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Scale-dependent effects of habitat fragmentation on the genetic diversity of Actinidia chinensis populations in China

  • 1.

    Wu, J. Key concepts and research topics in landscape ecology revisited: 30 years after the Allerton Park workshop. Landsc. Ecol. 28, 1–11 (2013).

    CAS  Article  Google Scholar 

  • 2.

    Wilson, M. C. et al. Habitat fragmentation and biodiversity conservation: key findings and future challenges. Landsc. Ecol. 31, 219–227 (2016).

    Article  Google Scholar 

  • 3.

    Leimu, R., Vergeer, P., Angeloni, F. & Ouborg, N. J. Habitat fragmentation, climate change, and inbreeding in plants. Ann. NY Acad. Sci. 1195, 84–98 (2010).

    PubMed  Article  Google Scholar 

  • 4.

    Young, A., Boyle, T. & Brown, T. The population genetic consequences of habitat fragmentation for plants. Trends Ecol. Evolution 11, 413–418 (1996).

    CAS  Article  Google Scholar 

  • 5.

    Yuan, N., Comes, H. P., Mao, Y., Qi, X. & Qiu, Y. Genetic effects of recent habitat fragmentation in the Thousand-Island Lake region of southeast China on the distylous herb Hedyotis chrysotricha (Rubiaceae). Am. J. Bot. 99, 1715–1725 (2012).

    PubMed  Article  Google Scholar 

  • 6.

    MacArthur, R. H. & Wilson, E. O. An equilibrium theory of insular zoogeography. Evolution 17, 373–387 (1963).

    Article  Google Scholar 

  • 7.

    MacArthur, R. H. & Wilson, E. O. The Theory of Island Biogeography (Princeton University Press, Princeton, NJ, 1967).

  • 8.

    Guo, Q. Island biogeography theory: emerging patterns and human effects. Earth Syst. Environ. Sci. 32, 1–5 (2015).

    Google Scholar 

  • 9.

    Wroblewska, A. High genetic diversity within island-like peripheral populations of Pedicularis sceptrum-carolinum, a species with a northern geographic distribution. Ann. Bot. Fenn. 50, 289–299 (2013).

    Article  Google Scholar 

  • 10.

    Csergo, A.-M. et al. Genetic structure of peripheral, island-like populations: a case study of Saponaria bellidifolia Sm. (Caryophyllaceae) from the Southeastern Carpathians. Plant Syst. Evol. 278, 33–41 (2009).

    Article  Google Scholar 

  • 11.

    Doyle, J. M., Hacking, C. C., Willoughby, J. R., Sundaram, M. & DeWoody, J. A. Mammalian genetic diversity as a function of habitat, body size, trophic class, and conservation status. J. Mammal. 96, 564–572 (2015).

    Article  Google Scholar 

  • 12.

    Reynolds, R. G. et al. Archipelagic genetics in a widespread Caribbean anole. J. Biogeogr. 44, 2631–2647 (2017).

    Article  Google Scholar 

  • 13.

    Costanzi, J.-M. & Steifetten, Ø. Island biogeography theory explains the genetic diversity of a fragmented rock ptarmigan (Lagopus muta) population. Ecol. Evol. 9, 3837–3849 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  • 14.

    Hermansen, T., Minchinton, T. & Ayre, D. Habitat fragmentation leads to reduced pollinator visitation, fruit production and recruitment in urban mangrove forests. Oecologia 185, 221–231 (2017).

    PubMed  Article  Google Scholar 

  • 15.

    Broeck, A. et al. Dispersal constraints for the conservation of the grassland herb Thymus pulegioides L. in a highly fragmented agricultural landscape. Conserv Genet. 16, 765–776 (2015).

    Article  Google Scholar 

  • 16.

    Browne, L. & Karubian, J. Habitat loss and fragmentation reduce effective gene flow by disrupting seed dispersal in a neotropical palm. Mol. Ecol. 27, 3055–3069 (2018).

    PubMed  Article  Google Scholar 

  • 17.

    Bijlsma, R. & Loeschcke, V. Genetic erosion impedes adaptive responses to stressful environments. Evol. Appl. 5, 117–129 (2012).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 18.

    Lienert, J. Habitat fragmentation effects on fitness of plant populations-a review. J. Nat. Conserv. 12, 53–72 (2004).

    Article  Google Scholar 

  • 19.

