperlipidaemia, hyperinsulinaemia, highly processed food and environmental toxins including plastics and air pollution. The relationship between the appearance of each of these potential causes and the onset of obesity is unknown. The cause(s) must precede obesity, the consequence, and temporally relate to its rising incidence. Macronutrients such as carbohydrates or fats are unlikely to cause obesity since these have long been constituents of human diets. Furthermore, food consumption and body weight have been well-regulated in most humans and other species until recent times. Thus, attention must focus on changes that have occurred in the last half-century and the relationship between such changes and specific populations that are impacted. The hypothesis presented here is that substances that have entered our bodies recently cause obesity by generating false and misleading information about energy status. We propose that this misinformation is caused by changes in the oxidation-reduction (redox) potential of metabolites that circulate and communicate to organs throughout the body. Examples are provided of food additives that generate reactive oxygen species and impact redox state, thereby, eliciting inappropriate tissue-specific functional changes, including insulin secretion. Reversal requires identification, neutralization, or removal of these compounds. This article is part of a discussion meeting issue 'Causes of obesity: theories, conjectures and evidence (Part I)'.
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Affiliation(s)
- Barbara E. Corkey
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
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10
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Feoktistova NY, Meschersky IG, Karmanova TN, Gureeva AV, Surov AV. Allele Diversity of the Major Histocompatibility Complex in the Common Hamster (Cricetus cricetus) in Urban and Rural Populations. BIOL BULL+ 2022. [DOI: 10.1134/s1062359022050077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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11
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Linking genetic, morphological, and behavioural divergence between inland island and mainland deer mice. Heredity (Edinb) 2022; 128:97-106. [PMID: 34952930 PMCID: PMC8814197 DOI: 10.1038/s41437-021-00492-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 02/03/2023] Open
Abstract
The island syndrome hypothesis (ISH) stipulates that, as a result of local selection pressures and restricted gene flow, individuals from island populations should differ from individuals within mainland populations. Specifically, island populations are predicted to contain individuals that are larger, less aggressive, more sociable, and that invest more in their offspring. To date, tests of the ISH have mainly compared oceanic islands to continental sites, and rarely smaller spatial scales such as inland watersheds. Here, using a novel set of genome-wide SNP markers in wild deer mice (Peromyscus maniculatus) we conducted a genomic assessment of predictions underlying the ISH in an inland riverine island system: analysing island-mainland population structure, and quantifying heritability of phenotypes thought to underlie the ISH. We found clear genomic differentiation between the island and mainland populations and moderate to high marker-based heritability estimates for overall variation in traits previously found to differ in line with the ISH between mainland and island locations. FST outlier analyses highlighted 12 loci associated with differentiation between mainland and island populations. Together these results suggest that the island populations examined are on independent evolutionary trajectories, the traits considered have a genetic basis (rather than phenotypic variation being solely due to phenotypic plasticity). Coupled with the previous results showing significant phenotypic differentiation between the island and mainland groups in this system, this study suggests that the ISH can hold even on a small spatial scale.
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12
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Orrock JL, Abueg L, Gammie S, Munshi‐South J. Exome sequencing of deer mice on two California Channel Islands identifies potential adaptation to strongly contrasting ecological conditions. Ecol Evol 2021; 11:17191-17201. [PMID: 34938502 PMCID: PMC8668806 DOI: 10.1002/ece3.8357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/12/2021] [Accepted: 10/20/2021] [Indexed: 11/23/2022] Open
Abstract
Understanding the forces that drive genotypic and phenotypic change in wild populations is a central goal of evolutionary biology. We examined exome variation in populations of deer mice from two of the California Channel Islands: Peromyscus maniculatus elusus from Santa Barbara Island and P. m. santacruzae from Santa Cruz Island exhibit significant differences in olfactory predator recognition, activity timing, aggressive behavior, morphology, prevalence of Sin Nombre virus, and population densities. We characterized variation in protein-coding regions using exome capture and sequencing of 25 mice from Santa Barbara Island and 22 mice from Santa Cruz Island. We identified and examined 386,256 SNPs using three complementary methods (BayeScan, pcadapt, and LFMM). We found strong differences in molecular variation between the two populations and 710 outlier SNPs in protein-coding genes that were detected by all three methods. We identified 35 candidate genes from this outlier set that were related to differences in phenotypes between island populations. Enrichment analyses demonstrated that patterns of molecular variation were associated with biological processes related to response to chemical stimuli and regulation of immune processes. Candidate genes associated with olfaction (Gfy, Tlr2, Vmn13r2, numerous olfactory receptor genes), circadian activity (Cry1), anxiety (Brca1), immunity (Cd28, Eif2ak4, Il12a, Syne1), aggression (Cyp19a, Lama2), and body size (Bc16, Syne1) exhibited non-synonymous mutations predicted to have moderate to large effects. Variation in olfaction-related genes, including a stop codon in the Santa Barbara Island population, suggests loss of predator-recognition traits at the molecular level, consistent with a lack of behavioral aversion to fox feces. These findings also suggest that divergent pathogen prevalence and population density may have influenced adaptive immunity and behavioral phenotypes, such as reduced aggression. Overall, our study indicates that ecological differences between islands are associated with signatures of selection in protein-coding genes underlying phenotypes that promote success in those environments.
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Affiliation(s)
- John L. Orrock
- Department of Integrative BiologyUniversity of WisconsinMadisonWisconsinUSA
| | - Linelle Abueg
- Louis Calder Center – Biological Field StationFordham UniversityArmonkNew YorkUSA
| | - Stephen Gammie
- Department of Integrative BiologyUniversity of WisconsinMadisonWisconsinUSA
| | - Jason Munshi‐South
- Louis Calder Center – Biological Field StationFordham UniversityArmonkNew YorkUSA
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Abstract
Although research performed in cities will not uncover new evolutionary mechanisms, it could provide unprecedented opportunities to examine the interplay of evolutionary forces in new ways and new avenues to address classic questions. However, while the variation within and among cities affords many opportunities to advance evolutionary biology research, careful alignment between how cities are used and the research questions being asked is necessary to maximize the insights that can be gained. In this review, we develop a framework to help guide alignment between urban evolution research approaches and questions. Using this framework, we highlight what has been accomplished to date in the field of urban evolution and identify several up-and-coming research directions for further expansion. We conclude that urban environments can be used as evolutionary test beds to tackle both new and long-standing questions in evolutionary biology.
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Affiliation(s)
- Sarah E. Diamond
- Department of Biology, Case Western Reserve University, Cleveland, Ohio 44106, USA;,
| | - Ryan A. Martin
- Department of Biology, Case Western Reserve University, Cleveland, Ohio 44106, USA;,
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14
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Chatelain M, Da Silva A, Celej M, Kurek E, Bulska E, Corsini M, Szulkin M. Replicated, urban-driven exposure to metallic trace elements in two passerines. Sci Rep 2021; 11:19662. [PMID: 34608262 PMCID: PMC8490372 DOI: 10.1038/s41598-021-99329-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/16/2021] [Indexed: 12/30/2022] Open
Abstract
While there are increasing examples of phenotypic and genotypic differences between urban and non-urban populations of plants and animals, few studies identified the mechanisms explaining those dissimilarities. The characterization of the urban landscape, which can only be achieved by measuring variability in relevant environmental factors within and between cities, is a keystone prerequisite to understand the effects of urbanization on wildlife. Here, we measured variation in bird exposure to metal pollution within 8 replicated urbanization gradients and within 2 flagship bird species in urban evolutionary ecology: the blue tit (Cyanistes caeruleus) and the great tit (Parus major). We report on a highly significant, positive linear relationship between the magnitude of urbanization-inferred as either tree cover, impervious surface cover, or an urbanization score computed from several environmental variables, and copper, zinc and lead concentrations in bird feathers. The reverse relationship was measured in the case of mercury, while cadmium and arsenic did not vary in response to the urbanization level. This result, replicated across multiple cities and two passerine species, strongly suggests that copper, zinc, lead and mercury pollution is likely to trigger the emergence of parallel responses at the phenotypic and/or genotypic level between urban environments worldwide.
