Functional connectivity in sympatric spiny rats reflects different dimensions of Amazonian forest‐association
dc.contributor.author | Dalapicolla, Jeronymo | |
dc.contributor.author | Prado, Joyce Rodrigues | |
dc.contributor.author | Percequillo, Alexandre Reis | |
dc.contributor.author | Knowles, L. Lacey | |
dc.date.accessioned | 2021-12-02T02:31:12Z | |
dc.date.available | 2023-01-01 21:31:10 | en |
dc.date.available | 2021-12-02T02:31:12Z | |
dc.date.issued | 2021-12 | |
dc.identifier.citation | Dalapicolla, Jeronymo; Prado, Joyce Rodrigues; Percequillo, Alexandre Reis; Knowles, L. Lacey (2021). "Functional connectivity in sympatric spiny rats reflects different dimensions of Amazonian forest‐association." Journal of Biogeography (12): 3196-3209. | |
dc.identifier.issn | 0305-0270 | |
dc.identifier.issn | 1365-2699 | |
dc.identifier.uri | https://hdl.handle.net/2027.42/171023 | |
dc.description.abstract | AimUnderstanding how the landscape influences gene flow is important in explaining biodiversity, especially when co‐distributed taxa across heterogeneous landscapes exhibit species‐specific habitat associations. Here, we test predictions about the effects of forest‐type on population connectivity in two sympatric species of spiny rats that differ in their forest associations. Specifically, we evaluate the hypothesis that seasonal floodplain forests (várzea) provide linear connectivity, facilitating gene flow among individuals, while non‐flooded forests (terra‐firme) may diminish the functional connectivity.LocationWestern Amazon, South America.TaxonProechimys simonsi (non‐flooded forests, terra‐firme) and Proechimys steerei (seasonal floodplain forests, várzea).MethodsWe analyse about 13,000 single nucleotide polymorphisms along with characterizations of landscape heterogeneity for two forest types to test for differences in the functional connectivity. Influence of the landscape and environmental variables are quantified using maximum‐likelihood population effect models to identify the relative importance of variables in explaining the gene flow.ResultsThere are significant differences in functional connectivity between species. However, the genomic data does not support the conventional hypotheses of higher connectivity for inhabitants of várzea than those of terra‐firme. Stronger genetic structure in P. steerei than P. simonsi based on isolation by distance models suggests reduced gene flow in species associated with várzea forests. Isolation by resistance reinforces that wetland habitats inhibit and promote the functional connectivity in P. simonsi and P. steerei, respectively, although large distances along the rivers can prevent gene flow in P. steerei.Main conclusionInterpreting differences between connectivity in taxa apparent from genetic analyses through the lens of a single dimension of Amazonian heterogeneity—that is, forest type—may be an oversimplification. Our statistical modelling and fit of the data to different models points to specific environmental and habitat differences between the ecological divergent spiny rat species that may contribute to differences in the genetic structure of these sympatric taxa. | |
dc.publisher | John Wiley & Sons | |
dc.subject.other | MLPE mixed models | |
dc.subject.other | phylogeography | |
dc.subject.other | RADseq | |
dc.subject.other | terra‐firme | |
dc.subject.other | várzea | |
dc.subject.other | landscape genetics | |
dc.subject.other | isolation by resistance | |
dc.title | Functional connectivity in sympatric spiny rats reflects different dimensions of Amazonian forest‐association | |
dc.type | Article | |
dc.rights.robots | IndexNoFollow | |
dc.subject.hlbsecondlevel | Geography and Maps | |
dc.subject.hlbtoplevel | Social Sciences | |
dc.description.peerreviewed | Peer Reviewed | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/171023/1/jbi14281_am.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/171023/2/jbi14281.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/171023/3/jbi14281-sup-0001-SupInfo.pdf | |
dc.identifier.doi | 10.1111/jbi.14281 | |
dc.identifier.source | Journal of Biogeography | |
