Skip to main content
SpringerLink
Log in

Phylogeography for Neotropical Species Conservation: Lineages Through Time and Space

  • Chapter
  • First Online:
Conservation Genetics in the Neotropics

Abstract

Phylogeography is the study of the spatial distribution of genealogical lineages, especially those found within and among closely related species. The discipline was originally considered a bridge between population genetics (microevolutionary processes) and phylogenetic systematics (macroevolutionary patterns). Therefore, phylogeographic studies are paramount to understanding the assembly of the world’s biota, especially in the Neotropics, one of the most biodiversity-rich regions in the world, harboring approximately one-third of all global species. Throughout this chapter, we show how phylogeography can provide information on the fine-scale genetic diversity of species/populations in the Neotropics. We briefly review the main hypotheses concerning neotropical diversification in terrestrial and freshwater organisms, which illustrate the complexity of processes responsible for the outstanding biodiversity levels in the region. We also present the main methodological approaches to assess these underlying diversification processes, and advocate that they should take this complexity into account to provide insightful guidance for biodiversity protection policies in the Neotropics at multiple evolutionary scales.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 229.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 299.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Change history

  • 28 November 2023

    A correction has been published.

Notes

  1. 1.

    The geologic time scale used in this paper follows the International Commission on Stratigraphy (Cohen et al. 2013).

  2. 2.

    A term introduced by Lieberman and Eldredge (1996), referring to the expansion of a species group’s boundary due to the temporary removal of a barrier.

References

  • Abreu-Jardim TP, Jardim L, Ballesteros-Mejia L et al (2021) Predicting impacts of global climatic change on genetic and phylogeographical diversity of a Neotropical tree frog. Divers Distrib 27(8):1519–1535

    Google Scholar 

  • Aguiar JM, da Fonseca GAB (2008) Conservation status of the Xenarthra. In: Viznaíno S, Loughry WJ (eds) The biology of the Xenarthra. University Press of Florida, Gainesville, pp 215–231

    Google Scholar 

  • Albert JS, Reis RE (2011) Introduction to Neotropical freshwaters. In Albert JS, Reis RE (eds) Historical biogeography of Neotropical freshwater fishes. University of California Press, Berkeley p 3–19

    Google Scholar 

  • Albert JS, Lovejoy NR, Crampton WGR (2006) Miocene tectonism and the separation of cis- and trans-Andean river basins: evidence from Neotropical fishes. J S Am Earth Sci 21:14–27

    Google Scholar 

  • Aleixo A (2004) Historical diversification of a terra-firme forest bird super species: a phylogeographic perspective on the role of different hypotheses of Amazonian diversification. Evolution 58:1303–1317

    CAS  PubMed  Google Scholar 

  • Alencar LRVD, Quental TB (2021) Linking population-level and microevolutionary processes to understand speciation dynamics at the macroevolutionary scale. Ecol Evol 11(11):5828–5843

    PubMed  PubMed Central  Google Scholar 

  • Alvarado-Serrano DF, Knowles LL (2014) Ecological niche models in phylogeographic studies: applications, advances and precautions. Mol Ecol Resour 14(2):233–248

    PubMed  Google Scholar 

  • Antonelli A, Zizka A, Antunes Carvalho F et al (2018) Amazonia is the primary source of Neotropical biodiversity. Proc Natl Acad Sci U S A 115(23):6034–6039

    Google Scholar 

  • Avendaño JE, Arbeláez-Cortés E, Cadena CD (2017) On the importance of geographic and taxonomic sampling in phylogeography: a reevaluation of diversification and species limits in a Neotropical thrush (Aves, Turdidae). Mol Phylogenet Evol 111:87–97

    PubMed  Google Scholar 

  • Avise JC (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge MA

    Google Scholar 

  • Avise JC, Arnold J, Ball RM et al (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Ann Rev Ecol Syst 18:489–522

    Google Scholar 

  • Barley AJ, White J, Diesmos AC et al (2013) The challenge of species delimitation at the extremes: diversification without morphological change in Philippine sun skinks. Evolution 67(12):3556–3572

    PubMed  Google Scholar 

  • Barluenga M, Stölting KN, Salzburger W et al (2006) Sympatric speciation in Nicaraguan crater lake cichlid fish. Nature 439:719–723

    CAS  PubMed  Google Scholar 

  • Barragán-Ruiz CE, Silva-Santos R, Saranholi BH et al (2021) Moderate genetic diversity and demographic reduction in the threatened giant anteater, Myrmecophaga tridactyla. Front Genet 12:1026

    Google Scholar 

  • Beerli P, Felsenstein J (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc Natl Acad Sci U S A 98(8):4563–4568

    CAS  PubMed  PubMed Central  Google Scholar 

  • Beheregaray LB (2008) Twenty years of phylogeography: the state of the field and the challenges for the southern hemisphere. Mol Ecol 17(17):3754–3774

    PubMed  Google Scholar 

  • Bertorelle G, Benazzo A, Mona S (2010) ABC as a flexible framework to estimate demography over space and time: some cons, many pros. Mol Ecol 19(13):2609–2625

    CAS  PubMed  Google Scholar 

  • Bloom DD, Lovejoy NR (2011) The biogeography of marine incursions in South America. In: Albert JS, Reis RE (eds) Historical biogeography of Neotropical freshwater fishes. University of California Press, Berkeley, pp 137–144

    Google Scholar 

  • Bonatelli IA, Perez MF, Peterson AT (2014) Interglacial microrefugia and diversification of a cactus species complex: phylogeography and palaeodistributional reconstructions for Pilosocereus aurisetus and allies. Mol Ecol 23(12):3044–3063