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Affiliation(s)
- Marion Chatelain
- Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland. .,Department of Zoology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria.
| | - Arnaud Da Silva
- grid.12847.380000 0004 1937 1290Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Marta Celej
- grid.12847.380000 0004 1937 1290Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Eliza Kurek
- grid.12847.380000 0004 1937 1290Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland
| | - Ewa Bulska
- grid.12847.380000 0004 1937 1290Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland ,grid.12847.380000 0004 1937 1290Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland
| | - Michela Corsini
- grid.12847.380000 0004 1937 1290Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Marta Szulkin
- grid.12847.380000 0004 1937 1290Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
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15
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Colella JP, Blumstein DM, MacManes MD. Disentangling environmental drivers of circadian metabolism in desert-adapted mice. J Exp Biol 2021; 224:jeb242529. [PMID: 34495305 PMCID: PMC8502254 DOI: 10.1242/jeb.242529] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/13/2021] [Indexed: 01/21/2023]
Abstract
Metabolism is a complex phenotype shaped by natural environmental rhythms, as well as behavioral, morphological and physiological adaptations. Metabolism has been historically studied under constant environmental conditions, but new methods of continuous metabolic phenotyping now offer a window into organismal responses to dynamic environments, and enable identification of abiotic controls and the timing of physiological responses relative to environmental change. We used indirect calorimetry to characterize metabolic phenotypes of the desert-adapted cactus mouse (Peromyscus eremicus) in response to variable environmental conditions that mimic their native environment versus those recorded under constant warm and constant cool conditions, with a constant photoperiod and full access to resources. We found significant sexual dimorphism, with males being more prone to dehydration than females. Under circadian environmental variation, most metabolic shifts occurred prior to physical environmental change and the timing was disrupted under both constant treatments. The ratio of CO2 produced to O2 consumed (the respiratory quotient) reached greater than 1.0 only during the light phase under diurnally variable conditions, a pattern that strongly suggests that lipogenesis contributes to the production of energy and endogenous water. Our results are consistent with historical descriptions of circadian torpor in this species (torpid by day, active by night), but reject the hypothesis that torpor is initiated by food restriction or negative water balance.
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Affiliation(s)
| | | | - Matthew D. MacManes
- University of New Hampshire, Department of Molecular, Cellular, and Biomedical Sciences, Durham, NH 03824, USA
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16
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Fossett TE, Hyman J. The effects of habituation on boldness of urban and rural song sparrows (Melospiza melodia). BEHAVIOUR 2021. [DOI: 10.1163/1568539x-bja10113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
As urbanization increases globally, wildlife species are changing their behaviour in many ways. Urban animals are often bolder, or less fearful of new stimuli, than rural animals. While adaptation can drive behavioural changes in urban animals, other factors, such as learning or habituation, can also lead to behavioural modifications. To determine how repeated exposure to a non-threatening human affects song sparrow (Melospiza melodia) behaviour in urban and rural habitat, we measured boldness as flight initiation distance (FID), for 5 consecutive days. We found that urban birds had consistently lower FID’s than their rural counterparts from days 1–4, yet there was no difference in rural and urban FID by trial 5. FID decreased over 5 days of repeated trials in the rural populations, but not the urban. These results suggest that habituation can occur quickly in rural birds and may account for the greater boldness we typically see in urban populations.
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Affiliation(s)
| | - Jeremy Hyman
- Western Carolina University, 1 University Way, Cullowhee, NC 28723, USA
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17
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Hantak MM, McLean BS, Li D, Guralnick RP. Mammalian body size is determined by interactions between climate, urbanization, and ecological traits. Commun Biol 2021; 4:972. [PMID: 34400755 PMCID: PMC8367959 DOI: 10.1038/s42003-021-02505-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 07/28/2021] [Indexed: 11/20/2022] Open
Abstract
Anthropogenically-driven climate warming is a hypothesized driver of animal body size reductions. Less understood are effects of other human-caused disturbances on body size, such as urbanization. We compiled 140,499 body size records of over 100 North American mammals to test how climate and human population density, a proxy for urbanization, and their interactions with species traits, impact body size. We tested three hypotheses of body size variation across urbanization gradients: urban heat island effects, habitat fragmentation, and resource availability. Our results demonstrate that both urbanization and temperature influence mammalian body size variation, most often leading to larger individuals, thus supporting the resource availability hypothesis. In addition, life history and other ecological factors play a critical role in mediating the effects of climate and urbanization on body size. Larger mammals and species that utilize thermal buffering are more sensitive to warmer temperatures, while flexibility in activity time appears to be advantageous in urbanized areas. This work highlights the value of using digitized, natural history data to track how human disturbance drives morphological variation. Anthropogenically-driven climate change is responsible for body size decreases in mammals. Using an important dataset of historically-collected data and data from continental-scale survey efforts from the National Ecological Observatory Network, Hantak et al. show that urbanization plays an important role in mediating this dynamic.
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Affiliation(s)
- Maggie M Hantak
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
| | - Bryan S McLean
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC, USA
| | - Daijiang Li
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.,Center for Computation & Technology, Louisiana State University, Baton Rouge, LA, USA
| | - Robert P Guralnick
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
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18
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Medina R, Wogan GOU, Bi K, Termignoni-García F, Bernal MH, Jaramillo-Correa JP, Wang IJ, Vázquez-Domínguez E. Phenotypic and genomic diversification with isolation by environment along elevational gradients in a neotropical treefrog. Mol Ecol 2021; 30:4062-4076. [PMID: 34160853 DOI: 10.1111/mec.16035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 01/03/2023]
Abstract
Understanding how geographic and environmental heterogeneity drive local patterns of genetic variation is a major goal of ecological genomics and a key question in evolutionary biology. The tropical Andes and inter-Andean valleys are shaped by markedly heterogeneous landscapes, where species experience strong selective processes. We examined genome-wide SNP data together with behavioural and ecological traits (mating calls and body size) known to contribute to genetic isolation in anurans in the banana tree-dwelling frog, Boana platanera, distributed across an environmental gradient in Central Colombia (northern South America). Here, we analysed the relationships between environmentally (temperature and precipitation) associated genetic and phenotypic differentiation and the potential drivers of isolation by environment along an elevation gradient. We identified candidate SNPs associated with temperature and body size, which follow a clinal pattern of genome-wide differentiation tightly coupled with phenotypic variation: as elevation increases, B. platanera exhibits larger body size and longer call duration with more pulses but lower pulse rate and frequency. Thus, the environmental landscape has rendered a scenario where isolation by environment and candidate loci show concordance with phenotypic divergence in this tropical frog along an elevation gradient in the Colombian Andes. Our study sets the basis for evaluating the role of temperature in the genetic structure and local adaptation in tropical treefrogs and its putative effect on life cycle (embryos, tadpoles, adults) along elevation gradients.
