Bayesian Skyline Plots disagree with range size changes based on Species Distribution Models for Holarctic birds.


Journal

Molecular ecology
ISSN: 1365-294X
Titre abrégé: Mol Ecol
Pays: England
ID NLM: 9214478

Informations de publication

Date de publication:
08 2021
Historique:
revised: 14 06 2021
received: 17 09 2020
accepted: 16 06 2021
pubmed: 22 6 2021
medline: 19 8 2021
entrez: 21 6 2021
Statut: ppublish

Résumé

During the Quaternary, large climate oscillations impacted the distribution and demography of species globally. Two approaches have played a major role in reconstructing changes through time: Bayesian Skyline Plots (BSPs), which reconstruct population fluctuations based on genetic data, and Species Distribution Models (SDMs), which allow us to back-cast the range occupied by a species based on its climatic preferences. In this paper, we contrast these two approaches by applying them to a large data set of 102 Holarctic bird species, for which both mitochondrial DNA sequences and distribution maps are available, to reconstruct their dynamics since the Last Glacial Maximum (LGM). Most species experienced an increase in effective population size (N

Identifiants

pubmed: 34152661
doi: 10.1111/mec.16032
doi:

Substances chimiques

DNA, Mitochondrial 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

3993-4004

Subventions

Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/M011194/1
Pays : United Kingdom

