Abstract
Landscape genetics is an interdisciplinary field that aims at assessing the influence of environmental and landscape factors on microevolutionary processes, especially gene flow and natural selection. It provides a powerful toolbox that can be applied to understand processes and patterns of biodiversity and establish informed conservation strategies in a spatial context. The Neotropics, home to extraordinary biodiversity, suffer from alarming rates of anthropogenic transformation and, hence, benefit from the landscape genetics framework. Here, we revisit fundamental concepts and provide an overview of common analytical methods. We then present a scientometric analysis of landscape genetic studies in the Neotropics and describe potential applications. Overall, there is ample opportunity for growth in neotropical studies. Based on our search criteria we compiled a total of 65 studies, with an increasing trend in publication over time. Brazil and Mexico are the main contributors to the literature, whereas most of the American tropical countries have not conducted landscape genetic studies. The studies tend to be population-based and focus on landscape features that influence genetic diversity and connectivity. Very few apply genomic tools to investigate local adaptation. Lastly, we discuss some of the challenges and opportunities for future (neo)tropical research.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Antonelli A (2021) The rise and fall of Neotropical biodiversity. Bot J Linn Soc 199:boab061. https://doi.org/10.1093/botlinnean/boab061
Antonelli A, Ariza M, Albert J et al (2018) Conceptual and empirical advances in Neotropical biodiversity research. PeerJ 6:e5644. https://doi.org/10.7717/peerj.5644
Balkenhol N, Fortin M (2015) Basics of study design: sampling landscape heterogeneity and genetic variation for landscape genetic studies. In: Landscape genetics: concepts, methods, applications. John Wiley & Sons, Ltd, West Sussex, pp 58–76
Balkenhol N, Cushman S, Storfer A, Waits L (2015) Landscape genetics: concepts, methods, applications. John Wiley & Sons, Ltd, West Sussex
Blair ME, Melnick DJ (2012) Scale-dependent effects of a heterogeneous landscape on genetic differentiation in the central American squirrel monkey (Saimiri oerstedii). PLoS One 7:e43027. https://doi.org/10.1371/journal.pone.0043027
Carvalho CS, Ribeiro MC, Cortes MC et al (2015) Contemporary and historic factors influence differently genetic differentiation and diversity in a tropical palm. Heredity (Edinb) 115:216–224. https://doi.org/10.1038/hdy.2015.30
Carvalho CS, Galetti M, Colevatti RG, Jordano P (2016) Defaunation leads to microevolutionary changes in a tropical palm. Sci Rep 6:31957. https://doi.org/10.1038/srep31957
Carvalho CS, Lanes ÉCM, Silva AR et al (2019) Habitat loss does not always entail negative genetic consequences. Front Genet 10:1101. https://doi.org/10.3389/fgene.2019.01101
Carvalho CS, Forester BR, Mitre SK et al (2021a) Combining genotype, phenotype, and environmental data to delineate site-adjusted provenance strategies for ecological restoration. Mol Ecol Resour 21:44–58. https://doi.org/10.1111/1755-0998.13191
Carvalho CS, García C, Lucas MS et al (2021b) Extant fruit-eating birds promote genetically diverse seed rain, but disperse to fewer sites in defaunated tropical forests. J Ecol 109:1055–1067. https://doi.org/10.1111/1365-2745.13534
Castilla AR, Pope NS, O’Connell M et al (2017) Adding landscape genetics and individual traits to the ecosystem function paradigm reveals the importance of species functional breadth. Proc Natl Acad Sci 114:201619271. https://doi.org/10.1073/pnas.1619271114
Catchen JM, Hohenlohe PA, Bernatchez L et al (2017) Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations. Mol Ecol Resour 17:362–365. https://doi.org/10.1111/1755-0998.12669
Ciocca DR, Delgado G (2017) The reality of scientific research in Latin America; an insider’s perspective. Cell Stress Chaperones 22:847–852. https://doi.org/10.1007/s12192-017-0815-8
