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Genetic structure of urban and non-urban populations differs between two common parid species

  • 1.

    Partecke, J., Gwinner, E. & Bensch, S. Is urbanisation of European blackbirds (Turdus merula) associated with genetic differentiation?. J. Ornithol. 147, 549–552 (2006).

    Article 

    Google Scholar 

  • 2.

    Perrier, C. et al. Great tits and the city: Distribution of genomic diversity and gene–environment associations along an urbanization gradient. Evol. Appl. 11, 593–613 (2018).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 3.

    Chace, J. F. & Walsh, J. J. Urban effects on native avifauna: A review. Landsc. Urban Plan. 74, 46–69 (2006).

    Article 

    Google Scholar 

  • 4.

    Evans, K. L. et al. Independent colonization of multiple urban centres by a formerly forest specialist bird species. Proc. R. Soc. B 276(1666), 2403–2410 (2009).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 5.

    Björklund, M., Ruiz, I. & Senar, J. C. Genetic differentiation in the urban habitat: The great tits (Parus major) of the parks of Barcelona city. Biol. J. Linn. Soc. 99, 9–19 (2010).

    Article 

    Google Scholar 

  • 6.

    Crooks, K. R. & Sanjayan, M. A. Connectivity conservation: Maintaining connections for nature. In Connectivity Conservation (eds Crooks, K. R. & Sanjayan, M. A.) 1–20 (Cambridge University Press, Cambridge, 2006).

    Google Scholar 

  • 7.

    Evans, K. L., Chamberlain, D. E., Hatchwell, B. J., Gregory, R. D. & Gaston, K. J. What makes an urban bird?. Glob. Change Biol. 17, 32–44 (2011).

    ADS 
    Article 

    Google Scholar 

  • 8.

    Seress, G. & Liker, A. Habitat urbanization and its effects on birds. Acta Zool. Acad. Sci. Hung. 61(4), 373–408 (2015).

    Article 

    Google Scholar 

  • 9.

    Miles, L. S., Rivkin, L. R., Johnson, M. T. J., Munshi-South, J. & Verrelli, B. C. Gene flow and genetic drift in urban environments. Mol. Ecol. 28, 4138–4151 (2019).

    PubMed 
    Article 

    Google Scholar 

  • 10.

    Shochat, E., Warren, P. S., Faeth, S. H., McIntyre, N. E. & Hope, D. From patterns to emerging processes in mechanistic urban ecology. Trends Ecol. Evol. 21, 186–191 (2006).

    PubMed 
    Article 

    Google Scholar 

  • 11.

    Chamberlain, D. E. et al. Avian productivity in urban landscapes: A review and meta-analysis. Ibis 151, 1–18 (2009).

    Article 

    Google Scholar 

  • 12.

    Delaney, K. S., Riley, S. P. D. & Fisher, R. N. A rapid, strong, and convergent genetic response to urban habitat fragmentation in four divergent and widespread vertebrates. PLoS ONE 5(9), e12767 (2010).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 13.

    Unfried, T. M., Hauser, L. & Marzluff, J. M. Effects of urbanization on Song Sparrow (Melospiza melodia) population connectivity. Conserv. Genet. 14(1), 41–53 (2013).

    Article 

    Google Scholar 

  • 14.

    Cureton, J. C. et al. Effects of urbanization on genetic diversity, gene flow, and population structure in the ornate box turtle (Terrapene ornato). Amphib-Reptil. 35, 87–97 (2014).

    Article 

    Google Scholar 

  • 15.

    Indykiewicz, P., Podlaszczuk, P., Janiszewska, A. & Minias, P. Extensive gene flow along the urban-rural gradient in a migratory colonial bird. J. Avian Biol. 49(6), e01723 (2018).

    Article 

    Google Scholar 

  • 16.

    Hurtado, G. & Mabry, K. E. Genetic structure of an abundant small mammal is influenced by low intensity urbanization. Conserv. Genet. 20, 705–715 (2019).

    CAS 
    Article 

    Google Scholar 

  • 17.

    Khimoun, A. et al. Urbanization without isolation: The absence of genetic structure among cities and forests in the tiny acorn ant Temnothorax nylanderi. Biol. Lett. 16, 20190741 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 18.