Informations de copyright

© 2021 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

Références

Aiello-Lammens, M. E., Boria, R. A., Radosavljevic, A., Vilela, B., & Anderson, R. P. (2015). spThin: An R package for spatial thinning of species occurrence records for use in ecological niche models. Ecography (Cop.), 38, 541-545. https://doi.org/10.1111/ecog.01132
Allen, J. R. M. et al (1999). Rapid environmental changes in southern Europe during the last glacial period. Nature, 400, 740-743. https://doi.org/10.1038/23432
Allen, J. R. M., Hickler, T., Singarayer, J. S., Sykes, M. T., Valdes, P. J., & Huntley, B. (2010). Last glacial vegetation of Northern Eurasia. Quaternary Science Reviews, 29, 2604-2618. https://doi.org/10.1016/j.quascirev.2010.05.031
Araújo, M. B., & Guisan, A. (2006). Five (or so) challenges for species distribution modelling. Journal of Biogeography, 33, 1677-1688. https://doi.org/10.1111/j.1365-2699.2006.01584.x
Araújo, M. B., & New, M. (2007). Ensemble forecasting of species distributions. Trends in Ecology & Evolution, 22, 42-47. https://doi.org/10.1016/j.tree.2006.09.010
Auer, T., Fink, D., & Strimas-Mackey, M. (2019). ebirdst: Tools for loading, plotting, mapping and analysis of eBird Status and Trends data products. R package version 0.1.0.
Bagchi, R. et al (2013). Evaluating the effectiveness of conservation site networks under climate change: Accounting for uncertainty. Global Change Biology, 19, 1236-1248. https://doi.org/10.1111/gcb.12123
Beyer, R., Krapp, M., & Manica, A. (2019). A systematic comparison of bias correction methods for paleoclimate simulations. Climate of the Past Discussion, 1-23, https://doi.org/10.5194/cp-2019-11
Beyer, R. M., Krapp, M., & Manica, A. (2020). High-resolution terrestrial climate, bioclimate and vegetation for the last 120,000 years. Sci. Data, 7, 1-9. https://doi.org/10.1038/s41597-020-0552-1
BirdLife International. (2018). BirdLife International and Handbook of the Birds of the World. 2018. Bird species distribution maps of the world. Version 2018.1. See http://datazone.birdlife.org/species/requestdis
BirdLife International and Handbook of the Birds of the World (2018). Bird species distribution maps of the world. Version 2018.1.
Bouckaert, R. (2015). bModelTest : Bayesian Site Model Selection for Nucleotide Data. bioRxiv, 1-17. https://doi.org/10.1101/020792
Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C. H., Xie, D., Suchard, M. A., Rambaut, A., & Drummond, A. J. (2014). BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Computational Biology, 10, 1-6. https://doi.org/10.1371/journal.pcbi.1003537
Burbrink, F. T., Chan, Y. L., Myers, E. A., Ruane, S., Smith, B. T., & Hickerson, M. J. (2016). Asynchronous demographic responses to Pleistocene climate change in Eastern Nearctic vertebrates. Ecology Letters. https://doi.org/10.1111/ele.12695
Calderón, L. et al (2016). Genomic evidence of demographic fluctuations and lack of genetic structure across flyways in a long distance migrant, the European turtle dove. BMC Evolutionary Biology, 16, 237. https://doi.org/10.1186/s12862-016-0817-7
Chikhi, L., Sousa, V. C., Luisi, P., Goossens, B., & Beaumont, M. A. (2010). The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes. Genetics, 186, 983-995. https://doi.org/10.1534/genetics.110.118661
Connor, E. F., Courtney, A. C., & Yoder, J. M. (2000). Individuals-area relationships: The relationship between animal population density and area. Ecology, 81, 734. https://doi.org/10.2307/177373
Drummond, A. J., & Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214. https://doi.org/10.1186/1471-2148-7-214
Drummond, A. J., Rambaut, A., Shapiro, B., & Pybus, O. G. (2005). Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular Biology and Evolution, 22, 1185-1192. https://doi.org/10.1093/molbev/msi103
Dunning, J. (2007). CRC handbook of avian body masses, 2nd ed. CRC Press.
Elith, J., & Leathwick, J. R. (2009). Species distribution models: Ecological explanation and prediction across space and time. Annual Review of Ecology Evolution and Systematics, 40, 677-697. https://doi.org/10.1146/annurev.ecolsys.110308.120159
Fan, Y., & Miguez-Macho, G. (2011). A simple hydrologic framework for simulating wetlands in climate and earth system models. Climate Dynamics, 37, 253-278. https://doi.org/10.1007/s00382-010-0829-8
Foote, A. D. et al (2013). Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts. Nature Communications, 4, 1677. https://doi.org/10.1038/ncomms2714
Fordham, D. A. et al (2012). Plant extinction risk under climate change: are forecast range shifts alone a good indicator of species vulnerability to global warming? Global Change Biology, 18, 1357-1371. https://doi.org/10.1111/j.1365-2486.2011.02614.x
Giesecke, T., Brewer, S., Finsinger, W., Leydet, M., & Bradshaw, R. H. W. (2017). Patterns and dynamics of European vegetation change over the last 15,000 years. Journal of Biogeography, 44, 1441-1456. https://doi.org/10.1111/jbi.12974