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Affiliation(s)
- Ricardo Medina
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México.,Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México.,Grupo de Herpetología, Eco-Fisiología & Etología, Departamento de Biología, Universidad del Tolima, Altos de Santa Helena, Ibagué, Colombia
| | - Guinevere O U Wogan
- Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley, California, USA.,Department of Integrative Biology, Oklahoma State University, Oklahoma, USA
| | - Ke Bi
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA.,Computational Genomics Resource Laboratory (CGRL, California Institute for Quantitative Biosciences (QB3, University of California, Berkeley, California, USA
| | - Flavia Termignoni-García
- Department of Organismic and Evolutionary Biology (OEB, Harvard University, Cambridge, Massachusetts, USA
| | - Manuel Hernando Bernal
- Grupo de Herpetología, Eco-Fisiología & Etología, Departamento de Biología, Universidad del Tolima, Altos de Santa Helena, Ibagué, Colombia
| | - Juan P Jaramillo-Correa
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley, California, USA
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
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19
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Zhou S, Krzton A, Gao S, Guo C, Xiang Z. Effects of human activity on the habitat utilization of Himalayan marmot ( Marmota himalayana) in Zoige wetland. Ecol Evol 2021; 11:8957-8968. [PMID: 34257938 PMCID: PMC8258216 DOI: 10.1002/ece3.7733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 05/13/2021] [Indexed: 11/10/2022] Open
Abstract
Human activity is increasingly and persistently disturbing nature and wild animals. Affected wildlife adopts multiple strategies to deal with different human influences. To explore the effect of human activity on habitat utilization of Himalayan marmot (Marmota himalayana), habitat utilization patterns of three neighboring marmot populations in habitats affected differently by human activities were recorded and compared. We found that (a) distance between reproductive burrows (a represent of reproductive pairs) becomes shorter under the influence of human activities, and more burrows were dug as temporary shelters, resulting in shorter distance between those shelters and shorter distance flee to those shelters and, consequently, shorter flight initiation distance when threatened. More burrows that are closer to the disturbed habitats improve the ability to escape from threats. (b) Reproductive burrow site selection of the species is determined by the availability of mounds in the habitat, and breeding pairs selectively build reproductive (also the hibernation) burrows on mounds, potentially to improve surveillance when basking and the drainage of burrows. Human activities generally drive breeding pairs away from the road to dig their reproductive burrows likely to reduce disturbance from vehicles. However, even heavy human activity exerts no pressure on the distance of reproductive burrows from the road or the mound volume of the high disturbance population, potentially because mounds are the best burrowing site to reproduce and hibernate in the habitat. Marmots deal with disturbance by digging more burrows in the habitat to flee more effectively and building reproductive burrows on mounds to gain better vigilance and drainage efficiency.
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Affiliation(s)
- Shuailing Zhou
- College of Life Science and TechnologyCentral South University of Forestry & TechnologyChangshaChina
| | - Ali Krzton
- Department of Research and InstructionRBD LibraryAuburn UniversityAuburnALUSA
| | - Shuai Gao
- College of Life Science and TechnologyCentral South University of Forestry & TechnologyChangshaChina
| | - Cheng Guo
- College of Life Science and TechnologyCentral South University of Forestry & TechnologyChangshaChina
| | - Zuofu Xiang
- College of Life Science and TechnologyCentral South University of Forestry & TechnologyChangshaChina
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20
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Salmón P, Jacobs A, Ahrén D, Biard C, Dingemanse NJ, Dominoni DM, Helm B, Lundberg M, Senar JC, Sprau P, Visser ME, Isaksson C. Continent-wide genomic signatures of adaptation to urbanisation in a songbird across Europe. Nat Commun 2021; 12:2983. [PMID: 34016968 PMCID: PMC8137928 DOI: 10.1038/s41467-021-23027-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 04/01/2021] [Indexed: 02/03/2023] Open
Abstract
Urbanisation is increasing worldwide, and there is now ample evidence of phenotypic changes in wild organisms in response to this novel environment. Yet, the genetic changes and genomic architecture underlying these adaptations are poorly understood. Here, we genotype 192 great tits (Parus major) from nine European cities, each paired with an adjacent rural site, to address this major knowledge gap in our understanding of wildlife urban adaptation. We find that a combination of polygenic allele frequency shifts and recurrent selective sweeps are associated with the adaptation of great tits to urban environments. While haplotypes under selection are rarely shared across urban populations, selective sweeps occur within the same genes, mostly linked to neural function and development. Collectively, we show that urban adaptation in a widespread songbird occurs through unique and shared selective sweeps in a core-set of behaviour-linked genes.
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Affiliation(s)
- Pablo Salmón
- Department of Biology, Lund University, Lund, Sweden.
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK.
| | - Arne Jacobs
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Dag Ahrén
- Department of Biology, Lund University, Lund, Sweden
| | - Clotilde Biard
- Sorbonne Université, UPEC, Paris 7, CNRS, INRA, IRD, Institut d'Écologie et des Sciences de l'Environnement de Paris, iEES Paris, F-75005, Paris, France
| | - Niels J Dingemanse
- Department of Biology, Ludwig Maximilians University Munich, Munich, Germany
| | - Davide M Dominoni
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Barbara Helm
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
- GELIFES - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Max Lundberg
- Department of Biology, Lund University, Lund, Sweden
| | | | - Philipp Sprau
- Department of Biology, Ludwig Maximilians University Munich, Munich, Germany
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
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21
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Locally adapted gut microbiomes mediate host stress tolerance. ISME JOURNAL 2021; 15:2401-2414. [PMID: 33658622 PMCID: PMC8319338 DOI: 10.1038/s41396-021-00940-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 01/29/2021] [Accepted: 02/11/2021] [Indexed: 01/04/2023]
Abstract
While evidence for the role of the microbiome in shaping host stress tolerance is becoming well-established, to what extent this depends on the interaction between the host and its local microbiome is less clear. Therefore, we investigated whether locally adapted gut microbiomes affect host stress tolerance. In the water flea Daphnia magna, we studied if the host performs better when receiving a microbiome from their source region than from another region when facing a stressful condition, more in particular exposure to the toxic cyanobacteria Microcystis aeruginosa. Therefore, a reciprocal transplant experiment was performed in which recipient, germ-free D. magna, isolated from different ponds, received a donor microbiome from sympatric or allopatric D. magna that were pre-exposed to toxic cyanobacteria or not. We tested for effects on host life history traits and gut microbiome composition. Our data indicate that Daphnia interact with particular microbial strains mediating local adaptation in host stress tolerance. Most recipient D. magna individuals performed better when inoculated with sympatric than with allopatric microbiomes. This effect was most pronounced when the donors were pre-exposed to the toxic cyanobacteria, but this effect was also pond and genotype dependent. We discuss how this host fitness benefit is associated with microbiome diversity patterns.
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22
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Hrnková J, Schneiderová I, Golovchenko M, Grubhoffer L, Rudenko N, Černý J. Role of Zoo-Housed Animals in the Ecology of Ticks and Tick-Borne Pathogens-A Review. Pathogens 2021; 10:210. [PMID: 33669161 PMCID: PMC7919684 DOI: 10.3390/pathogens10020210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/11/2021] [Accepted: 02/13/2021] [Indexed: 12/11/2022] Open
Abstract
Ticks are ubiquitous ectoparasites, feeding on representatives of all classes of terrestrial vertebrates and transmitting numerous pathogens of high human and veterinary medical importance. Exotic animals kept in zoological gardens, ranches, wildlife parks or farms may play an important role in the ecology of ticks and tick-borne pathogens (TBPs), as they may serve as hosts for local tick species. Moreover, they can develop diseases of varying severity after being infected by TBPs, and theoretically, can thus serve as reservoirs, thereby further propagating TBPs in local ecosystems. The definite role of these animals in the tick-host-pathogen network remains poorly investigated. This review provides a summary of the information currently available regarding ticks and TBPs in connection to captive local and exotic wildlife, with an emphasis on zoo-housed species.
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Affiliation(s)
- Johana Hrnková
- Centre for Infectious Animal Diseases and Zoonoses, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, 165 00 Suchdol, Czech Republic;
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, 165 00 Suchdol, Czech Republic;
| | - Irena Schneiderová
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, 165 00 Suchdol, Czech Republic;
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 2 128 00 Prague, Czech Republic
| | - Marina Golovchenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic; (M.G.); (L.G.); (N.R.)
| | - Libor Grubhoffer
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic; (M.G.); (L.G.); (N.R.)