Cleary KA, Waits LP, Finegan B (2017) Comparative landscape genetics of two frugivorous bats in a biological corridor undergoing agricultural intensification. Mol Ecol 26:4603–4617. https://doi.org/10.1111/mec.14230
Collevatti RG, dos Santos JS, Rosa FF et al (2020) Multi-scale landscape influences on genetic diversity and adaptive traits in a neotropical savanna tree. Front Genet 11:259. https://doi.org/10.3389/fgene.2020.00259
Curtis PG, Slay CM, Harris NL et al (2018) Classifying drivers of global forest loss. Science 361(6407):1108–1111. https://doi.org/10.1126/science.aau3445
Cushman SA, Landguth EL (2010) Scale dependent inference in landscape genetics. Landsc Ecol 25:967–979. https://doi.org/10.1007/s10980-010-9467-0
Cushman SA, McRae BH, McGarigal K (2015) Basics of landscape ecology: an introduction to landscapes and population processes for landscape geneticists. In: Landscape genetics: concepts, methods, applications. John Wiley & Sons, Ltd, Chichester, pp 9–34
Dahdouh-Guebas F, Ahimbisibwe J, Van Moll R, Koedam N (2003) Neo-colonial science by the most industrialised upon the least developed countries in peer-reviewed publishing. Scientometrics 56:329–343. https://doi.org/10.1023/A:1022374703178
Dixo M, Metzger JP, Morgante JS, Zamudio KR (2009) Habitat fragmentation reduces genetic diversity and connectivity among toad populations in the Brazilian Atlantic Coastal Forest. Biol Conserv 142:1560–1569. https://doi.org/10.1016/j.biocon.2008.11.016
do Amaral TS, dos Santos JS, Rosa FF et al (2021) Agricultural landscape heterogeneity matter: responses of neutral genetic diversity and adaptive traits in a neotropical savanna tree. Front Genet 11:606222. https://doi.org/10.3389/fgene.2020.606222
Fahrig L (2003) Effects of habitat fragmentation on biodiversity. Annu Rev Ecol Evol Syst 34:487–515. https://doi.org/10.1146/annurev.ecolsys.34.011802.132419
Forester BR, Lasky JR, Wagner HH, Urban DL (2018) Comparing methods for detecting multilocus adaptation with multivariate genotype-environment associations. Mol Ecol 27:2215–2233. https://doi.org/10.1111/mec.14584
François O, Martins H, Caye K, Schoville SD (2016) Controlling false discoveries in genome scans for selection. Mol Ecol 25:454–469. https://doi.org/10.1111/mec.13513
Fusco NA, Carlen EJ, Munshi-South J (2021) Urban landscape genetics: are biologists keeping up with the pace of urbanization? Curr Landsc Ecol Rep 6:35–45. https://doi.org/10.1007/s40823-021-00062-3
Gallego-García N, Forero-Medina G, Vargas-Ramírez M et al (2019) Landscape genomic signatures indicate reduced gene flow and forest-associated adaptive divergence in an endangered neotropical turtle. Mol Ecol 28:2757–2771. https://doi.org/10.1111/mec.15112
García-Rodríguez A, Guarnizo CE, Crawford AJ et al (2021) Idiosyncratic responses to drivers of genetic differentiation in the complex landscapes of Isthmian Central America. Heredity (Edinb) 126:251–265. https://doi.org/10.1038/s41437-020-00376-8
Grimm NB, Faeth SH, Golubiewski NE et al (2008) Global change and the ecology of cities. Science 319:756–760. https://doi.org/10.1126/science.1150195
Hall LA, Beissinger SR (2014) A practical toolbox for design and analysis of landscape genetics studies. Landsc Ecol 29:1487–1504. https://doi.org/10.1007/s10980-014-0082-3
Hand BK, Lowe WH, Kovach RP et al (2015) Landscape community genomics: understanding eco-evolutionary processes in complex environments. Trends Ecol Evol 30:161–168. https://doi.org/10.1016/j.tree.2015.01.005
Hansen MC, Potapov PV, Moore R et al (2013) High-resolution global maps of 21st-century forest cover change. Science 342:850–853. https://doi.org/10.1126/science.1244693
Hansen A, Barnett K, Jantz P et al (2019) Global humid tropics forest structural condition and forest structural integrity maps. Sci Data 6:232. https://doi.org/10.1038/s41597-019-0214-3