    Munshi-South, J., Zolnik, C. P. & Harris, S. E. Population genomics of the Anthropocene: Urbanization is negatively associated with genome-wide variation in white-footed mouse populations. Evol. Appl. 9, 546–564 (2016).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 19.

    Brewer, V. N., Lane, S. J., Sewall, K. B. & Mabry, K. E. Effects of low-density urbanization on genetic structure in the Song Sparrow. PLoS ONE 15(6), e0234008 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 20.

    Slatkin, M. Gene flow in natural populations. Annu. Rev. Ecol. Syst. 16, 393–430 (1985).

    Article 

    Google Scholar 

  • 21.

    Balloux, F. & Lugon-Moulin, N. The estimation of population differentiation with microsatellite markers. Mol. Ecol. 11, 155–165 (2002).

    PubMed 
    Article 

    Google Scholar 

  • 22.

    Vangestel, C., Mergeay, J., Dawson, D. A., Vandomme, V. & Lens, L. Spatial heterogeneity in genetic relatedness among house sparrows along an urban—rural gradient as revealed by individual-based analysis. Mol. Ecol. 20, 4643–4653 (2011).

    PubMed 
    Article 

    Google Scholar 

  • 23.

    Barnett, J. R., Ruiz-Gutierrez, V., Coulon, A. & Lovette, I. J. Weak genetic structuring indicates ongoing gene flow across White-ruffed Manakin (Corapipo altera) populations in a highly fragmented Costa Rica landscape. Conserv. Genet. 9, 1403–1412 (2008).

    Article 

    Google Scholar 

  • 24.

    Riegert, J., Fainová, D. & Bystrická, D. Genetic variability, body characteristics and reproductive parameters of neighbouring rural and urban common kestrel (Falco tinnuculus) populations. Popul. Ecol. 52, 73–79 (2009).

    Article 

    Google Scholar 

  • 25.

    MacDougall-Shackleton, E. A., Clinchy, M., Zanette, L. & Neff, B. D. Songbird genetic diversity is lower in anthropogenically versus naturally fragmented landscapes. Conserv. Genet. 12, 1195–1203 (2011).

    Article 

    Google Scholar 

  • 26.

    Caizergues, A. E. et al. Testing for parallel genomic and epigenomic footprints of adaptation to urban life in a passerine bird. bioRxiv. https://doi.org/10.1101/2021.02.10.430452

  • 27.

    Schmidt, C., Domaratzki, M., Kinnunen, R. P., Bowman, J. & Garroway, C. J. Continent-wide effects of urbanization on bird and mammal genetic diversity. Proc. R. Soc. B. 287, 20192497 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 28.

    Cramp, S. & Perrins, C. M. The Birds of the Western Palearctic Vol. 7 (Oxford University Press, 1993).

    Google Scholar 

  • 29.

    Dauwe, T. et al. Great and Blue tit feathers as biomonitors for heavy metal pollution. Ecol. Indic. 1, 227–234 (2002).

    CAS 
    Article 

    Google Scholar 

  • 30.

    Bańbura, J. & Bańbura, M. Blue tits Cyanistes caeruleus and great tits Parus major as urban habitat breeders. Inter Stud. Sparrows 36, 66–72 (2012).

    Article 

    Google Scholar 

  • 31.

    Charmantier, A., Doutrelant, C., Dubuc-Messier, G., Fargevieille, A. & Szulkin, M. Mediterranean blue tits as a case study of local adaptation. Evol. Appl. 9, 135–152 (2016).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 32.

    Lemoine, M. et al. Low but contrasting neutral genetic differentiation shaped by winter temperature in European Great Tits. Biol. J. Linn. Soc. 118, 668–685 (2016).

    Article 

    Google Scholar 

  • 33.

    Porlier, M. Garant, D. Perret, P. and Charmantier, A. Habitat-linked population genetic differentiation in the Blue tit Cyanistes caeruleus. J. Hered. 103, 781–791 (2012).

  • 34.

    Szulkin, M., Gagnaire, P. A., Bierne, N. & Charmantier, A. Population genomic footprints of fine-scale differentiation between habitats in Mediterranean blue tits. Mol. Ecol. 25, 542–558 (2016).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 35.