- Faculty of Sciences, University of South Bohemia, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Natalie Rudenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic; (M.G.); (L.G.); (N.R.)
| | - Jiří Černý
- Centre for Infectious Animal Diseases and Zoonoses, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, 165 00 Suchdol, Czech Republic;
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, 165 00 Suchdol, Czech Republic;
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23
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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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24
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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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25
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Elizabeth Alter S, Tariq L, Creed JK, Megafu E. Evolutionary responses of marine organisms to urbanized seascapes. Evol Appl 2021; 14:210-232. [PMID: 33519966 PMCID: PMC7819572 DOI: 10.1111/eva.13048] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 12/19/2022] Open
Abstract
Many of the world's major cities are located in coastal zones, resulting in urban and industrial impacts on adjacent marine ecosystems. These pressures, which include pollutants, sewage, runoff and debris, temperature increases, hardened shorelines/structures, and light and acoustic pollution, have resulted in new evolutionary landscapes for coastal marine organisms. Marine environmental changes influenced by urbanization may create new selective regimes or may influence neutral evolution via impacts on gene flow or partitioning of genetic diversity across seascapes. While some urban selective pressures, such as hardened surfaces, are similar to those experienced by terrestrial species, others, such as oxidative stress, are specific to aquatic environments. Moreover, spatial and temporal scales of evolutionary responses may differ in the ocean due to the spatial extent of selective pressures and greater capacity for dispersal/gene flow. Here, we present a conceptual framework and synthesis of current research on evolutionary responses of marine organisms to urban pressures. We review urban impacts on genetic diversity and gene flow and examine evidence that marine species are adapting, or are predicted to adapt, to urbanization over rapid evolutionary time frames. Our findings indicate that in the majority of studies, urban stressors are correlated with reduced genetic diversity. Genetic structure is often increased in urbanized settings, but artificial structures can also act as stepping stones for some hard-surface specialists, promoting range expansion. Most evidence for rapid adaptation to urban stressors comes from studies of heritable tolerance to pollutants in a relatively small number of species; however, the majority of marine ecotoxicology studies do not test directly for heritability. Finally, we highlight current gaps in our understanding of evolutionary processes in marine urban environments and present a framework for future research to address these gaps.
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Affiliation(s)
- S. Elizabeth Alter
- Department of Biology & ChemistryCalifornia State University, Monterey BayChapman Academic Science CenterSeasideCAUSA
- Department of BiologyYork CollegeCity University of New YorkJamaicaNYUSA
- Department of IchthyologyAmerican Museum of Natural HistoryNew YorkNYUSA
| | - Laraib Tariq
- Department of BiologyYork CollegeCity University of New YorkJamaicaNYUSA
| | - James Keanu Creed
- Department of BiologyYork CollegeCity University of New YorkJamaicaNYUSA
- Department of IchthyologyAmerican Museum of Natural HistoryNew YorkNYUSA
| | - Emmanuel Megafu
- Department of BiologyYork CollegeCity University of New YorkJamaicaNYUSA
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26
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Wei X, Huang M, Yue Q, Ma S, Li B, Mu Z, Peng C, Gao W, Liu W, Zheng J, Weng X, Sun X, Zuo Q, Bo S, Yuan X, Zhang W, Yang G, Ding Y, Wang X, Wang T, Hua P, Wang Z. Long-term urbanization impacts the eastern golden frog ( Pelophylax plancyi) in Shanghai City: Demographic history, genetic structure, and implications for amphibian conservation in intensively urbanizing environments. Evol Appl 2021; 14:117-135. [PMID: 33519960 PMCID: PMC7819575 DOI: 10.1111/eva.13156] [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: 04/17/2020] [Revised: 10/11/2020] [Accepted: 10/20/2020] [Indexed: 11/29/2022] Open
Abstract
Understanding the mechanisms of how urbanization influences the evolution of native species is vital for urban wildlife ecology and conservation in the Anthropocene. With thousands of years of agriculture-dominated historical urbanization followed by 40 years of intensive and rapid urbanization, Shanghai provides an ideal environment to study how the two-stage urbanization process influences the evolution of indigenous wildlife, especially of anuran species. Therefore, in this study, we used mitochondrial Cyt-b gene, microsatellite (SSR), and single nucleotide polymorphism (SNP) data to evaluate the demographic history and genetic structure of the eastern golden frog (Pelophylax plancyi), by sampling 407 individuals from 15 local populations across Shanghai, China. All local populations experienced bottlenecks during historical urbanization, while the local populations in urban areas maintained comparable contemporary effective population sizes (N e) and genetic diversity with suburban and rural populations. Nevertheless, the rapid modern urbanization has already imposed significant negative effects to the integrity of populations. The 15 local populations were differentiated into eight genetic clusters, showing a spatial distribution pattern consistent with the current urbanization gradient and island-mainland geography. Although moderate gene flow still occurred from the rural peripheral cluster to urban and suburban clusters, population fragmentation was more serious in the urban and suburban populations, where higher urbanization levels within 2-km radius areas showed significant negative relationships to the N e and genetic diversity of local populations. Therefore, to protect urban wildlife with limited dispersal ability, improving conditions in fragmented habitat remnants might be most essential for local populations living in more urbanized areas. Meanwhile, we highlight the need to preserve large unfragmented rural habitats and to construct corridor networks to connect discrete urban habitat remnants for the long-term wildlife conservation in intensively urbanizing environments.
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Affiliation(s)
- Xu Wei
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Meiling Huang
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Qu Yue
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Shuo Ma
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Ben Li
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Zhiqiang Mu
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Chuan Peng
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Wenxuan Gao
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Wenli Liu
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Jiaxin Zheng
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Xiaodong Weng
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Xiaohui Sun
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Qingqiu Zuo
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Shunqi Bo
- Shanghai Landscaping & City Appearance Administrative BureauShanghai Forestry BureauShanghaiChina
| | - Xiao Yuan
- Shanghai Landscaping & City Appearance Administrative BureauShanghai Forestry BureauShanghaiChina
| | - Wei Zhang
- Natural History Research Centre of Shanghai Natural History MuseumShanghai Science and Technology MuseumShanghaiChina
| | - Gang Yang
- Natural History Research Centre of Shanghai Natural History MuseumShanghai Science and Technology MuseumShanghaiChina
| | - Youzhong Ding
- School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Xiaoming Wang
- School of Life SciencesEast China Normal UniversityShanghaiChina
- Shanghai Science and Technology MuseumShanghaiChina
| | - Tianhou Wang
- School of Life SciencesEast China Normal UniversityShanghaiChina
- Institute of Eco‐ChongmingShanghaiChina
| | - Panyu Hua
- School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Zhenghuan Wang
- School of Life SciencesEast China Normal UniversityShanghaiChina
- Joint Translational Science and Technology Research InstituteEast China Normal UniversityShanghaiChina
- Yangtze Delta Estuarine Wetland Ecosystem Observation and Research StationMinistry of Education & Shanghai Science and Technology CommitteeShanghaiChina
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27
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Adaptive Evolution in Cities: Progress and Misconceptions. Trends Ecol Evol 2020; 36:239-257. [PMID: 33342595 DOI: 10.1016/j.tree.2020.11.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/01/2020] [Accepted: 11/09/2020] [Indexed: 12/14/2022]
Abstract
Current narratives suggest that urban adaptation - the adaptive evolution of organisms to cities - is pervasive across taxa and cities. However, in reviewing hundreds of studies, we find only six comprehensive examples of species adaptively evolving to urbanization. We discuss the utility and shortcomings of methods for studying urban adaptation. We then review diverse systems offering preliminary evidence for urban adaptation and outline a research program for advancing its study. Urban environments constitute diverse, interacting selective agents that test the limits of adaptation. Understanding urban adaptation therefore offers unique opportunities for addressing fundamental questions in evolutionary biology and for better conserving biodiversity in cities. However, capitalizing on these opportunities requires appropriate research methods and dissemination of accurate narratives.
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28
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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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29
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Westby KM, Medley KA. Cold Nights, City Lights: Artificial Light at Night Reduces Photoperiodically Induced Diapause in Urban and Rural Populations of Aedes albopictus (Diptera: Culicidae). JOURNAL OF MEDICAL ENTOMOLOGY 2020; 57:1694-1699. [PMID: 32638000 DOI: 10.1093/jme/tjaa139] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Indexed: 05/12/2023]
Abstract
As the planet becomes increasingly urbanized, it is imperative that we understand the ecological and evolutionary consequences of urbanization on species. One common attribute of urbanization that differs from rural areas is the prevalence of artificial light at night (ALAN). For many species, light is one of the most important and reliable environmental cues, largely governing the timing of daily and seasonal activity patterns. Recently, it has been shown that ALAN can alter behavioral, phenological, and physiological traits in diverse taxa. For temperate insects, diapause is an essential trait for winter survival and commences in response to declining daylight hours in the fall. Diapause is under strong selection pressure in the mosquito, Aedes albopictus (Skuse); local adaptation and rapid evolution has been observed along a latitudinal cline. It is unknown how ALAN affects this photosensitive trait or if local adaptation has occurred along an urbanization gradient. Using a common garden experiment, we experimentally demonstrated that simulated ALAN reduces diapause incidence in this species by as much as 40%. There was no difference, however, between urban and rural demes. We also calculated diapause incidence from wild demes in urban areas to determine whether wild populations exhibited lower than predicted incidence compared to estimates from total nocturnal darkness. In early fall, lower than predicted diapause incidence was recorded, but all demes reached nearly 100% diapause before terminating egg laying. It is possible that nocturnal resting behavior in vegetation limits the amount of ALAN exposure this species experiences potentially limiting local adaptation.