    Luquet, E. et al. Genetic erosion in wild populations makes resistance to a pathogen more costly. Evolution 66, 1942–1952 (2012).

    PubMed  Article  Google Scholar 

  • 20.

    Toczydlowski, R. H. & Waller, D. M. Drift happens: molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests. Mol. Ecol. 28, 2459–2475 (2019).

    PubMed  Article  PubMed Central  Google Scholar 

  • 21.

    Jimenez, J. F., Sanchez-Gomez, P., Canovas, J. L., Hensen, I. & Aouissat, M. Influence of natural habitat fragmentation on the genetic structure of Canarian populations of Juniperus turbinata. Silva Fenn. 51, 1–14 (2017).

    Article  Google Scholar 

  • 22.

    Garciaverdugo, C. et al. Do island plant populations really have lower genetic variation than mainland populations? Effects of selection and distribution range on genetic diversity estimates. Mol. Ecol. 24, 726–741 (2015).

    CAS  Article  Google Scholar 

  • 23.

    Vandepitte, K., Jacquemyn, H., Roldan-Ruiz, I. & Honnay, O. Landscape genetics of the self-compatible forest herb Geum urbanum: effects of habitat age, fragmentation and local environment. Mol. Ecol. 16, 4171–4179 (2007).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 24.

    Krauss, J. et al. Habitat fragmentation causes immediate and time-delayed biodiversity loss at different trophic levels. Ecol. Lett. 13, 597–605 (2010).

    PubMed  PubMed Central  Article  Google Scholar 

  • 25.

    Heinken, T. & Weber, E. Consequences of habitat fragmentation for plant species: do we know enough? Perspect. Plant Ecol. Syst. 15, 205–216 (2013).

    Article  Google Scholar 

  • 26.

    Duminil, J. et al. Large-scale pattern of genetic differentiation within African rainforest trees: insights on the roles of ecological gradients and past climate changes on the evolution of Erythrophleum spp (Fabaceae). BMC Evol. Biol. 13, 195- (2013).

    PubMed  PubMed Central  Article  Google Scholar 

  • 27.

    Yuan, N. et al. A comparative study on genetic effects of artificial and natural habitat fragmentation on Loropetalum chinense (Hamamelidaceae) in Southeast China. Heredity 114, 544 (2014).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • 28.

    Muyle, A. et al. Dioecy in plants: an evolutionary dead end? Insights from a population genomics study in the Silene genus. Preprint at https://www.biorxiv.org/content/10.1101/414771v1.full (2018).

  • 29.

    Fuller, M. R. & Doyle, M. W. Gene flow simulations demonstrate resistance of long-lived species to genetic erosion from habitat fragmentation. Conserv Genet. 19, 1439–1448 (2018).

    Article  Google Scholar 

  • 30.

    Hu, Y. et al. Genetic structuring and recent demographic history of red pandas (Ailurus fulgens) inferred from microsatellite and mitochondrial DNA. Mol. Ecol. 20, 2662–2675 (2011).

    PubMed  Article  Google Scholar 

  • 31.

    Moore, J. A., Miller, H. C., Daugherty, C. H. & Nelson, N. J. Fine-scale genetic structure of a long-lived reptile reflects recent habitat modification. Mol. Ecol. 17, 4630–4641 (2008).

    CAS  PubMed  Article  Google Scholar 

  • 32.

    Martínez-López, V., García, C., Zapata, V., Robledano, F. & De la Rúa, P. Intercontinental long-distance seed dispersal across the Mediterranean Basin explains population genetic structure of a bird-dispersed shrub. Mol. Ecol. 29, 1408–1420 (2020).

    PubMed  Article  Google Scholar 

  • 33.

    Grover, A. & Sharma, P. C. Development and use of molecular markers: past and present. Crit. Rev. Biotechnol. 36, 290–302 (2016).

    CAS  PubMed  Article  Google Scholar 

  • 34.

    Vieira, M. L. C., Santini, L., Diniz, A. L. & Munhoz, C. D. F. Microsatellite markers: what they mean and why they are so useful. Genet Mol. Biol. 39, 312–328 (2016).

    PubMed  PubMed Central  Article  Google Scholar 

  • 35.

    Selkoe, K. A. & Toonen, R. J. Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol. Lett. 9, 615–629 (2006).

    PubMed  Article  Google Scholar 

  • 36.