    Dubuc-Messier, G. et al. Gene flow does not prevent personality and morphological differentiation between two blue tit populations. J. Evol. Biol. 31, 1127–1137 (2018).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 36.

    Postma, E. D., Tex, R.-J., Noordwijk, A. J. & Mateman, A. C. Neutral markers mirror small-scale quantitative genetic differentiation in an avian island population. Biol. J. Linn. Soc. 97, 867–875 (2009).

    Article 

    Google Scholar 

  • 37.

    Salmón, P. et al. Repeated genomic signature of adaptation to urbanisation in a songbird across Europe. bioRxiv. https://doi.org/10.1101/2020.05.05.078568 (2020).

  • 38.

    Dhondt, A. A. Effects of competition on great and blue tit reproduction: Intensity and importance in relation to habitat quality. J. Anim. Ecol. 79, 257–265 (2010).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 39.

    Nilsson, A. L. K., Lindström, Å., Jonzén, N., Nilsson, S. G. & Karlsson, L. The effect of climate change on partial migration: The blue tit paradox. Glob. Change Biol. 12, 2014–2022. https://doi.org/10.1111/j.1365-2486.2006.01237.x (2006).

    ADS 
    Article 

    Google Scholar 

  • 40.

    Nilsson, A. L. K., Alerstam, T. & Nilsson, J. Å. Diffuse, short and slow migration among Blue Tits. J. Ornithol. 149, 365–373. https://doi.org/10.1007/s10336-008-0280-3 (2008).

    Article 

    Google Scholar 

  • 41.

    Bańbura, J. et al. Spatial and temporal variation in heterophil-to-lymphocyte ratios of nestling passerine birds: Comparison of blue tits and great tits. PLoS ONE 8(9), e74226 (2013).

  • 42.

    Adamou, A.-E., Bańbura, M. & Bańbura, J. Subtle differences in breeding performance between Great Tits Parus major and Afrocanarian Blue Tits Cyanistes teneriffae in the peripheral zone of the species geographic ranges in NE Algeria. Eur. Zool. J. 87, 263–271 (2020).

    Article 

    Google Scholar 

  • 43.

    Dhondt, A. A. & Eyckerman, R. Competition between the great tit and the blue tit outside the breeding season in field experiments. Ecology 61, 1291–1296 (1980).

    Article 

    Google Scholar 

  • 44.

    Ortego, J., Garcia-Navas, V., Ferrer, E. S. & Sanz, J. J. Genetic structure reflects natal dispersal movements at different spatial scales in the blue tit Cyanistes caeruleus. Anim. Behav. 82, 131–137 (2011).

    Article 

    Google Scholar 

  • 45.

    Langin, K. M. et al. Characterizing range-wide divergence in an alpine-endemic bird: A comparison of genetic and genomic approaches. Conserv. Genet. 19(6), 1471–1485 (2018).

    CAS 
    Article 

    Google Scholar 

  • 46.

    Roques, S., Chancerel, E., Boury, C., Pierre, M. & Acolas, M. L. From microsatellites to single nucleotide polymorphisms for the genetic monitoring of a critically endangered sturgeon. Ecol. Evol. 9(12), 7017–7029 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 47.

    Zimmerman, S. J., Aldridge, C. L. & Oyler-McCance, S. J. An empirical comparison of population genetic analyses using microsatellite and SNP data for a species of conservation concern. BMC Genom. 21, 1–16 (2020).

    Article 
    CAS 

    Google Scholar 

  • 48.

    Markowski, M. et al. Effects of experimental lead exposure on physiological indices of nestling great tits Parus major: Haematocrit and heterophile-to-lymphocyte ratio. Conserv. Physiol. 7, coz067 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 49.

    Bańbura, J. et al. Habitat and year-to-year variation in haemoglobin concentration in nestling blue tits Cyanistes caeruleus. Comp. Biochem. Phys. A 148, 572–577 (2007).

    Article 
    CAS 

    Google Scholar 

  • 50.

    Kiedrzyński, M. The impact of forest management on the flora and vegetation of old oak-stands (an example from The Spała Forests, central Poland). Nat. Conserv. 65, 51–62 (2008).

    Google Scholar 

  • 51.