Holderegger R, Wagner HH (2006) A brief guide to landscape genetics. Landsc Ecol 21:793–796. https://doi.org/10.1007/s10980-005-6058-6
Jaffé R, Pope N, Acosta AL et al (2016) Beekeeping practices and geographic distance, not land use, drive gene flow across tropical bees. Mol Ecol 25:5345–5358. https://doi.org/10.1111/mec.13852
Joost S, Bonin A, Bruford MW et al (2007) A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation. Mol Ecol 16:3955–3969. https://doi.org/10.1111/j.1365-294X.2007.03442.x
Khelifa R, Amano T, Nuñez MA (2022) A solution for breaking the language barrier. Trends Ecol Evol 37:109–112. https://doi.org/10.1016/j.tree.2021.11.003
Khimoun A, Peterman W, Eraud C et al (2017) Landscape genetic analyses reveal fine-scale effects of forest fragmentation in an insular tropical bird. Mol Ecol 26:4906–4919. https://doi.org/10.1111/mec.14233
Landguth EL, Cushman SA, Schwartz MK et al (2010) Quantifying the lag time to detect barriers in landscape genetics. Mol Ecol 19:4179–4191. https://doi.org/10.1111/j.1365-294X.2010.04808.x
Lanes ÉC, Pope NS, Alves R et al (2018) Landscape genomic conservation assessment of a narrow-endemic and a widespread morning glory from amazonian savannas. Front Plant Sci 9:532. https://doi.org/10.3389/fpls.2018.00532
Latorre-Cardenas MC, Gutiérrez-Rodríguez C, Rico Y, Martínez-Meyer E (2021) Do landscape and riverscape shape genetic patterns of the Neotropical otter, Lontra longicaudis, in eastern Mexico? Landsc Ecol 36:69–87. https://doi.org/10.1007/s10980-020-01114-5
Lowry DB, Hoban S, Kelley JL et al (2017) Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation. Mol Ecol Resour 17:142–152. https://doi.org/10.1111/1755-0998.12635
Luikart G, England PR, Tallmon D et al (2003) The power and promise of population genomics: from genotyping to genome typing. Nat Rev Genet 4:981–994. https://doi.org/10.1038/nrg1226
Maas B, Pakeman RJ, Godet L et al (2021) Women and global south strikingly underrepresented among top-publishing ecologists. Conserv Lett 14:e12797. https://doi.org/10.1111/conl.12797
Manel S, Schwartz MK, Luikart G, Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. Trends Ecol Evol 18:189–197. https://doi.org/10.1016/S0169-5347(03)00008-9
Manel S, Joost S, Epperson BK et al (2010) Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field. Mol Ecol 19:3760–3772. https://doi.org/10.1111/j.1365-294X.2010.04717.x
Martin LJ, Blossey B, Ellis E (2012) Mapping where ecologists work: biases in the global distribution of terrestrial ecological observations. Front Ecol Environ 10:195–201. https://doi.org/10.1890/110154
Mastretta-Yanes A, Xue AT, Moreno-Letelier A et al (2018) Long-term in situ persistence of biodiversity in tropical sky islands revealed by landscape genomics. Mol Ecol 27:432–448. https://doi.org/10.1111/mec.14461
McRae BH (2006) Isolation by resistance. Evolution 60:1551. https://doi.org/10.1554/05-321.1
Medina R, Wogan GOU, Bi K et al (2021) Phenotypic and genomic diversification with isolation by environment along elevational gradients in a neotropical treefrog. Mol Ecol 30:4062–4076. https://doi.org/10.1111/mec.16035
Metzger JP (2001) O que é ecologia de paisagens. Biota Neotrop 1:1–9. https://doi.org/10.1093/hmg/ddn246
Monteiro WP, Veiga JC, Silva AR et al (2019) Everything you always wanted to know about gene flow in tropical landscapes (but were afraid to ask). PeerJ 7:e6446. https://doi.org/10.7717/peerj.6446
Moraes AM, Ruiz-Miranda CR, Galetti PM et al (2018) Landscape resistance influences effective dispersal of endangered golden lion tamarins within the Atlantic Forest. Biol Conserv 224:178–187. https://doi.org/10.1016/j.biocon.2018.05.023
Morin PA, Luikart G, Wayne RK (2004) SNPs in ecology, evolution and conservation. Trends Ecol Evol 19:208–216. https://doi.org/10.1016/j.tree.2004.01.009
Murphy MA, Dezzani R, Pilliod DS, Storfer A (2010) Landscape genetics of high mountain frog metapopulations. Mol Ecol 19:3634–3649. https://doi.org/10.1111/j.1365-294X.2010.04723.x