dc.identifier.citedreference | Patton, J. L., & Leite, R. N. ( 2015 ). Genus Proechimys J. A. Allen, 1889. In J. L. Patton, U. F. J. Pardiñas, & G. D’Elía (Eds.), Mammals of South America, Vol. 2: Rodents (pp. 950 – 989 ). University of Chicago Press. | |
dc.identifier.citedreference | Pinheiro, J., Bates, D., DebRoy, S., & Sarkar, D. ( 2020 ). nlme: Linear and nonlinear mixed effects models. https://cran.r‐project.org/package=nlme | |
dc.identifier.citedreference | Pirani, R. M., Werneck, F. P., Thomaz, A. T., Kenney, M. L., Sturaro, M. J., Ávila‐Pires, T. C. S., Peloso, P. L. V., Rodrigues, M. T., & Knowles, L. L. ( 2019 ). Testing main Amazonian rivers as barriers across time and space within widespread taxa. Journal of Biogeography, 46 ( 11 ), 2444 – 2456. https://doi.org/10.1111/jbi.13676 | |
dc.identifier.citedreference | Pope, N. ( 2020 ). r2vcftools: An R interface for vcftools. R package version 0.0.0.9000. https://github.com/nspope/r2vcftools | |
dc.identifier.citedreference | Prado, J. R., Percequillo, A. R., Thomaz, A. T., & Knowles, L. L. ( 2019 ). Similar but different: Revealing the relative roles of species‐traits versus biome properties structuring genetic variation in South American marsh rats. Journal of Biogeography, 46 ( 4 ), 770 – 783. https://doi.org/10.1111/jbi.13529 | |
dc.identifier.citedreference | Puechmaille, S. J. ( 2016 ). The program structure does not reliably recover the correct population structure when sampling is uneven: Subsampling and new estimators alleviate the problem. Molecular Ecology Resources, 16 ( 3 ), 608 – 627. https://doi.org/10.1111/1755‐0998.12512 | |
dc.identifier.citedreference | R Core Team. ( 2020 ). R: A language and environment for statistical computing. R Foundation for Statistical Computing. https://www.r‐project.org/. | |
dc.identifier.citedreference | Ribas, C. C., Aleixo, A., Nogueira, A. C. R., Miyaki, C. Y., & Cracraft, J. ( 2012 ). A palaeobiogeographic model for biotic diversification within Amazonia over the past three million years. Proceedings of the Royal Society of London B: Biological Sciences, 279 ( 1729 ), 681 – 689. https://doi.org/10.1098/rspb.2011.1120 | |
dc.identifier.citedreference | Rutten, A., Cox, K., Scheppers, T., Broecke, V., Leirs, H., Casaer, J., & Leirs, H. ( 2019 ). Analysing the recolonisation of a highly fragmented landscape by wild boar using a landscape genetic approach. Wildlife Biology, 2019 ( 1 ), 1 – 11. https://doi.org/10.2981/wlb.00542 | |
dc.identifier.citedreference | Salo, J., Kalliola, R., Häkkinen, I., Mäkinen, Y., Niemelä, P., Puhakka, M., & Coley, P. D. ( 1986 ). River dynamics and the diversity of Amazon lowland forest. Nature, 322 ( 6076 ), 254 – 258. https://doi.org/10.1038/322254a0 | |
dc.identifier.citedreference | Shirk, A. J., Landguth, E. L., & Cushman, S. A. ( 2017 ). A comparison of individual‐based genetic distance metrics for landscape genetics. Molecular Ecology Resources, 17 ( 6 ), 1308 – 1317. https://doi.org/10.1111/1755‐0998.12684 | |
dc.identifier.citedreference | Shirk, A. J., Landguth, E. L., & Cushman, S. A. ( 2018 ). A comparison of regression methods for model selection in individual‐based landscape genetic analysis. Molecular Ecology Resources, 18 ( 1 ), 55 – 67. https://doi.org/10.1111/1755‐0998.12709 | |
dc.identifier.citedreference | Sikes, R. S. ( 2016 ). 2016 Guidelines of the American Society of Mammalogists for the use of wild mammals in research and education. Journal of Mammalogy, 97 ( 3 ), 663 – 688. https://doi.org/10.1093/jmammal/gyw078 | |
dc.identifier.citedreference | Silk, M. J., Harrison, X. A., & Hodgson, D. J. ( 2020 ). Perils and pitfalls of mixed‐effects regression models in biology. PeerJ, 8, e9522. https://doi.org/10.7717/peerj.9522 | |
dc.identifier.citedreference | Smith, B. T., McCormack, J. E., Cuervo, A. M., Hickerson, M. J., Aleixo, A., Cadena, C. D., Pérez‐Emán, J., Burney, C. W., Xie, X., Harvey, M. G., Faircloth, B. C., Glenn, T. C., Derryberry, E. P., Prejean, J., Fields, S., & Brumfield, R. T. ( 2014 ). The drivers of tropical speciation. Nature, 515 ( 7527 ), 406 – 409. https://doi.org/10.1038/nature13687 | |