Grant, W. S. (2015). Problems and cautions with sequence mismatch analysis and Bayesian skyline plots to infer historical demography. Journal of Heredity, 106, 333-346. https://doi.org/10.1093/jhered/esv020
Grant, W. S., Liu, M., Gao, T., & Yanagimoto, T. (2012). Limits of Bayesian skyline plot analysis of mtDNA sequences to infer historical demographies in Pacific herring (and other species). Molecular Phylogenetics and Evolution, 65, 203-212. https://doi.org/10.1016/j.ympev.2012.06.006
Gregory, R. D., Van Strien, A., Vorisek, P., Meyling, A. W. G., Noble, D. G., Foppen, R. P. B., & Gibbons, D. W. (2005). Developing indicators for European birds. Philosophical Transaction of the Royal Society B Biol. Sci., 360, 269-288. https://doi.org/10.1098/rstb.2004.1602
Guisan, A., Thuiller, W., & Zimmermann, N. E. (2017). Habitat suitability and distribution models. Cambridge University Press. https://doi.org/10.1017/9781139028271
Heled, J., & Drummond, A. J. (2008). Bayesian inference of population size history from multiple loci. BMC Evolutionary Biology, 15, 1-15. https://doi.org/10.1186/1471-2148-8-289.
Heller, R., Chikhi, L., & Siegismund, H. R. (2013). The confounding effect of population structure on Bayesian skyline plot inferences of demographic history. PLoS One, 8, e62992. https://doi.org/10.1371/journal.pone.0062992
Hijmans, R. J., Cameron, S. E., Parra, J. L., Jones, P. G., & Jarvis, A. (2005). Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology, 25, 1965-1978. https://doi.org/10.1002/joc.1276
Ho, S. Y. M. (2007). Calibrating molecular estimates of substitution rates and divergence times in birds. Journal of Avian Biology, 38, 409-414. https://doi.org/10.1111/j.2007.0908-8857.04168.x
Ho, S. Y. W., & Shapiro, B. (2011). Skyline-plot methods for estimating demographic history from nucleotide sequences. Molecular Ecology Resources, 11, 423-434. https://doi.org/10.1111/j.1755-0998.2011.02988.x
Hope, A. G., Ho, S. Y. W., Malaney, J. L., Cook, J. A., & Talbot, S. L. (2014). Accounting for rate variation among lineages in comparative demographic analyses. Evolution (N., Y). 68, 2689-2700. https://doi.org/10.1111/evo.12469
Howard, C., Stephens, P. A., Pearce-Higgins, J. W., Gregory, R. D., & Willis, S. G. (2014). Improving species distribution models: The value of data on abundance. Methods in Ecology and Evolution, 5, 506-513. https://doi.org/10.1111/2041-210X.12184
Howell, N., Smejkal, C. B., Mackey, D. A., Chinnery, P. F., Turnbull, D. M., & Herrnstadt, C. (2003). The Pedigree Rate of Sequence Divergence in the Human Mitochondrial Genome: There Is a Difference Between Phylogenetic and Pedigree Rates. American Journal of Human Genetics, 72, 659-670. https://doi.org/10.1086/368264
Jetz, W., Thomas, G. H., Joy, J. B., Hartmann, K., & Mooers, A. O. (2012). The global diversity of birds in space and time. Nature, 491, 444-448. https://doi.org/10.1038/nature11631
Johnston, A. et al (2015). Abundance models improve spatial and temporal prioritization of conservation resources. Ecological Applications, 25, 1749-1756. https://doi.org/10.1890/14-1826.1
Kaplan, J. O. (2002). Wetlands at the Last Glacial Maximum: Distribution and methane emissions. Geophysical Research Letters, 29, 3-1-3-4. https://doi.org/10.1029/2001GL013366
Kingman, J. F. C. (1982). On the genealogy of large populations. Journal of Applied Probability, 19, 27. https://doi.org/10.2307/3213548
Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870-1874. https://doi.org/10.1093/molbev/msw054
Lafleur, P. M. (2008). Connecting Atmosphere and Wetland: Energy and Water Vapour Exchange. Geography Compass, 2, 1027-1057. https://doi.org/10.1111/j.1749-8198.2007.00132.x
Leigh, J. W., & Bryant, D. (2015). Popart: Full-Feature Software for Haplotype Network Construction. Methods in Ecology and Evolution, 6, 1110-1116. https://doi.org/10.1111/2041-210X.12410
Lorenzen, E. D. et al (2012). Species-specific responses of LateQuaternary megafauna to climate and humans. Nature, 479, 359-364. https://doi.org/10.1038/nature10574
Lu, B., Zheng, Y., Murphy, R. W., & Zeng, X. (2012). Coalescence patterns of endemic Tibetan species of stream salamanders (Hynobiidae: Batrachuperus). Molecular Ecology, 21, 3308-3324. https://doi.org/10.1111/j.1365-294X.2012.05606.x
Mazet, O., Rodríguez, W., & Chikhi, L. (2015). Demographic inference using genetic data from a single individual: Separating population size variation from population structure. Theoretical Population Biology, 104, 46-58. https://doi.org/10.1016/j.tpb.2015.06.003
Miller, E. F., Manica, A., & Amos, W. (2018). Global demographic history of human populations inferred from whole mitochondrial genomes. Royal Society of Open Science, 5, 180543. https://doi.org/10.1098/rsos.180543
Nabholz, B., Lanfear, R., & Fuchs, J. (2016). Body mass-corrected molecular rate for bird mitochondrial DNA. Molecular Ecology, 25, 4438-4449. https://doi.org/10.1111/mec.13780
Pannell, J. R. (2003). Coalescence in a Metapopulation with Recurrent Local Extinction and Recolonzation. Evolution (N., Y). 57, 949-961. https://doi.org/10.1111/j.0014-3820.2003.tb00307.x.