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Affiliation(s)
- Katie M Westby
- Tyson Research Center, Washington University in Saint Louis, Eureka, MO
| | - Kim A Medley
- Tyson Research Center, Washington University in Saint Louis, Eureka, MO
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30
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Slatculescu AM, Clow KM, McKay R, Talbot B, Logan JJ, Thickstun CR, Jardine CM, Ogden NH, Knudby AJ, Kulkarni MA. Species distribution models for the eastern blacklegged tick, Ixodes scapularis, and the Lyme disease pathogen, Borrelia burgdorferi, in Ontario, Canada. PLoS One 2020; 15:e0238126. [PMID: 32915794 PMCID: PMC7485816 DOI: 10.1371/journal.pone.0238126] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/10/2020] [Indexed: 12/31/2022] Open
Abstract
The blacklegged tick, Ixodes scapularis, is established in several regions of Ontario, Canada, and continues to spread into new geographic areas across the province at a rapid rate. This poses a significant public health risk since I. scapularis transmits the Lyme disease-causing bacterium, Borrelia burgdorferi, and other pathogens of potential public health concern. The objective of this study was to develop species distribution models for I. scapularis and B. burgdorferi to predict and compare the potential distributions of the tick vector and the Lyme disease pathogen as well as the ecological factors most important for species establishment. Ticks were collected via tick dragging at 120 sites across southern, central, and eastern Ontario between 2015 and 2018 and tested for tick-borne pathogens. A maximum entropy (Maxent) approach was used to model the potential distributions of I. scapularis and B. burgdorferi. Two independent datasets derived from tick dragging at 25 new sites in 2019 and ticks submitted by the public to local health units between 2015 and 2017 were used to validate the predictive accuracy of the models. The model for I. scapularis showed high suitability for blacklegged ticks in eastern Ontario and some regions along the shorelines of the Great Lakes, and moderate suitability near Algonquin Provincial Park and the Georgian Bay with good predictive accuracy (tick dragging 2019: AUC = 0.898; ticks from public: AUC = 0.727). The model for B. burgdorferi showed a similar predicted distribution but was more constrained to eastern Ontario, particularly between Ottawa and Kingston, and along Lake Ontario, with similarly good predictive accuracy (tick dragging 2019: AUC = 0.958; ticks from public: AUC = 0.863. The ecological variables most important for predicting the distributions of I. scapularis and B. burgdorferi included elevation, distance to deciduous and coniferous forest, proportions of agricultural land, water, and infrastructure, mean summer/spring temperature, and cumulative annual degree days above 0°C. Our study presents a novel application of species distribution modelling for I. scapularis and B. burgdorferi in Ontario, Canada, and provides an up to date projection of their potential distributions for public health knowledge users.
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Affiliation(s)
| | - Katie M. Clow
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Roman McKay
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Benoit Talbot
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - James J. Logan
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Charles R. Thickstun
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Claire M. Jardine
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
- Canadian Wildlife Health Cooperative, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Nicholas H. Ogden
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Saint-Hyacinthe, Quebec, Canada
| | - Anders J. Knudby
- Department of Geography, Environment, and Geomatics, University of Ottawa, Ottawa, Ontario, Canada
| | - Manisha A. Kulkarni
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
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31
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Garroway CJ, Schmidt C. Genomic evidence for parallel adaptation to cities. Mol Ecol 2020; 29:3397-3399. [PMID: 32772443 DOI: 10.1111/mec.15589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 07/31/2020] [Indexed: 11/26/2022]
Abstract
Urban evolutionary biology is the study of rapid evolutionary change in response to humans and our uses of land to support city dwellers. Because cities are relatively modern additions to the natural world, research on urban evolution tends to focus on microevolutionary change that has happened across a few to many hundreds of generations. These questions still fall under the broad purview of evolutionary ecology. However, the severity, rapidity and replication of environmental changes that drive evolution in this context make it worthy of specific attention. Urban evolution provides the opportunity to study the earliest stages of evolution in a context that is scientifically interesting and societally important. The newness of urban populations and their proximity to natural populations also creates challenges when trying to detect population genetic change. In a From the Cover article in this issue of Molecular Ecology, Mueller et al. use whole genome resequencing data to address some of these challenges while exploring genetic changes associated with urbanization in three replicate urban-rural burrowing owl (Athene cunicularia) populations. Combining multiple approaches across these sample sites Mueller et al. find evidence for selection on genes whose function is related to synapses, neuron projections, brain connectivity and cognitive function in general. That selection was parallel suggests that phenotypes related to brain processes were probably particularly important for urban adaptation.
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Affiliation(s)
- Colin J Garroway
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Chloé Schmidt
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
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32
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Falvey CH, Aviles-Rodriguez KJ, Hagey TJ, Winchell KM. The finer points of urban adaptation: intraspecific variation in lizard claw morphology. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa123] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Abstract
Human activity drastically transforms landscapes, generating novel habitats to which species must adaptively respond. Consequently, urbanization is increasingly recognized as a driver of phenotypic change. The structural environment of urban habitats presents a replicated natural experiment to examine trait–environment relationships and phenotypic variation related to locomotion. We use geometric morphometrics to examine claw morphology of five species of Anolis lizards in urban and forest habitats. We find that urban lizards undergo a shift in claw shape in the same direction but varying magnitude across species. Urban claws are overall taller, less curved, less pointed and shorter in length than those of forest lizards. These differences may enable more effective attachment or reduce interference with toepad function on smooth anthropogenic substrates. We also find an increase in shape disparity, a measurement of variation, in urban populations, suggesting relaxed selection or niche expansion rather than directional selection. This study expands our understanding of the relatively understudied trait of claw morphology and adds to a growing number of studies demonstrating phenotypic changes in urban lizards. The consistency in the direction of the shape changes we observed supports the intriguing possibility that urban environments may lead to predictable convergent adaptive change.
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Affiliation(s)
- Cleo H Falvey
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | | | - Travis J Hagey
- Department of Sciences & Mathematics, Mississippi University for Women, Columbus, MS, USA
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33
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Garcia-Elfring A, Barrett RDH, Millien V. Genomic Signatures of Selection along a Climatic Gradient in the Northern Range Margin of the White-Footed Mouse (Peromyscus leucopus). J Hered 2020; 110:684-695. [PMID: 31300816 DOI: 10.1093/jhered/esz045] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 07/10/2019] [Indexed: 02/07/2023] Open
Abstract
Identifying genetic variation involved in thermal adaptation is likely to yield insights into how species adapt to different climates. Physiological and behavioral responses associated with overwintering (e.g., torpor) are thought to serve important functions in climate adaptation. In this study, we use 2 isolated Peromyscus leucopus lineages on the northern margin of the species range to identify single nucleotide polymorphisms (SNPs) showing a strong environmental association and test for evidence of parallel evolution. We found signatures of clinal selection in each lineage, but evidence of parallelism was limited, with only 2 SNPs showing parallel allele frequencies across transects. These parallel SNPs map to a gene involved in protection against iron-dependent oxidative stress (Fxn) and to a gene with unknown function but containing a forkhead-associated domain (Fhad1). Furthermore, within transects, we find significant clinal patterns in genes enriched for functions associated with glycogen homeostasis, synaptic function, intracellular Ca2+ balance, H3 histone modification, as well as the G2/M transition of cell division. Our results are consistent with recent literature on the cellular and molecular basis of climate adaptation in small mammals and provide candidate genomic regions for further study.