dc.identifier.citedreference | Taylor, P. D., Fahrig, L., Henein, K., & Merriam, G. ( 1993 ). Connectivity is a vital element of landscape structure. Oikos, 68 ( 3 ), 571 – 573. https://doi.org/10.2307/3544927 | |
dc.identifier.citedreference | Thom, G., Xue, A. T., Sawakuchi, A. O., Ribas, C. C., Hickerson, M. J., Aleixo, A., & Miyaki, C. ( 2020 ). Quaternary climate changes as speciation drivers in the Amazon floodplains. Science Advances, 6 ( 11 ), eaax4718. https://doi.org/10.1126/sciadv.aax4718 | |
dc.identifier.citedreference | Tracy, C. A., & Widom, H. ( 1994 ). Level spacing distributions and the Bessel kernel. Communications in Mathematical Physics, 161 ( 2 ), 289 – 309. https://doi.org/10.1007/BF02099779 | |
dc.identifier.citedreference | van Soelen, E. E., Kim, J.‐H., Santos, R. V., Dantas, E. L., Vasconcelos de Almeida, F., Pires, J. P., Roddaz, M., & Sinninghe Damsté, J. S. ( 2017 ). A 30 Ma history of the Amazon River inferred from terrigenous sediments and organic matter on the Ceará Rise. Earth and Planetary Science Letters, 474, 40 – 48. https://doi.org/10.1016/J.EPSL.2017.06.025 | |
dc.identifier.citedreference | Vormisto, J., Tuomisto, H., & Oksanen, J. ( 2004 ). Palm distribution patterns in Amazonian rainforests: What is the role of topographic variation? Journal of Vegetation Science, 15 ( 4 ), 485 – 494. https://doi.org/10.1111/j.1654‐1103.2004.tb02287.x | |
dc.identifier.citedreference | Voss, R. S., & Emmons, L. H. ( 1996 ). Mammalian diversity in Neotropical lowland rainforests: A preliminary assessment. Bulletin of the American Museum of Natural History, 230, 1 – 115. | |
dc.identifier.citedreference | Voss, R. S., Lunde, D. P., & Simmons, N. B. ( 2001 ). The mammals of Paracou, French Guiana: A Neotropical lowland rainforest fauna part 2. Nonvolant species. Bulletin of the American Museum of Natural History, 263, 3 – 236. https://doi.org/10.1206/0003‐0090(2001)263<0003:TMOPFG>2.0.CO;2 | |
dc.identifier.citedreference | Wittmann, F., Schöngart, J., & Junk, W. J. ( 2010 ). Phytogeography, species diversity, community structure and dynamics of Central Amazonian floodplain forests. In W. J. Junk, M. T. F. Piedade, F. Wittmann, J. Schöngart, & P. Parolin (Eds.), Amazonian floodplain forests: Ecophysiology, biodiversity and sustainable management (pp. 61 – 102 ). Springer. | |
dc.identifier.citedreference | Woods, C. A., & Kilpatrick, C. W. ( 2005 ). Infraorder Hystricognathi Brandt, 1855. In D. E. Wilson, & D. M. Reeder (Eds.), Mammal species of the world. A taxonomic and geographic reference (Volume 2, pp. 1538 – 1600 ). Johns Hopkins University Press. | |
dc.identifier.citedreference | Wright, S. ( 1943 ). Isolation by distance. Genetics, 28 ( 2 ), 114 – 138. https://doi.org/10.1093/genetics/28.2.114 | |
dc.identifier.citedreference | Yang, J., Benyamin, B., McEvoy, B. P., Gordon, S., Henders, A. K., Nyholt, D. R., Madden, P. A., Heath, A. C., Martin, N. G., Montgomery, G. W., Goddard, M. E., & Visscher, P. M. ( 2010 ). Common SNPs explain a large proportion of the heritability for human height. Nature Genetics, 42 ( 7 ), 565 – 569. https://doi.org/10.1038/ng.608 | |
dc.identifier.citedreference | Albert, J. S., Val, P., Hoorn, C., Albert, J. S., Val, P., & Hoorn, C. ( 2018 ). The changing course of the Amazon River in the Neogene: Center stage for Neotropical diversification. Neotropical Ichthyology, 16 ( 3 ), e180033. https://doi.org/10.1590/1982‐0224‐20180033 | |
dc.identifier.citedreference | Aleixo, A. ( 2006 ). Historical diversification of floodplain forest specialist species in the Amazon: A case study with two species of the avian genus Xiphorhynchus (Aves: Dendrocolaptidae). Biological Journal of the Linnean Society, 89 ( 2 ), 383 – 395. https://doi.org/10.1111/j.1095‐8312.2006.00703.x | |
dc.identifier.citedreference | Balkenhol, N., Cushman, S., Storfer, A., & Waits, L. ( 2015 ). Landscape genetics: Concepts, methods, applications. John Wiley & Sons. | |