Penny, D. (2005). Relativity for molecular clocks. Nature, 436, 183-184. https://doi.org/10.1038/436183a
Potts, J. M., & Elith, J. (2006). Comparing species abundance models. Ecological Modelling, 199, 153-163. https://doi.org/10.1016/j.ecolmodel.2006.05.025
Pybus, O. G., Rambaut, A., & Harvey, P. H. (2000). An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics, 155, 1429-1437.
Roberts, D. R. et al (2017). Cross-validation strategies for data with temporal, spatial, hierarchical, or phylogenetic structure. Ecography (Cop.), 40, 913-929. https://doi.org/10.1111/ecog.02881
Sanchez, G., Tomano, S., Yamashiro, C., Fujita, R., Wakabayashi, T., Sakai, M., & Umino, T. (2016). Population genetics of the jumbo squid Dosidicus gigas (Cephalopoda: Ommastrephidae) in the northern Humboldt Current system based on mitochondrial and microsatellite DNA markers. Fisheries Research, 175, 1-9. https://doi.org/10.1016/j.fishres.2015.11.005
Segawa, T., Takeuchi, N., Fujita, K., Aizen, V. B., Willerslev, E., & Yonezawa, T. (2018). Demographic analysis of cyanobacteria based on the mutation rates estimated from an ancient ice core. Heredity (Edinb), 1-12, https://doi.org/10.1038/s41437-017-0040-3
Städler, T., Haubold, B., Merino, C., Stephan, W., & Pfaffelhuber, P. (2009). The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations. Genetics, 182, 205-216. https://doi.org/10.1534/genetics.108.094904
Stiller, M. et al (2010). Withering away-25,000 years of genetic decline preceded cave bear extinction. Molecular Biology and Evolution, 27, 975-978. https://doi.org/10.1093/molbev/msq083.
Stockwell, D. R., & Peterson, A. T. (2002). Effects of sample size on accuracy of species distribution models. Ecological Modelling, 148, 1-13. https://doi.org/10.1016/S0304-3800(01)00388-X
Svenning, J.-C., Eiserhardt, W. L., Normand, S., Ordonez, A., & Sandel, B. (2015). The influence of paleoclimate on present-day patterns in biodiversity and ecosystems. Annual Review of Ecology Evolution and Systematics, 46, 551-572. https://doi.org/10.1146/annurev-ecolsys-112414-054314
Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22, 4673-4680. https://doi.org/10.1093/nar/22.22.4673
Thuiller, W., Georges, D., Engler, R., & Breiner, F. (2019) biomod2: Ensemble Platform for Species Distribution Modeling.
Townsend, P. A. (2011). Ecological niche conservatism: A time-structured review of evidence. Journal of Biogeography, 38, 817-827. https://doi.org/10.1111/j.1365-2699.2010.02456.x
Twitchett, R. J. (2006). The palaeoclimatology, palaeoecology and palaeoenvironmental analysis of mass extinction events. Palaeogeography, Palaeoclimatology, Palaeoecology, 232, 190-213. https://doi.org/10.1016/j.palaeo.2005.05.019
Valavi, R., Elith, J., Lahoz-Monfort, J. J., & Guillera-Arroita, G. (2019). blockCV: An r package for generating spatially or environmentally separated folds for k-fold cross-validation of species distribution models. Methods in Ecology and Evolution, 10, 225-232. https://doi.org/10.1111/2041-210X.13107
Valdes, P. J., Beerling, D. J., & Jonhson, C. E. (2005). The ice age methane budget. Geophysical Research Letters, 32, 1-4. https://doi.org/10.1029/2004GL021004
Van Meerbeeck, C. J., Renssen, H., & Roche, D. M. (2009). How did Marine Isotope Stage 3 and Last Glacial Maximum climates differ? - Perspectives from equilibrium simulations. Climate of the Past, 5, 33-51. https://doi.org/10.5194/cp-5-33-2009
Veloz, S. D., Williams, J. W., Blois, J. L., He, F., Otto-Bliesner, B., & Liu, Z. (2012). No-analog climates and shifting realized niches during the late quaternary: Implications for 21st-century predictions by species distribution models. Global Change Biology, 18, 1698-1713. https://doi.org/10.1111/j.1365-2486.2011.02635.x
Vignaud, T. M. et al (2014). Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline. Molecular Ecology. https://doi.org/10.1111/mec.12754
Villalta, I., Amor, F., Galarza, J. A., Dupont, S., Ortega, P., Hefetz, A., Dahbi, A., Cerdá, X., & Boulay, R. (2018). Origin and distribution of desert ants across the Gibraltar Straits. Molecular Phylogenetics and Evolution, 118, 122-134. https://doi.org/10.1016/j.ympev.2017.09.026
Voous, K. H. (1977) List of recent Holarctic bird species. Ibis (Lond. 1859).

Auteurs

Eleanor F Miller (EF)

Department of Zoology, University of Cambridge, Cambridge, UK.

Rhys E Green (RE)

Department of Zoology, University of Cambridge, Cambridge, UK.

Andrew Balmford (A)

Department of Zoology, University of Cambridge, Cambridge, UK.

Pierpaolo Maisano Delser (P)

Department of Zoology, University of Cambridge, Cambridge, UK.

Robert Beyer (R)

Department of Zoology, University of Cambridge, Cambridge, UK.

Marius Somveille (M)

BirdLife International, Cambridge, UK.

Michela Leonardi (M)

Department of Zoology, University of Cambridge, Cambridge, UK.

William Amos (W)

Department of Zoology, University of Cambridge, Cambridge, UK.

Andrea Manica (A)

Department of Zoology, University of Cambridge, Cambridge, UK.

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