Murphy M, Dyer R, Cushman SA (2015) Graph theory and network models in landscape genetics. In: Landscape genetics: concepts, methods, applications. John Wiley & Sons, Ltd, Chichester, pp 165–180
Nuñez MA, Chiuffo MC, Pauchard A, Zenni RD (2021) Making ecology really global. Trends Ecol Evol 36:766–769. https://doi.org/10.1016/j.tree.2021.06.004
Otero-Jiménez B, Li K, Tucker PK (2020) Landscape drivers of connectivity for a forest rodent in a coffee agroecosystem. Landsc Ecol 35:1249–1261. https://doi.org/10.1007/s10980-020-00999-6
Peterman WE (2018) ResistanceGA: an R package for the optimization of resistance surfaces using genetic algorithms. Methods Ecol Evol 9:1638–1647. https://doi.org/10.1111/2041-210X.12984
Peterman WE, Connette GM, Semlitsch RD, Eggert LS (2014) Ecological resistance surfaces predict fine-scale genetic differentiation in a terrestrial woodland salamander. Mol Ecol 23:2402–2413. https://doi.org/10.1111/mec.12747
Peterman WE, Winiarski KJ, Moore CE et al (2019) A comparison of popular approaches to optimize landscape resistance surfaces. Landsc Ecol 34:2197–2208. https://doi.org/10.1007/s10980-019-00870-3
Pillay R, Venter M, Aragon-Osejo J et al (2022) Tropical forests are home to over half of the world’s vertebrate species. Front Ecol Environ 20:10–15. https://doi.org/10.1002/fee.2420
Raven PH, Gereau RE, Phillipson PB et al (2020) The distribution of biodiversity richness in the tropics. Sci Adv 6:eabc6228. https://doi.org/10.1126/sciadv.abc6228
Rellstab C, Gugerli F, Eckert AJ et al (2015) A practical guide to environmental association analysis in landscape genomics. Mol Ecol 24:4348–4370. https://doi.org/10.1111/mec.13322
Richardson JL, Burak MK, Hernandez C et al (2017) Using fine-scale spatial genetics of Norway rats to improve control efforts and reduce leptospirosis risk in urban slum environments. Evol Appl 10:323–337. https://doi.org/10.1111/eva.12449
Rico Y (2019) Landscape genetics of Mexican biodiversity: a review. Acta Univ 29:1–23. https://doi.org/10.15174/au.2019.1894
Roslin T, Traugott M, Jonsson M et al (2019) Introduction: special issue on species interactions, ecological networks and community dynamics – untangling the entangled bank using molecular techniques. Mol Ecol 28:157–164. https://doi.org/10.1111/mec.14974
Santos AS, Gaiotto FA (2020) Knowledge status and sampling strategies to maximize cost-benefit ratio of studies in landscape genomics of wild plants. Sci Rep 10:3706. https://doi.org/10.1038/s41598-020-60788-8
Santos AS, Cazetta E, Morante Filho JC et al (2015) Lessons from a palm: genetic diversity and structure in anthropogenic landscapes from Atlantic Forest, Brazil. Conserv Genet 16:1295–1302. https://doi.org/10.1007/s10592-015-0740-2
Schemske DW, Mittelbach GG, Cornell HV et al (2009) Is there a latitudinal gradient in the importance of biotic interactions? Annu Rev Ecol Evol Syst 40:245–269. https://doi.org/10.1146/annurev.ecolsys.39.110707.173430
Schlötterer C (2004) The evolution of molecular markers — just a matter of fashion? Nat Rev Genet 5:63–69. https://doi.org/10.1038/nrg1249
Sexton JP, Hangartner SB, Hoffmann AA (2014) Genetic isolation by environmental or distance: which pattern of gene flow is most common? Evolution 68:1–15. https://doi.org/10.1111/evo.12258
Shirk AJ, Landguth EL, Cushman SA (2017) A comparison of individual-based genetic distance metrics for landscape genetics. Mol Ecol Resour 17:1308–1317. https://doi.org/10.1111/1755-0998.12684
Soares LASS, Cazetta E, Santos LR et al (2019) Anthropogenic disturbances eroding the genetic diversity of a threatened palm tree: a multiscale approach. Front Genet 10:1–12. https://doi.org/10.3389/fgene.2019.01090
Souza CM, Shimbo JZ, Rosa MR et al (2020) Reconstructing three decades of land use and land cover changes in brazilian biomes with landsat archive and earth engine. Remote Sens 12:2735. https://doi.org/10.3390/rs12172735