dc.identifier.citedreference | Barlow, J., Lennox, G. D., Ferreira, J., Berenguer, E., Lees, A. C., Nally, R. M., Thomson, J. R., Ferraz, S. F. D. B., Louzada, J., Oliveira, V. H. F., Parry, L., Ribeiro de Castro Solar, R., Vieira, I. C. G., Aragão, L. E. O. C., Begotti, R. A., Braga, R. F., Cardoso, T. M., de Oliveira, R. C., Souza Jr., C. M., … Gardner, T. A. ( 2016 ). Anthropogenic disturbance in tropical forests can double biodiversity loss from deforestation. Nature, 535 ( 7610 ), 144 – 147. https://doi.org/10.1038/nature18326 | |
dc.identifier.citedreference | Bredin, Y. K., Hawes, J. E., Peres, C. A., & Haugaasen, T. ( 2020 ). Structure and composition of terra firme and seasonally flooded várzea forests in the western Brazilian Amazon. Forests, 11 ( 12 ), 1 – 20. https://doi.org/10.3390/f11121361 | |
dc.identifier.citedreference | Cadena, C. D., Gutiérrez‐Pinto, N., Dávila, N., & Terry Chesser, R. ( 2011 ). No population genetic structure in a widespread aquatic songbird from the Neotropics. Molecular Phylogenetics and Evolution, 58 ( 3 ), 540 – 545. https://doi.org/10.1016/j.ympev.2010.12.014 | |
dc.identifier.citedreference | Carnaval, A. C., & Moritz, C. ( 2008 ). Historical climate modelling predicts patterns of current biodiversity in the Brazilian Atlantic forest. Journal of Biogeography, 35 ( 7 ), 1187 – 1201. https://doi.org/10.1111/j.1365‐2699.2007.01870.x | |
dc.identifier.citedreference | Carvalho, C. S., Lanes, É. C. M., Silva, A. R., Caldeira, C. F., Carvalho‐Filho, N., Gastauer, M., Imperatriz‐Fonseca, V. L., Nascimento Júnior, W., Oliveira, G., Siqueira, J. O., Viana, P. L., & Jaffé, R. ( 2019 ). Habitat loss does not always entail negative genetic consequences. Frontiers in Genetics, 10, 1101. https://doi.org/10.3389/fgene.2019.01101 | |
dc.identifier.citedreference | Castilla, A. R., Méndez‐Vigo, B., Marcer, A., Martínez‐Minaya, J., Conesa, D., Picó, F. X., & Alonso‐Blanco, C. ( 2020 ). Ecological, genetic and evolutionary drivers of regional genetic differentiation in Arabidopsis thaliana. BMC Evolutionary Biology, 20 ( 1 ), 1 – 13. https://doi.org/10.1186/s12862‐020‐01635‐2 | |
dc.identifier.citedreference | Cheng, H., Sinha, A., Cruz, F. W., Wang, X., Edwards, R. L., d’Horta, F. M., Ribas, C. C., Vuille, M., Stott, L. D., & Auler, A. S. ( 2013 ). Climate change patterns in Amazonia and biodiversity. Nature Communications, 4 ( 1 ), 1411. https://doi.org/10.1038/ncomms2415 | |
dc.identifier.citedreference | Clarke, R. T., Rothery, P., & Raybould, A. F. ( 2002 ). Confidence limits for regression relationships between distance matrices: Estimating gene flow with distance. Journal of Agricultural, Biological, and Environmental Statistics, 7 ( 3 ), 361 – 372. https://doi.org/10.1198/108571102320 | |
dc.identifier.citedreference | Colinvaux, P. A., De Oliveira, P. E., Moreno, J. E., Miller, M. C., & Bush, M. B. ( 1996 ). A long pollen record from lowland Amazonia: Forest and cooling in glacial times. Science, 274 ( 5284 ), 85 – 88. https://doi.org/10.1126/science.274.5284.85 | |
dc.identifier.citedreference | Constantine, J. A., Dunne, T., Ahmed, J., Legleiter, C., & Lazarus, E. D. ( 2014 ). Sediment supply as a driver of river meandering and floodplain evolution in the Amazon Basin. Nature Geoscience, 7 ( 12 ), 899 – 903. https://doi.org/10.1038/ngeo2282 | |
dc.identifier.citedreference | Da Silva, M. N., & Patton, J. L. ( 1998 ). Molecular phylogeography and the evolution and conservation of amazonian mammals. Molecular Ecology, 7, 475 – 486. https://doi.org/10.1046/j.1365‐294x.1998.00276.x | |
dc.identifier.citedreference | Dalapicolla, J., Alves, R., Jaffé, R., Vasconcelos, S., Pires, E. S., Nunes, G. L., Pereira, J. B. D. S., Guimarães, J. T. F., Dias, M. C., Fernandes, T. N., Scherer, D., Santos, F. M. G., Castilho, A., Santos, M. P., Calderón, E. N., Martins, R. L., Fonseca, R. N., Esteves, F. D. A., Caldeira, C. F., & Oliveira, G. ( 2021 ). Conservation implications of genetic structure in the narrowest endemic quillwort from the Eastern Amazon. Ecology and Evolution, 11 ( 15 ), 10119 – 10132. https://doi.org/10.1002/ECE3.7812 | |