    Huang, H. et al. Genetic diversity in the genus Actinidia (in Chinese). Chin. Biodivers. 8, 1–12 (2000).

    CAS  Google Scholar 

  • 37.

    Logan, D. P. & Xu, X. Germination of kiwifruit, Actinidia chinensis, after passage through Silvereyes, Zosterops lateralis. New Zeal. J. Ecol. 30, 407–411 (2006).

    Google Scholar 

  • 38.

    Costa, G., Testolin, R. & Vizzotto, G. Kiwifruit pollination: an unbiased estimate of wind and bee contribution. N. Zeal J. Crop Hort. 21, 189–195 (1993).

    Article  Google Scholar 

  • 39.

    Huang, H. The Genus Actinidia, A World Monograph (Science Press, Beijing, 2014).

  • 40.

    Lv, K. et al. Habitat fragmentation influences gene structure and gene differentiation among the Loxoblemmus aomoriensis populations in the Thousand Island Lake. Mitochondrial DNA A 29, 222–227 (2017).

    Article  CAS  Google Scholar 

  • 41.

    Liu, Y. F. et al. Rapid radiations of both kiwifruit hybrid lineages and their parents shed light on a two-layer mode of species diversification. N. Phytol. 215, 877–890 (2017).

    CAS  Article  Google Scholar 

  • 42.

    Huang, W. G., Cipriani, G., Morgante, M. & Testolin, R. Microsatellite DNA in Actinidia chinensis: isolation, characterisation, and homology in related species. Theor. Appl. Genet. 97, 1269–1278 (1998).

    CAS  Article  Google Scholar 

  • 43.

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

    Article  CAS  Google Scholar 

  • 44.

    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. Resour. 10, 564–567 (2010).

    PubMed  Article  PubMed Central  Google Scholar 

  • 45.

    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 

  • 46.

    Pallant, J. SPSS survival manual: a step by step guide to data analysis using SPSS. Aust. N.Z. J. Public Health 37, 597–598 (2013).

    Google Scholar 

  • 47.

    Excoffier, L., Smouse, P. E. & Quattro, J. M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131, 479–491 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 48.

    Smouse, P. E., Long, J. C. & Sokal, R. R. Multiple regression and correlation extensions of the mantel test of matrix correspondence. Syst. Biol. 35, 627–632 (1986).

    Google Scholar 

  • 49.

    Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 50.

    Evanno, G., Regnaut, S. & Goudet, J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14, 2611–2620 (2005).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 51.

    Earl, D. & Vonholdt, B. M. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4, 359–361 (2012).

    Article  Google Scholar 

  • 52.

    Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30, 2725–2729 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 53.

    Pickrell, J. K. & Pritchard, J. K. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8, e1002967 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 54.

    Cornuet, J. M. & Luikart, G. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144, 2001–2014 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 55.

    Di Rienzo, A. et al. Mutational processes of simple-sequence repeat loci in human populations. Proc. Natl Acad. Sci. USA 91, 3166–3170 (1994).

    PubMed  Article  PubMed Central  Google Scholar 

  • 56.

    Wang, S. et al. Population size and time since island isolation determine genetic diversity loss in insular frog populations. Mol. Ecol. 23, 637–648 (2014).

    PubMed  Article  PubMed Central  Google Scholar 

  • 57.

    Luikart, G., Allendorf, F., Cornuet, J. & Sherwin, W. Distortion of allele frequency distributions provides a test for recent population bottlenecks. J. Hered. 89, 238–247 (1998).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 58.

    Cornuet, J.-M. et al. DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data. Bioinformatics 30, 1187–1189 (2014).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 59.

    Ewers, R. M. & Didham, R. K. The effect of fragment shape and species’ sensitivity to habitat edges on animal population size. Conserv Biol. 21, 926–936 (2007).

    PubMed  Article  Google Scholar 

  • 60.

    Ortego, J., Bonal, R. & Munoz, A. Genetic consequences of habitat fragmentation in long-lived tree species: the case of the Mediterranean holm oak (Quercus ilex, L.). J. Hered. 101, 717–726 (2010).

    CAS  PubMed  Article  Google Scholar 

  • 61.

    Fletcher, J. R. J. et al. Is habitat fragmentation good for biodiversity? Biol. Conserv 226, 9–15 (2018).

    Article  Google Scholar 

  • 62.

    Fattorini, S., Borges, P. A. V., Dapporto, L. & Strona, G. What can the parameters of the species-area relationship (SAR) tell us? Insights from Mediterranean islands. J. Biogeogr. 44, 1018–1028 (2017).