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Affiliation(s)
- Alan Garcia-Elfring
- Redpath Museum, McGill University, Montreal, QC, Canada.,Department of Biology, McGill University, Montreal, QC, Canada
| | - Rowan D H Barrett
- Redpath Museum, McGill University, Montreal, QC, Canada.,Department of Biology, McGill University, Montreal, QC, Canada
| | - Virginie Millien
- Redpath Museum, McGill University, Montreal, QC, Canada.,Department of Biology, McGill University, Montreal, QC, Canada
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34
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Mueller JC, Carrete M, Boerno S, Kuhl H, Tella JL, Kempenaers B. Genes acting in synapses and neuron projections are early targets of selection during urban colonization. Mol Ecol 2020; 29:3403-3412. [DOI: 10.1111/mec.15451] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 04/08/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Jakob C. Mueller
- Department of Behavioural Ecology & Evolutionary Genetics Max Planck Institute for Ornithology Seewiesen Germany
| | - Martina Carrete
- Department of Conservation Biology Estación Biológica de Doñana – CSIC Sevilla Spain
- Department of Physical, Chemical and Natural Systems University Pablo de Olavide Sevilla Spain
| | - Stefan Boerno
- Sequencing Core Facility Max Planck Institute for Molecular Genetics Berlin Germany
| | - Heiner Kuhl
- Sequencing Core Facility Max Planck Institute for Molecular Genetics Berlin Germany
- Department of Ecophysiology and Aquaculture Leibniz‐Institute of Freshwater Ecology and Inland Fisheries Berlin Germany
| | - José L. Tella
- Department of Conservation Biology Estación Biológica de Doñana – CSIC Sevilla Spain
| | - Bart Kempenaers
- Department of Behavioural Ecology & Evolutionary Genetics Max Planck Institute for Ornithology Seewiesen Germany
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35
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Mull N, Jackson R, Sironen T, Forbes KM. Ecology of Neglected Rodent-Borne American Orthohantaviruses. Pathogens 2020; 9:E325. [PMID: 32357540 PMCID: PMC7281597 DOI: 10.3390/pathogens9050325] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 12/31/2022] Open
Abstract
The number of documented American orthohantaviruses has increased significantly over recent decades, but most fundamental research has remained focused on just two of them: Andes virus (ANDV) and Sin Nombre virus (SNV). The majority of American orthohantaviruses are known to cause disease in humans, and most of these pathogenic strains were not described prior to human cases, indicating the importance of understanding all members of the virus clade. In this review, we summarize information on the ecology of under-studied rodent-borne American orthohantaviruses to form general conclusions and highlight important gaps in knowledge. Information regarding the presence and genetic diversity of many orthohantaviruses throughout the distributional range of their hosts is minimal and would significantly benefit from virus isolations to indicate a reservoir role. Additionally, few studies have investigated the mechanisms underlying transmission routes and factors affecting the environmental persistence of orthohantaviruses, limiting our understanding of factors driving prevalence fluctuations. As landscapes continue to change, host ranges and human exposure to orthohantaviruses likely will as well. Research on the ecology of neglected orthohantaviruses is necessary for understanding both current and future threats to human health.
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Affiliation(s)
- Nathaniel Mull
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA; (R.J.); (K.M.F.)
| | - Reilly Jackson
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA; (R.J.); (K.M.F.)
| | - Tarja Sironen
- Department of Virology, University of Helsinki, 00290 Helsinki, Finland;
- Department of Veterinary Biosciences, University of Helsinki, 00790 Helsinki, Finland
| | - Kristian M. Forbes
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA; (R.J.); (K.M.F.)
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36
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Perry GH. How human behavior can impact the evolution of genetically-mediated behavior in wild non-human species. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2020; 206:337-342. [PMID: 32201915 DOI: 10.1007/s00359-020-01415-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/24/2020] [Accepted: 02/27/2020] [Indexed: 11/29/2022]
Abstract
Humans intensely modify the ecosystems we inhabit. Many of the impacts that this behavior can have on other species also sharing these spaces are obvious. A prime example is the devastating current extinction crisis. Yet some populations of non-human, non-domesticated species survive or even appear to thrive in heavily disturbed or human-built habitats. Theoretically, this apparent paradox could be facilitated partly by the evolution of genetically-mediated trait adaptations to the impacts of human behavior. At the least, persistence in strongly modified habitats would provide requisite selection pressures for this process to potentially occur in the future. In fact, we have a growing number of well-characterized examples of morphological trait adaptations to human behavior. However, our knowledge of genetically-mediated behavioral adaptations in similar contexts is less well developed. In this review I set up and discuss several evolutionary scenarios by which human behavior might have impacted the evolution of genetically mediated behavior in non-human, non-domestic species and highlight several approaches that could be used in future studies of this process.
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Affiliation(s)
- George H Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Biology, Pennsylvania State University, University Park, USA. .,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, USA. .,DFG Center for Advanced Studies, University of Tübingen, Tübingen, Germany.
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37
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Campbell-Staton SC, Winchell KM, Rochette NC, Fredette J, Maayan I, Schweizer RM, Catchen J. Parallel selection on thermal physiology facilitates repeated adaptation of city lizards to urban heat islands. Nat Ecol Evol 2020; 4:652-658. [DOI: 10.1038/s41559-020-1131-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 01/28/2020] [Indexed: 12/22/2022]
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38
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Liker A. Biologia Futura: adaptive changes in urban populations. Biol Futur 2020; 71:1-8. [DOI: 10.1007/s42977-020-00005-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/17/2020] [Indexed: 12/12/2022]
Abstract
AbstractCities represent novel environments where altered ecological conditions can generate strong selection pressures leading to the evolution of specific urban phenotypes. Is there evidence for such adaptive changes in urban populations which have colonized their new environments relatively recently? A growing number of studies suggest that rapid adaptations may be widespread in wild urban populations, including increased tolerance to various anthropogenic stressors, and physiological, morphological and behavioural changes in response to the altered resources and predation risk. Some of these adaptive changes are based on genetic differentiation, although other mechanisms, such as phenotypic plasticity and epigenetic effects, are also frequently involved.
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39
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Heras J, Chakraborty M, Emerson JJ, German DP. Genomic and biochemical evidence of dietary adaptation in a marine herbivorous fish. Proc Biol Sci 2020; 287:20192327. [PMID: 32070255 PMCID: PMC7062031 DOI: 10.1098/rspb.2019.2327] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/26/2020] [Indexed: 01/30/2023] Open
Abstract
Adopting a new diet is a significant evolutionary change, and can profoundly affect an animal's physiology, biochemistry, ecology and genome. To study this evolutionary transition, we investigated the physiology and genomics of digestion of a derived herbivorous fish, Cebidichthys violaceus. We sequenced and assembled its genome (N50 = 6.7 Mb) and digestive transcriptome, and revealed the molecular changes related to digestive enzymes (carbohydrases, proteases and lipases), finding abundant evidence of molecular adaptation. Specifically, two gene families experienced expansion in copy number and adaptive amino acid substitutions: amylase and carboxyl ester lipase (cel), which are involved in the digestion of carbohydrates and lipids, respectively. Both show elevated levels of gene expression and increased enzyme activity. Because carbohydrates are abundant in the prickleback's diet and lipids are rare, these findings suggest that such dietary specialization involves both exploiting abundant resources and scavenging rare ones, especially essential nutrients, like essential fatty acids.