dc.identifier.citedreference | Dormann, C. F., Elith, J., Bacher, S., Buchmann, C., Carl, G., Carré, G., Marquéz, J. R. G., Gruber, B., Lafourcade, B., Leitão, P. J., Münkemüller, T., McClean, C., Osborne, P. E., Reineking, B., Schröder, B., Skidmore, A. K., Zurell, D., & Lautenbach, S. ( 2013 ). Collinearity: A review of methods to deal with it and a simulation study evaluating their performance. Ecography, 36 ( 1 ), 27 – 46. https://doi.org/10.1111/j.1600‐0587.2012.07348.x | |
dc.identifier.citedreference | Dray, S., & Dufour, A. B. ( 2007 ). The ade4 package: Implementing the duality diagram for ecologists. Journal of Statistical Software, 22 ( 4 ), 1 – 20. https://doi.org/10.18637/jss.v022.i04 | |
dc.identifier.citedreference | Emmons, L. H. ( 1982 ). Ecology of Proechimys (Rodentia, Echimyidae) in southeastern Peru. Tropical Ecology, 23 ( 2 ), 280 – 290. | |
dc.identifier.citedreference | Excoffier, L., Foll, M., & Petit, R. J. ( 2009 ). Genetic consequences of range expansions. Annual Review of Ecology, Evolution, and Systematics, 40 ( 1 ), 481 – 501. https://doi.org/10.1146/annurev.ecolsys.39.110707.173414 | |
dc.identifier.citedreference | Fabre, P. H., Patton, J. L., & Leite, Y. L. R. ( 2016 ). Family Echimyidae (hutias, South American spiny‐rats and coypu). In D. E. Wilson, T. E. J. Lacher, & R. A. Mittermeier (Eds.), Handbook of the mammals of the world. Vol 6. Lagomorphs and rodents I (pp. 552 – 641 ). Lynx Edicions. | |
dc.identifier.citedreference | Fenderson, L. E., Kovach, A. I., & Llamas, B. ( 2020 ). Spatiotemporal landscape genetics: Investigating ecology and evolution through space and time. Molecular Ecology, 29 ( 2 ), 218 – 246. https://doi.org/10.1111/mec.15315 | |
dc.identifier.citedreference | Fernandes, A. M., Gonzalez, J., Wink, M., & Aleixo, A. ( 2013 ). Multilocus phylogeography of the Wedge‐billed Woodcreeper Glyphorynchus spirurus (Aves, Furnariidae) in lowland Amazonia: Widespread cryptic diversity and paraphyly reveal a complex diversification pattern. Molecular Phylogenetics and Evolution, 66 ( 1 ), 270 – 282. https://doi.org/10.1016/j.ympev.2012.09.033 | |
dc.identifier.citedreference | Frichot, E., & Francois, O. ( 2014 ). LEA: An R package for landscape and ecological association studies. http://membres‐timc.imag.fr/Olivier.Francois/lea.html | |
dc.identifier.citedreference | Frichot, E., Mathieu, F., Trouillon, T., Bouchard, G., & François, O. ( 2014 ). Fast and efficient estimation of individual ancestry coefficients. Genetics, 196 ( 4 ), 973 – 983. https://doi.org/10.1534/genetics.113.160572 | |
dc.identifier.citedreference | Gascon, C., Malcolm, J. R., Patton, J. L., da Silva, M. N. F., Bogart, J. P., Lougheed, S. C., Peres, C. A., Neckel, S., & Boag, P. T. ( 2000 ). Riverine barriers and the geographic distribution of Amazonian species. Proceedings of the National Academy of Sciences of the United States of America, 97 ( 25 ), 13672 – 13677. https://doi.org/10.1073/pnas.230136397 | |
dc.identifier.citedreference | Godoy, J. R., Petts, G., & Salo, J. ( 1999 ). Riparian flooded forests of the Orinoco and Amazon basins: A comparative review. Biodiversity and Conservation, 8 ( 4 ), 551 – 586. https://doi.org/10.1023/A:1008846531941 | |
dc.identifier.citedreference | Goslee, S. C., & Urban, D. L. ( 2007 ). The ecodist package for dissimilarity‐based analysis of ecological data. Journal of Statistical Software, 22 ( 7 ), 1 – 19. https://doi.org/10.18637/jss.v022.i07 | |
dc.identifier.citedreference | Gruber, B., & Georges, A. ( 2019 ). dartR: Importing and analysing SNP and silicodart data generated by genome‐wide restriction fragment analysis. https://cran.r‐project.org/package=dartR | |
dc.identifier.citedreference | Gumbricht, T., Roman‐Cuesta, R. M., Verchot, L., Herold, M., Wittmann, F., Householder, E., Herold, N., & Murdiyarso, D. ( 2017 ). An expert system model for mapping tropical wetlands and peatlands reveals South America as the largest contributor. Global Change Biology, 23 ( 9 ), 3581 – 3599. https://doi.org/10.1111/gcb.13689 | |
dc.identifier.citedreference | Häggi, C., Chiessi, C. M., Merkel, U., Mulitza, S., Prange, M., Schulz, M., & Schefuß, E. ( 2017 ). Response of the Amazon rainforest to late Pleistocene climate variability. Earth and Planetary Science Letters, 479, 50 – 59. https://doi.org/10.1016/J.EPSL.2017.09.013 | |