Storfer A, Murphy MA, Evans JS et al (2007) Putting the “landscape” in landscape genetics. Heredity (Edinb) 98:128–142. https://doi.org/10.1038/sj.hdy.6800917
Storfer A, Murphy MA, Spear SF et al (2010) Landscape genetics: where are we now? Mol Ecol 19:3496–3514. https://doi.org/10.1111/j.1365-294X.2010.04691.x
Storfer A, Patton A, Fraik AK (2018) Navigating the interface between landscape genetics and landscape genomics. Front Genet 9:68. https://doi.org/10.3389/fgene.2018.00068
Symondson WOC, Harwood JD (2014) Special issue on molecular detection of trophic interactions: unpicking the tangled bank. Mol Ecol 23:3601–3604. https://doi.org/10.1111/mec.12831
ter Steege H, Pitman NCA, Sabatier D et al (2013) Hyperdominance in the Amazonian tree Flora. Science(80- ) 342:1243092. https://doi.org/10.1126/science.1243092
Thomassen HA, Buermann W, Milá B et al (2010) Modeling environmentally associated morphological and genetic variation in a rainforest bird, and its application to conservation prioritization. Evol Appl 3:1–16. https://doi.org/10.1111/j.1752-4571.2009.00093.x
Torres-Vanegas F, Hadley AS, Kormann UG et al (2019) The landscape genetic signature of pollination by trapliners: evidence from the tropical herb, Heliconia tortuosa. Front Genet 10:1206. https://doi.org/10.3389/fgene.2019.01206
Tscharntke T, Hochberg ME, Rand TA et al (2007) Author sequence and credit for contributions in multiauthored publications. PLoS Biol 5:e18. https://doi.org/10.1371/journal.pbio.0050018
Valenzuela-Toro AM, Viglino M (2021) How latin american researchers suffer in science. Nature 598:374–375. https://doi.org/10.1038/d41586-021-02601-8
Van Strien MJ, Keller D, Holderegger R (2012) A new analytical approach to landscape genetic modelling: least-cost transect analysis and linear mixed models. Mol Ecol 21:4010–4023. https://doi.org/10.1111/j.1365-294X.2012.05687.x
Vasconcellos MM, Colli GR, Weber JN et al (2019) Isolation by instability: historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna. Mol Ecol 28:1748–1764. https://doi.org/10.1111/mec.15045
Wagner HH, Fortin MJ (2012) A conceptual framework for the spatial analysis of landscape genetic data. Conserv Genet 14:253–261. https://doi.org/10.1007/s10592-012-0391-5
Wagner HH, Fortin MJ (2015) Basics of spatial data analysis: linking landscape and genetic data for landscape genetic studies. In: Landscape genetics: concepts, methods, applications. John Wiley & Sons, Ltd, Chichester, pp 77–98
Waits LP, Storfer A (2015) Basics of population genetics: quantifying neutral and adaptive genetic variation for landscape genetic studies. In: Landscape genetics: concepts, methods, applications. John Wiley & Sons, Ltd, Chichester, pp 35–57
Wang IJ, Bradburd GS (2014) Isolation by environment. Mol Ecol 23:5649–5662. https://doi.org/10.1111/mec.12938
Wojciechowski J, Ceschin F, Pereto SCAS et al (2017) Latin American scientific contribution to ecology. An Acad Bras Cienc 89:2663–2674. https://doi.org/10.1590/0001-3765201720160535
Zeller KA, McGarigal K, Whiteley AR (2012) Estimating landscape resistance to movement: a review. Landsc Ecol 27:777–797. https://doi.org/10.1007/s10980-012-9737-0
Zimmerman SJ, Aldridge CL, Oyler-McCance SJ (2020) An empirical comparison of population genetic analyses using microsatellite and SNP data for a species of conservation concern. BMC Genomics 21:382. https://doi.org/10.1186/s12864-020-06783-9
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2023 The Author(s), under exclusive license to Springer Nature Switzerland AG
About this chapter
Cite this chapter
da Silva Carvalho, C., Côrtes, M.C. (2023). Landscape Genetics in the Neotropics. In: Galetti Jr., P.M. (eds) Conservation Genetics in the Neotropics. Springer, Cham. https://doi.org/10.1007/978-3-031-34854-9_7
Download citation
DOI: https://doi.org/10.1007/978-3-031-34854-9_7
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-031-34853-2
Online ISBN: 978-3-031-34854-9
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)