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Affiliation(s)
- Joseph Heras
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA 92697-2525, USA
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Khimoun A, Doums C, Molet M, Kaufmann B, Peronnet R, Eyer PA, Mona S. Urbanization without isolation: the absence of genetic structure among cities and forests in the tiny acorn ant Temnothorax nylanderi. Biol Lett 2020; 16:20190741. [PMID: 31992150 DOI: 10.1098/rsbl.2019.0741] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Urban alteration of neutral and adaptive evolutionary processes is still underexplored. Using a genome-wide SNP dataset, we investigated (i) urban-induced modifications of population demography, genetic diversity and population structure and (ii) signature of divergent selection between urban and forest populations in the ant species, Temnothorax nylanderi. Our results did not reveal an impact of urbanization on neutral processes since we observed: (i) analogous genetic diversity among paired urban/forest sites and two control populations; (ii) weak population genetic structure explained neither by habitat (urban versus forest) nor by geography; (iii) a remarkably similar demographic history across populations with an ancestral growth followed by a recent decline, regardless of their current habitat or geographical location. The micro-geographical home range of ants may explain their resilience to urbanization. Finally, we detected 19 candidate loci discriminating urban/forest populations and associated with core cellular components, molecular function or biological process. Two of these loci were associated with a gene ontology term that was previously found to belong to a module of co-expressed genes related to caste phenotype. These results call for transcriptomics analyses to identify genes associated with ant social traits and to infer their potential role in urban adaptation.
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Affiliation(s)
- A Khimoun
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000 Dijon, France
| | - C Doums
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE, Sorbonne Université, 75005 Paris, France.,EPHE, PSL University, 75005 Paris, France
| | - M Molet
- Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), UMR 7618, Sorbonne Université, Université Paris Est Créteil, Université Paris Diderot, CNRS, INRA, IRD, 75005 Paris, France
| | - B Kaufmann
- Université de Lyon, UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université Lyon 1, ENTPE, CNRS, Villeurbanne 69622, France
| | - R Peronnet
- Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), UMR 7618, Sorbonne Université, Université Paris Est Créteil, Université Paris Diderot, CNRS, INRA, IRD, 75005 Paris, France
| | - P A Eyer
- Department of Entomology, Texas A&M University, 2143 TAMU, College Station, TX 77843-2143, USA
| | - S Mona
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE, Sorbonne Université, 75005 Paris, France.,EPHE, PSL University, 75005 Paris, France
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41
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Selmoni O, Vajana E, Guillaume A, Rochat E, Joost S. Sampling strategy optimization to increase statistical power in landscape genomics: A simulation-based approach. Mol Ecol Resour 2019; 20:154-169. [PMID: 31550072 PMCID: PMC6972490 DOI: 10.1111/1755-0998.13095] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/05/2019] [Accepted: 09/18/2019] [Indexed: 02/06/2023]
Abstract
An increasing number of studies are using landscape genomics to investigate local adaptation in wild and domestic populations. Implementation of this approach requires the sampling phase to consider the complexity of environmental settings and the burden of logistical constraints. These important aspects are often underestimated in the literature dedicated to sampling strategies. In this study, we computed simulated genomic data sets to run against actual environmental data in order to trial landscape genomics experiments under distinct sampling strategies. These strategies differed by design approach (to enhance environmental and/or geographical representativeness at study sites), number of sampling locations and sample sizes. We then evaluated how these elements affected statistical performances (power and false discoveries) under two antithetical demographic scenarios. Our results highlight the importance of selecting an appropriate sample size, which should be modified based on the demographic characteristics of the studied population. For species with limited dispersal, sample sizes above 200 units are generally sufficient to detect most adaptive signals, while in random mating populations this threshold should be increased to 400 units. Furthermore, we describe a design approach that maximizes both environmental and geographical representativeness of sampling sites and show how it systematically outperforms random or regular sampling schemes. Finally, we show that although having more sampling locations (between 40 and 50 sites) increase statistical power and reduce false discovery rate, similar results can be achieved with a moderate number of sites (20 sites). Overall, this study provides valuable guidelines for optimizing sampling strategies for landscape genomics experiments.
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Affiliation(s)
- Oliver Selmoni
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Elia Vajana
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Annie Guillaume
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Estelle Rochat
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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Homola JJ, Loftin CS, Cammen KM, Helbing CC, Birol I, Schultz TF, Kinnison MT. Replicated Landscape Genomics Identifies Evidence of Local Adaptation to Urbanization in Wood Frogs. J Hered 2019; 110:707-719. [PMID: 31278891 PMCID: PMC6785938 DOI: 10.1093/jhered/esz041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 06/28/2019] [Indexed: 12/20/2022] Open
Abstract
Native species that persist in urban environments may benefit from local adaptation to novel selection factors. We used double-digest restriction-side associated DNA (RAD) sequencing to evaluate shifts in genome-wide genetic diversity and investigate the presence of parallel evolution associated with urban-specific selection factors in wood frogs (Lithobates sylvaticus). Our replicated paired study design involved 12 individuals from each of 4 rural and urban populations to improve our confidence that detected signals of selection are indeed associated with urbanization. Genetic diversity measures were less for urban populations; however, the effect size was small, suggesting little biological consequence. Using an FST outlier approach, we identified 37 of 8344 genotyped single nucleotide polymorphisms with consistent evidence of directional selection across replicates. A genome-wide association study analysis detected modest support for an association between environment type and 12 of the 37 FST outlier loci. Discriminant analysis of principal components using the 37 FST outlier loci produced correct reassignment for 87.5% of rural samples and 93.8% of urban samples. Eighteen of the 37 FST outlier loci mapped to the American bullfrog (Rana [Lithobates] catesbeiana) genome, although none were in coding regions. This evidence of parallel evolution to urban environments provides a powerful example of the ability of urban landscapes to direct evolutionary processes.
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Affiliation(s)
- Jared J Homola
- School of Biology and Ecology, University of Maine, Orono, ME
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI
| | - Cynthia S Loftin
- the US Geological Survey, Maine Cooperative Fish and Wildlife Research Unit, Orono, ME
| | | | - Caren C Helbing
- the Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Inanc Birol
- the Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Thomas F Schultz
- the Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University, Beaufort, NC
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Zhao H, Wang H, Liu T, Liu S, Jin L, Huang X, Dai W, Sun K, Feng J. Gene expression vs. sequence divergence: comparative transcriptome sequencing among natural Rhinolophus ferrumequinum populations with different acoustic phenotypes. Front Zool 2019; 16:37. [PMID: 31528181 PMCID: PMC6743130 DOI: 10.1186/s12983-019-0336-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/04/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Although the sensory drive hypothesis can explain the geographic variation in echolocation frequencies of some bat species, the molecular mechanisms underlying this phenomenon are still unclear. The three lineages of greater horseshoe bat (Rhinolophus ferrumequinum) in China (northeast, central-east, and southwest) have significant geographic variation in resting frequencies (RF) of echolocation calls. Because their cochleae have an acoustic fovea that is highly sensitive to a narrow range of frequencies, we reported the transcriptomes of cochleae collected from three genetic lineages of R. ferrumequinum, which is an ideal organism for studying geographic variation in echolocation signals, and tried to understand the mechanisms behind this bat phenomenon by analyzing gene expression and sequence variation. RESULTS A total of 8190 differentially expressed genes (DEGs) were identified. We identified five modules from all DEGs that were significantly related to RF or forearm length (FL). DEGs in the RF-related modules were significantly enriched in the gene categories involved in neural activity, learning, and response to sound. DEGs in the FL-related modules were significantly enriched in the pathways related to muscle and actin functions. Using 21,945 single nucleotide polymorphisms, we identified 18 candidate unigenes associated with hearing, five of which were differentially expressed among the three populations. Additionally, the gene ERBB4, which regulates diverse cellular processes in the inner ear such as cell proliferation and differentiation, was in the largest module. We also found 49 unigenes that were under positive selection from 4105 one-to-one orthologous gene pairs between the three R. ferrumequinum lineages and three other Chiroptera species. CONCLUSIONS The variability of gene expression and sequence divergence at the molecular level might provide evidence that can help elucidate the genetic basis of geographic variation in echolocation signals of greater horseshoe bats.