dc.identifier.citedreference | Harrison, X. A., Donaldson, L., Correa‐Cano, M. E., Evans, J., Fisher, D. N., Goodwin, C. E. D., Robinson, B. S., Hodgson, D. J., & Inger, R. ( 2018 ). A brief introduction to mixed effects modelling and multi‐model inference in ecology. PeerJ, 2018 ( 5 ), e4794. https://doi.org/10.7717/peerj.4794 | |
dc.identifier.citedreference | Harvey, M. G., Aleixo, A., Ribas, C. C., & Brumfield, R. T. ( 2017 ). Habitat association predicts genetic diversity and population divergence in Amazonian birds. American Naturalist, 190 ( 5 ), 631 – 648. https://doi.org/10.1086/693856 | |
dc.identifier.citedreference | Hawkins, B. A., Porter, E. E., & Diniz‐Filho, J. A. F. ( 2003 ). Productivity and history as predictors of the latitudinal diversity gradient of terrestrial birds. Ecology, 84 ( 6 ), 1608 – 1623. https://doi.org/10.1890/0012‐9658(2003)084[1608:PAHAPO]2.0.CO;2 | |
dc.identifier.citedreference | He, Q., Edwards, D. L., & Knowles, L. L. ( 2013 ). Integrative testing of how environments from the past to the present shape genetic structure across landscapes. Evolution, 67 ( 12 ), 3386 – 3402. https://doi.org/10.1111/evo.12159 | |
dc.identifier.citedreference | Hess, L. L., Melack, J. M., Affonso, A. G., Barbosa, C., Gastil‐Buhl, M., & Novo, E. M. L. M. ( 2015 ). Wetlands of the Lowland Amazon Basin: Extent, vegetative cover, and dual‐season inundated area as mapped with JERS‐1 synthetic aperture radar. Wetlands, 35 ( 4 ), 745 – 756. https://doi.org/10.1007/s13157‐015‐0666‐y | |
dc.identifier.citedreference | Hijmans, R., & van Etten, J. ( 2015 ). raster: Geographic data analysis and modeling. In R package version 3.4‐10. https://CRAN.R‐project.org/package=raster | |
dc.identifier.citedreference | Hoban, S., Bruford, M., D’Urban Jackson, J., Lopes‐Fernandes, M., Heuertz, M., Hohenlohe, P. A., Paz‐Vinas, I., Sjögren‐Gulve, P., Segelbacher, G., Vernesi, C., Aitken, S., Bertola, L. D., Bloomer, P., Breed, M., Rodríguez‐Correa, H., Funk, W. C., Grueber, C. E., Hunter, M. E., Jaffe, R., … Laikre, L. ( 2020 ). Genetic diversity targets and indicators in the CBD post‐2020 Global Biodiversity Framework must be improved. Biological Conservation, 248, 108654. https://doi.org/10.1016/j.biocon.2020.108654 | |
dc.identifier.citedreference | Hoorn, C., Wesselingh, F. P., ter Steege, H., Bermudez, M. A., Mora, A., Sevink, J., Sanmartín, I., Sanchez‐Meseguer, A., Anderson, C. L., Figueiredo, J. P., Jaramillo, C., Riff, D., Negri, F. R., Hooghiemstra, H., Lundberg, J., Stadler, T., Särkinen, T., & Antonelli, A. ( 2010 ). Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science, 330 ( 6006 ), 927 – 931. https://doi.org/10.1126/science.1194585 | |
dc.identifier.citedreference | Jaeger, B. C. ( 2017 ). r2glmm: Computes R squared for mixed (multilevel) models. https://cran.r‐project.org/package=r2glmm | |
dc.identifier.citedreference | Jaeger, B. C., Edwards, L. J., Das, K., & Sen, P. K. ( 2017 ). An R 2 statistic for fixed effects in the generalized linear mixed model. Journal of Applied Statistics, 44 ( 6 ), 1086 – 1105. https://doi.org/10.1080/02664763.2016.1193725 | |
dc.identifier.citedreference | Jaffé, R., Veiga, J. C., Pope, N. S., Lanes, É. C. M., Carvalho, C. S., Alves, R., Andrade, S. C. S., Arias, M. C., Bonatti, V., Carvalho, A. T., Castro, M. S., Contrera, F. A. L., Francoy, T. M., Freitas, B. M., Giannini, T. C., Hrncir, M., Martins, C. F., Oliveira, G., Saraiva, A. M., … Imperatriz‐Fonseca, V. L. ( 2019 ). Landscape genomics to the rescue of a tropical bee threatened by habitat loss and climate change. Evolutionary Applications, 12 ( 6 ), 1164 – 1177. https://doi.org/10.1111/eva.12794 | |
dc.identifier.citedreference | Jombart, T., & Ahmed, I. ( 2011 ). adegenet 1.3‐1: New tools for the analysis of genome‐wide SNP data. Bioinformatics, 27 ( 21 ), 3070 – 3071. https://doi.org/10.1093/bioinformatics/btr521 | |