    Glądalski, M. et al. Effects of human-related disturbance on breeding success of urban and non-urban blue tits (Cyanistes caeruleus). Urban Ecosyst. 19, 1325–1334 (2016).

    Article 

    Google Scholar 

  • 52.

    Markowski, M. et al. Spatial and temporal variation of lead, cadmium, and zinc in feathers of great tit and blue tit nestlings in Central Poland. Arch. Environ. Contam. Toxicol. 67, 507–518 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 53.

    Richard, M. & Thorpe, R. S. Highly polymorphic microsatellites in the lacertid Gallotia Gallowi from the western Canary Islands. Mol. Ecol. 9, 1919–1952 (2000).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 54.

    Saladin, V., Bonfils, D., Binz, T. & Richner, H. Isolation and characterization of 16 microsatellite loci in the Great Tit Parus major. Mol. Ecol. Notes 3, 520–522 (2003).

    CAS 
    Article 

    Google Scholar 

  • 55.

    Dawson, D. A., Hanotte, O., Greig, C., Stewart, I. R. K. & Burke, T. Polymorphic microsatellites in the blue tit Parus caeruleus and their cross-species utility in 20 songbird families. Mol. Ecol. 9, 1941–1944 (2000).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 56.

    van Oosterhout, C., Hutchinson, W. F., Wills, D. P. & Shipley, P. MICRO-CHECKER: Software for identifying and correcting genotyping errors in microsatellite data. Mol. Ecol. Res. 4, 535–538 (2004).

    Google Scholar 

  • 57.

    Guo, S. W. & Thompson, E. A. Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48, 361–372 (1992).

    CAS 
    MATH 
    Article 

    Google Scholar 

  • 58.

    Excoffier, L. & Lischer, H. E. L. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Res. 10, 564–567 (2010).

    Article 

    Google Scholar 

  • 59.

    Goudet, J. FSTAT (version 12): A computer program to calculate F-statistics. J. Hered. 86, 485–486 (1995).

    Article 

    Google Scholar 

  • 60.

    Kalinowski, S. T., Taper, M. L. & Marshall, T. C. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol. Ecol. 16, 1099–1106 (2007).

    PubMed 
    Article 

    Google Scholar 

  • 61.

    Peakall, R. & Smouse, P. E. GENALEX 6: Genetic analysis in Excel: Population genetic software for teaching and research. Mol. Ecol. Notes 6, 288–295 (2006).

    Article 

    Google Scholar 

  • 62.

    Peakall, R. & Smouse, P. E. GENALEX 6.5: Genetic analysis in Excel. Population genetic software for teaching and research: An update. Bioinformatics 28, 2537–2539 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 63.

    Slatkin, M. A measure of subdivision based on microsatellite allele frequencies. Genetics 139, 457–462 (1995).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 64.

    Hardy, O. J., Charbonnel, N., Fréville, H. & Heuertz, M. Microsatellite allele sizes: A simple test to assess their significance on genetic differentiation. Genetics 163, 1467–1482 (2003).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 65.

    Hardy, O. J. & Vekemans, X. SPAGeDi: A versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol. Ecol. Notes 2, 618–620 (2002).

    Article 
    CAS 

    Google Scholar 

  • 66.

    Hedrick, P. W. A standardized genetic differentiation measure. Evolution 59, 1633–1638 (2005).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 67.

    Meirmans, P. G. Using the AMOVA framework to estimate a standardized genetic differentiation measure. Evolution 60, 2399–2402 (2006).

    Article 

    Google Scholar 

  • 68.

    Nei, M. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89, 583–590 (1978).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 69.

    Dray, S. & Dufour, A. The ade4 Package: Implementing the duality diagram for ecologists. J. Stat. Softw. 22(4), 1–20. https://doi.org/10.18637/jss.v022.i04 (2007).

    Article 

    Google Scholar 

  • 70.

    Jombart, T. adegenet: A R package for the multivariate analysis of genetic markers. Bioinformatics 24(11), 1403–1405 (2008).

    CAS 
    Article 

    Google Scholar 

  • 71.

    TIBCO Software Inc. Statistica (Data Analysis Software System), Version 13. http://statistica.io. (2017).


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