    Article  Google Scholar 

  • 63.

    Matthews, T. J. et al. Island species-area relationships and species accumulation curves are not equivalent: an analysis of habitat island datasets. Global Ecol. Biogeogr. 25, 607–618 (2016).

    Article  Google Scholar 

  • 64.

    Matthews, T., Cottee-Jones, H., Whittaker, R. & Brotons, L. Habitat fragmentation and the species-area relationship: a focus on total species richness obscures the impact of habitat loss on habitat specialists. Divers Distrib. 20, 1136–1146 (2014).

    Article  Google Scholar 

  • 65.

    McGlaughlin, M. E. et al. Do the island biogeography predictions of MacArthur and Wilson hold when examining genetic diversity on the near mainland California Channel Islands? Examples from endemic Acmispon (Fabaceae). Bot. J. Linn. Soc. 174, 289–304 (2014).

    Article  Google Scholar 

  • 66.

    Jangjoo, M., Matter, S. F., Roland, J. & Keyghobadi, N. Connectivity rescues genetic diversity after a demographic bottleneck in a butterfly population network. Proc. Natl Acad. Sci. USA 113, 10914–10919 (2016).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 67.

    Reisch, C. et al. Genetic diversity of calcareous grassland plant species depends on historical landscape configuration. BMC Ecol. 17, 1–13 (2017).

    Article  Google Scholar 

  • 68.

    Bottin, L. et al. Genetic diversity and population structure of an insular tree, Santalum austrocaledonicum in New Caledonian archipelago. Mol. Ecol. 14, 1979–1989 (2005).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 69.

    Breed, M. F. et al. Mating patterns and pollinator mobility are critical traits in forest fragmentation genetics. Heredity 115, 108–114 (2015).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 70.

    Llorens, T. M., Byrne, M., Yates, C. J., Nistelberger, H. M. & Coates, D. J. Evaluating the influence of different aspects of habitat fragmentation on mating patterns and pollen dispersal in the bird-pollinated Banksia sphaerocarpa var.caesia. Mol. Ecol. 21, 314–328 (2012).

    CAS  PubMed  Article  Google Scholar 

  • 71.

    Rosche, C. et al. Sex ratio rather than population size affects genetic diversity in Antennaria dioica. Plant Biol. 20, 789–796 (2018).

    CAS  PubMed  Article  Google Scholar 

  • 72.

    Liu, Y., Li, D., Yan, L. & Huang, H. The microgeographical patterns of morphological and molecular variation of a mixed ploidy population in the species complex Actinidia chinensis. PLoS ONE 10, e0117596 (2015).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • 73.

    Guijun, Y., Ferguson, A. R. & McNeilage, M. A. Ploidy races in Actinidia chinensis. Euphytica 78, 175–183 (1994).

    Article  Google Scholar 

  • 74.

    Chat, J., Jáuregui, B., Petit, R. J. & Nadot, S. Reticulate evolution in kiwifruit (Actinidia, Actinidiaceae) identified by comparing their maternal and paternal phylogenies. Am. J. Bot. 91, 736–747 (2004).

    CAS  PubMed  Article  Google Scholar 

  • 75.

    Crowhurst, R. N. et al. Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening. BMC Genomics 9, 351 (2008).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • 76.

    Zheng, Y. Q., Li, Z. Z. & Huang, H. W. Preliminary study on SSR analysis in kiwifruit cultivars. J. WH Bot. Res. 21, 444–448 (2003).

    Google Scholar 

  • 77.

    Llorens, T. M., Ayre, D. J. & Whelan, R. J. Anthropogenic fragmentation may not alter pre-existing patterns of genetic diversity and differentiation in perennial shrubs. Mol. Ecol. 27, 1541–1555 (2018).

    PubMed  Article  Google Scholar 

  • 78.

    Van de Peer, Y., Mizrachi, E. & Marchal, K. The evolutionary significance of polyploidy. Nat. Rev. Genet. 18, 411–424 (2017).

    PubMed  Article  CAS  Google Scholar 

  • 79.

    Bommarco, R., Lindborg, R., Marini, L. & Ockinger, E. Extinction debt for plants and flower-visiting insects in landscapes with contrasting land use history. Divers. Distrib. 20, 591–599 (2014).

    Article  Google Scholar 


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