dc.identifier.citedreference | Jombart, T., Devillard, S., & Balloux, F. ( 2010 ). Discriminant analysis of principal components: A new method for the analysis of genetically structured populations. BMC Genetics, 11 ( 1 ), 1 – 15. https://doi.org/10.1186/1471‐2156‐11‐94 | |
dc.identifier.citedreference | Junk, W. J., & Piedade, M. T. ( 1993 ). Herbaceous plants of the Amazon floodplain near Manaus: Species diversity and adaptations to the flood pulse. Amazoniana: Limnologia et Oecologia Regionalis Systematis Fluminis Amazonas, 12 ( 3/4 ), 467 – 484. http://hdl.handle.net/21.11116/0000‐0004‐896E‐7 | |
dc.identifier.citedreference | Knowles, L. L., Massatti, R., He, Q., Olson, L. E., & Lanier, H. C. ( 2016 ). Quantifying the similarity between genes and geography across Alaska’s alpine small mammals. Journal of Biogeography, 43 ( 7 ), 1464 – 1476. https://doi.org/10.1111/jbi.12728 | |
dc.identifier.citedreference | Lanier, H. C., Massatti, R., He, Q., Olson, L. E., & Knowles, L. L. ( 2015 ). Colonization from divergent ancestors: Glaciation signatures on contemporary patterns of genomic variation in Collared Pikas ( Ochotona collaris ). Molecular Ecology, 24 ( 14 ), 3688 – 3705. https://doi.org/10.1111/mec.13270 | |
dc.identifier.citedreference | Lara, M., & Patton, J. L. ( 2000 ). Evolutionary diversification of spiny rats (genus Trinomys, Rodentia: Echimyidae) in the Atlantic Forest of Brazil. Zoological Journal of the Linnean Society, 130 ( 4 ), 661 – 686. https://doi.org/10.1006/zjls.2000.0240 | |
dc.identifier.citedreference | Leite, R. N., & Rogers, D. S. ( 2013 ). Revisiting Amazonian phylogeography: Insights into diversification hypotheses and novel perspectives. Organisms Diversity & Evolution, 13 ( 4 ), 639 – 664. https://doi.org/10.1007/s13127‐013‐0140‐8 | |
dc.identifier.citedreference | Leite, Y. L. R. ( 2003 ). Evolution and systematics of the Atlantic Tree Rats, genus Phyllomys (Rodentia: Echimyidae) with description of two new species. In J. A. Rodriguez‐Robles, D. A. Good, & D. B. Wake (Eds.), University of California publications in zoology (Vol. 132, pp. 1 – 118 ). University of California Press. | |
dc.identifier.citedreference | Lessa, E. P., Cook, J. A., & Patton, J. L. ( 2003 ). Genetic footprints of demographic expansion in North America, but not Amazonia, during the Late Quaternary. Proceedings of the National Academy of Sciences of the United States of America, 100 ( 18 ), 10331 – 10334. https://doi.org/10.1073/pnas.1730921100 | |
dc.identifier.citedreference | Li, H., Qu, W., Obrycki, J. J., Meng, L., Zhou, X., Chu, D., & Li, B. ( 2020 ). Optimizing sample size for population genomic study in a global invasive lady beetle, Harmonia axyridis. Insects, 11 ( 5 ), 290. https://doi.org/10.3390/insects11050290 | |
dc.identifier.citedreference | Li, W., Zhang, P., Ye, J., Li, L., & Baker, P. A. ( 2011 ). Impact of two different types of El Niño events on the Amazon climate and ecosystem productivity. Journal of Plant Ecology, 4 ( 1–2 ), 91 – 99. https://doi.org/10.1093/jpe/rtq039 | |
dc.identifier.citedreference | Manel, S., & Holderegger, R. ( 2013 ). Ten years of landscape genetics. Trends in Ecology and Evolution, 28 ( 10 ), 614 – 621. https://doi.org/10.1016/j.tree.2013.05.012 | |
dc.identifier.citedreference | Manel, S., Schwartz, M. K., Luikart, G., & Taberlet, P. ( 2003 ). Landscape genetics: Combining landscape ecology and population genetics. Trends in Ecology and Evolution, 18 ( 4 ), 189 – 197. https://doi.org/10.1016/S0169‐5347(03)00008‐9 | |
dc.identifier.citedreference | Mantel, N. ( 1967 ). The detection of disease clustering and a generalized regression approach. Cancer Research, 27 ( 2 ), 209 – 220. http://www.ncbi.nlm.nih.gov/pubmed/6018555 | |
dc.identifier.citedreference | Massatti, R., & Knowles, L. L. ( 2014 ). Microhabitat differences impact phylogeographic concordance of codistributed species: Genomic evidence in montane sedges ( Carex L.) from the Rocky Mountains. Evolution, 68 ( 10 ), 2833 – 2846. https://doi.org/10.1111/evo.12491 | |
dc.identifier.citedreference | Massatti, R., & Knowles, L. L. ( 2016 ). Contrasting support for alternative models of genomic variation based on microhabitat preference: Species‐specific effects of climate change in alpine sedges. Molecular Ecology, 25 ( 16 ), 3974 – 3986. https://doi.org/10.1111/mec.13735 | |