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Affiliation(s)
- Hanbo Zhao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Hui Wang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Sen Liu
- Institute of Resources & Environment, Henan Polytechnic University, Jiaozuo, 454000 China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Xiaobin Huang
- Vector Laboratory, Institute of Pathogens and Vectors, Branch of Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, 671003 China
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
- College of Life Science, Jilin Agricultural University, Changchun, 130118 China
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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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Larsen PA, Matocq MD. Emerging genomic applications in mammalian ecology, evolution, and conservation. J Mammal 2019. [DOI: 10.1093/jmammal/gyy184] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Peter A Larsen
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science; Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, USA
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Mueller JC, Kuhl H, Boerno S, Tella JL, Carrete M, Kempenaers B. Evolution of genomic variation in the burrowing owl in response to recent colonization of urban areas. Proc Biol Sci 2019; 285:rspb.2018.0206. [PMID: 29769357 PMCID: PMC5966595 DOI: 10.1098/rspb.2018.0206] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/16/2018] [Indexed: 11/12/2022] Open
Abstract
When a species successfully colonizes an urban habitat it can be expected that its population rapidly adapts to the new environment but also experiences demographic perturbations. It is, therefore, essential to gain an understanding of the population structure and the demographic history of the urban and neighbouring rural populations before studying adaptation at the genome level. Here, we investigate populations of the burrowing owl (Athene cunicularia), a species that colonized South American cities just a few decades ago. We assembled a high-quality genome of the burrowing owl and re-sequenced 137 owls from three urban-rural population pairs at 17-fold median sequencing coverage per individual. Our data indicate that each city was independently colonized by a limited number of founders and that restricted gene flow occurred between neighbouring urban and rural populations, but not between urban populations of different cities. Using long-range linkage disequilibrium statistics in an approximate Bayesian computation approach, we estimated consistently lower population sizes in the recent past for the urban populations in comparison to the rural ones. The current urban populations all show reduced standing variation in rare single nucleotide polymorphisms (SNPs), but with different subsets of rare SNPs in different cities. This lowers the potential for local adaptation based on rare variants and makes it harder to detect consistent signals of selection in the genome.
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Affiliation(s)
- Jakob C Mueller
- Department of Behavioural Ecology & Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Heiner Kuhl
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Stefan Boerno
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jose L Tella
- Department of Conservation Biology, Estación Biológica de Doñana - CSIC, Sevilla, Spain
| | - Martina Carrete
- Department of Conservation Biology, Estación Biológica de Doñana - CSIC, Sevilla, Spain.,Department of Physical, Chemical and Natural Systems, University Pablo de Olavide, Sevilla, Spain
| | - Bart Kempenaers
- Department of Behavioural Ecology & Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
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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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Li JX, Zhu XH, Li Y, Liu Y, Qian ZH, Zhang XX, Sun Y, Ji LY. Adaptive genetic differentiation in Pterocarya stenoptera (Juglandaceae) driven by multiple environmental variables were revealed by landscape genomics. BMC PLANT BIOLOGY 2018; 18:306. [PMID: 30482158 PMCID: PMC6260741 DOI: 10.1186/s12870-018-1524-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/14/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND The investigation of the genetic basis of local adaptation in non-model species is an interesting focus of evolutionary biologists and molecular ecologists. Identifying these adaptive genetic variabilities on the genome responsible can provide insight into the genetic mechanism of local adaptation. RESULTS We investigated the spatial distribution of genetic variation in 22 natural populations of Pterocarya stenoptera across its distribution area in China to provide insights into the complex interplay between multiple environmental variables and adaptive genetic differentiation. The Bayesian analysis of population structure showed that the 22 populations of P. stenoptera were subdivided into two groups. Redundancy analysis demonstrated that this genetic differentiation was caused by the divergent selection of environmental difference. A total of 44 outlier loci were mutually identified by Arlequin and BayeScan, 43 of which were environment-associated loci (EAL). The results of latent factor mixed model analysis showed that solar radiation in June (Sr6), minimum temperature of the coldest month (Bio6), temperature seasonality (Bio4), and water vapor pressure in January (Wvp1) were associated with the highest numbers of EAL. Sr6 was associated with the ecological habitat of "prefered light", and Bio6 and Wvp1 were associated with the ecological habitat of "warm and humid environment". CONCLUSIONS Our results provided empirical evidence that environmental variables related to the ecological habitats of species play key roles in driving adaptive differentiation of species genome.
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Affiliation(s)
- Jia-Xin Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
| | - Xiu-Hong Zhu
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
| | - Yong Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
| | - Ying Liu
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, No.135, Xingang Xi Road, Guangzhou, 510275 China
| | - Zhi-Hao Qian
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
| | - Xue-Xia Zhang
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
| | - Yue Sun
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
| | - Liu-Yang Ji
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
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Beninde J, Feldmeier S, Veith M, Hochkirch A. Admixture of hybrid swarms of native and introduced lizards in cities is determined by the cityscape structure and invasion history. Proc Biol Sci 2018; 285:rspb.2018.0143. [PMID: 30051861 DOI: 10.1098/rspb.2018.0143] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/16/2018] [Indexed: 12/15/2022] Open
Abstract
Introductions of non-native lineages increase opportunities for hybridization. Non-native lineages of the common wall lizard, Podarcis muralis, are frequently introduced in cities where they hybridize with native populations. We aimed at unravelling the invasion history and admixture of native and non-native wall lizards in four German cities using citywide, comprehensive sampling. We barcoded and genotyped 826 lizards and tested if gene flow in populations composed of admixed native and introduced lineages is facilitated by similar environmental factors to those in native populations by comparing fine-scale landscape genetic patterns. In cities with non-native lineages, lizards commonly occurred in numerous clusters of hybrid swarms, which showed variable lineage composition, consisting of up to four distinct evolutionary lineages. Hybrid swarms held vast genetic diversity and showed recent admixture with other hybrid swarms. Landscape genetic analyses showed differential effects of cityscape structures across cities, but identified water bodies as strong barriers to gene flow in both native and admixed populations. By contrast, railway tracks facilitated gene flow of admixed populations only. Our study shows that cities represent unique settings for hybridization, caused by multiple introductions of non-native taxa. Cityscape structure and invasion histories of cities will determine future evolutionary pathways at these novel hybrid zones.
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Affiliation(s)
- Joscha Beninde
- Department of Biogeography, Trier University, 54286 Trier, Germany
| | | | - Michael Veith
- Department of Biogeography, Trier University, 54286 Trier, Germany
| | - Axel Hochkirch
- Department of Biogeography, Trier University, 54286 Trier, Germany
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50
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Brans KI, Stoks R, De Meester L. Urbanization drives genetic differentiation in physiology and structures the evolution of pace-of-life syndromes in the water flea Daphnia magna. Proc Biol Sci 2018; 285:rspb.2018.0169. [PMID: 30051844 DOI: 10.1098/rspb.2018.0169] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/22/2018] [Indexed: 11/12/2022] Open
Abstract
Natural and human-induced stressors elicit changes in energy metabolism and stress physiology in populations of a wide array of species. Cities are stressful environments that may lead to differential selection on stress-coping mechanisms. Given that city ponds are exposed to the urban heat island effect and receive polluted run-off, organisms inhabiting these ecosystems might show genetic differentiation for physiological traits enabling them to better cope with higher overall stress levels. A common garden study with 62 Daphnia magna genotypes from replicated urban and rural populations revealed that urban Daphnia have significantly higher concentrations of total body fat, proteins and sugars. Baseline activity levels of the antioxidant defence enzymes superoxide dismutase (SOD) and glutathione-S-transferase (GST) were higher in rural compared with city populations, yet urban animals were equally well protected against lipid peroxidation. Our results add to the recent evidence of urbanization-driven changes in stress physiology and energy metabolism in terrestrial organisms. Combining our results with data on urban life history evolution in Daphnia revealed that urban genotypes show a structured pace-of-life syndrome involving both life-history and physiological traits, whereas this is absent in rural populations.
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Affiliation(s)
- Kristien I Brans
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Ch. Deberiotstraat 32, 3000, Leuven, Belgium
| | - Robby Stoks
- Laboratory of Evolutionary Stress Ecology and Ecotoxicology, KU Leuven, Ch. Deberiotstraat 32, 3000, Leuven, Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Ch. Deberiotstraat 32, 3000, Leuven, Belgium
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