dc.identifier.citedreference | Matocq, M. D., Patton, J. L., & Da Silva, M. N. F. ( 2000 ). Population genetic structure of two ecologically distinct amazonian spiny rats: Separating history and current ecology. Evolution, 54 ( 4 ), 1423 – 1432. https://doi.org/10.1111/j.0014‐3820.2000.tb00574.x | |
dc.identifier.citedreference | McLaughlin, J. F., & Winker, K. ( 2020 ). An empirical examination of sample size effects on population demographic estimates in birds using single nucleotide polymorphism (SNP) data. PeerJ, 8, e9939. https://doi.org/10.7717/peerj.9939 | |
dc.identifier.citedreference | McRae, B. H. ( 2006 ). Isolation by resistance. Evolution, 60 ( 8 ), 1551 – 1561. https://doi.org/10.1111/j.0014‐3820.2006.tb00500.x | |
dc.identifier.citedreference | McRae, B. H., & Beier, P. ( 2007 ). Circuit theory predicts gene flow in plant and animal populations. Proceedings of the National Academy of Sciences of the United States of America, 104 ( 50 ), 19885 – 19890. https://doi.org/10.1073/pnas.0706568104 | |
dc.identifier.citedreference | Miller, J. M., Cullingham, C. I., & Peery, R. M. ( 2020 ). The influence of a priori grouping on inference of genetic clusters: Simulation study and literature review of the DAPC method. Heredity, 125 ( 5 ), 269 – 280. https://doi.org/10.1038/s41437‐020‐0348‐2 | |
dc.identifier.citedreference | Murphy, M. O., Jones, K. S., Price, S. J., & Weisrock, D. W. ( 2018 ). A genomic assessment of population structure and gene flow in an aquatic salamander identifies the roles of spatial scale, barriers, and river architecture. Freshwater Biology, 63 ( 5 ), 407 – 419. https://doi.org/10.1111/fwb.13071 | |
dc.identifier.citedreference | Nakagawa, S., & Schielzeth, H. ( 2013 ). A general and simple method for obtaining R 2 from generalized linear mixed‐effects models. Methods in Ecology and Evolution, 4 ( 2 ), 133 – 142. https://doi.org/10.1111/j.2041‐210x.2012.00261.x | |
dc.identifier.citedreference | Nazareno, A. G., Bemmels, J. B., Dick, C. W., & Lohmann, L. G. ( 2017 ). Minimum sample sizes for population genomics: An empirical study from an Amazonian plant species. Molecular Ecology Resources, 17 ( 6 ), 1136 – 1147. https://doi.org/10.1111/1755‐0998.12654 | |
dc.identifier.citedreference | Oksanen, J., Blanchet, F. G., Friendly, M., Kindt, R., Legendre, P., O’Hara, R. B., Simpson, G. L., Solymos, P., Stevens, M. H. H., Szoecs, E., & Wagner, H. ( 2019 ). vegan: Community ecology package. http://cran.r‐project.org/package=vegan | |
dc.identifier.citedreference | Papadopoulou, A., & Knowles, L. L. ( 2016 ). Toward a paradigm shift in comparative phylogeography driven by trait‐based hypotheses. Proceedings of the National Academy of Sciences of the United States of America, 113 ( 29 ), 8018 – 8024. https://doi.org/10.1073/pnas.1601069113 | |
dc.identifier.citedreference | Patterson, N., Price, A. L., & Reich, D. ( 2006 ). Population structure and eigenanalysis. PLoS Genetics, 2 ( 12 ), 2074 – 2093. https://doi.org/10.1371/journal.pgen.0020190 | |
dc.identifier.citedreference | Patton, J. L., Da Silva, M. N., & Malcolm, J. R. ( 2000 ). Mammals of the Rio Juruá and the evolutionary and ecological diversification of Amazonia. Bulletin American Museum of Natural History, 244, 1 – 306. https://doi.org/10.1206/0003‐0090(2000)244%3C0001:MOTRJA%3E2.0.CO;2 | |
dc.identifier.citedreference | Patton, J. L., Pardiñas, U. F. J., & D’Elía, G. ( 2015 ). Mammals of South America, Vol. 2. Rodents. The University of Chicago Press. | |
dc.identifier.citedreference | Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., & Hoekstra, H. E. ( 2012 ). Double digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non‐model species. PLoS One, 7 ( 5 ), e37135. https://doi.org/10.1371/journal.pone.0037135 | |
dc.working.doi | NO | en |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
Files in this item
Remediation of Harmful Language
The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.
Accessibility
If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.