    CAS  PubMed  Google Scholar 

  • Bonatelli IA, Gehara M, Carstens BC et al (2022) Comparative and predictive phylogeography in the south American diagonal of open formations: unravelling the biological and environmental influences on multitaxon demography. Mol Ecol 31(1):331–342

    PubMed  Google Scholar 

  • Borowiec ML, Dikow RB, Frandsen PB et al (2022) Deep learning as a tool for ecology and evolution. Methods Ecol Evol 13(8):1640–1660

    Google Scholar 

  • Boubli JP, Ribas C, Alfaro JWL et al (2015) Spatial and temporal patterns of diversification on the Amazon: a test of the riverine hypothesis for all diurnal primates of Rio Negro and Rio Branco in Brazil. Mol Phylogenet Evol 82:400–412

    PubMed  Google Scholar 

  • Bruschi DP, Peres EA, Lourenço LB et al (2019) Signature of the paleo-course changes in the São Francisco River as source of genetic structure in Neotropical Pithecopus nordestinus (Phyllomedusinae, Anura) treefrog. Front Genet 10:728

    PubMed  PubMed Central  Google Scholar 

  • Burke KD, Williams JW, Chandler MA et al (2018) Pliocene and Eocene provide best analogs for near-future climates. Proc Natl Acad Sci U S A 115(52):13288–13293

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bush MB (1994) Amazonian speciation: a necessarily complex model. J Biogeogr 21:5–17

    Google Scholar 

  • Buzatti RSDO, Pfeilsticker TR, De Magalhaes RF et al (2018) Genetic and historical colonization analyses of an endemic savanna tree, Qualea grandiflora, reveal ancient connections between Amazonian savannas and Cerrado core. Front Plant Sci 9:981

    PubMed  PubMed Central  Google Scholar 

  • Camargo A, Morando M, Avila LJ et al (2012) Species delimitation with ABC and other coalescent-based methods: a test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae). Evolution 66(9):2834–2849

    PubMed  Google Scholar 

  • Capurucho JMG, Cornelius C, Borges SH et al (2013) Combining phylogeography and landscape genetics of Xenopipo atronitens (Aves: Pipridae), a white sand campina specialist, to understand Pleistocene landscape evolution in Amazonia. Biol J Linn Soc 110(1):60–76

    Google Scholar 

  • Cardoso YP, Jardim de Queiroz L, Bahechar IA et al (2021) Multilocus phylogeny and historical biogeography of Hypostomus shed light on the processes of fish diversification in La Plata Basin. Sci Rep 11:5073

    CAS  PubMed  PubMed Central  Google Scholar 

  • Carnaval AC, Hickerson MJ, Haddad CF et al (2009) Stability predicts genetic diversity in the Brazilian Atlantic forest hotspot. Science 323(5915):785–789

    CAS  PubMed  Google Scholar 

  • Carstens BC, Pelletier TA, Reid NM et al (2013) How to fail at species delimitation. Mol Ecol 22(17):4369–4383

    PubMed  Google Scholar 

  • Carvalho SB, Velo-Anton G, Tarroso P et al (2017) Spatial conservation prioritization of biodiversity spanning the evolutionary continuum. Nat Ecol Evol 1(6):1–8

    Google Scholar 

  • Carvalho AF, Menezes RST, Miranda EA et al (2021) Comparative phylogeography and palaeomodelling reveal idiosyncratic responses to climate changes in Neotropical paper wasps. Biol J Linn Soc 132(4):955–969

    Google Scholar 

  • Castroviejo-Fisher S, Guayasamin JM, Gonzalez-Voyer A et al (2014) Neotropical diversification seen through glass frogs. J Biogeogr 41(1):66–80

    Google Scholar 

  • Cavers S, Dick CW (2013) Phylogeography of Neotropical trees. J Biogeogr 40:615–617

    Google Scholar 

  • Cioffi MB, Ráb P, Ezaz T, Bertollo LAC et al (2019) Deciphering the evolutionary history of arowana fishes (Teleostei, Osteoglossiformes, Osteoglossidae): insight from comparative cytogenomics. Int J Mol Sci 20(17):4296

    PubMed  Google Scholar 

  • Cohen KM, Finney SC, Gibbard PL et al (2013, Updated) The ICS international chronostratigraphic chart. Episodes 36:199–204. https://stratigraphy.org/ICSchart/ChronostratChart2022-02.pdf. Accessed 15 Aug 2022

  • Coimbra RTF, Magalhães RF, Lemes P (2022) Integrative phylogeography reveals conservation priorities for the Giant anteater Myrmecophaga tridactyla in Brazil. Diversity 14:542

    CAS  Google Scholar 

  • Colinvaux PA (1998) A new vicariance model for Amazonian endemics. Glob Ecol Biogeogr Let 7(2):95–96

    Google Scholar 

  • Collevatti RG, Lima NE, Vitorino LC (2020) The diversification of extant angiosperms in the South America dry diagonal. In: Rull V, Carnaval C (eds) Neotropical diversification: patterns and processes. Springer, Berlin, pp 547–568

    Google Scholar 

  • Connor EF (1986) The role of Pleistocene Forest refugia in the evolution and biogeography of tropical biotas. Trends Ecol Evol 1(6):165–168

    CAS  PubMed  Google Scholar 

  • Csilléry K, Blum MG, Gaggiotti OE (2010) Approximate Bayesian computation (ABC) in practice. Trends Ecol Evol 25(7):410–418

    PubMed  Google Scholar 

  • de Oliveira FFR, Gehara M, Solé M et al (2021) Quaternary climatic fluctuations influence the demographic history of two species of sky-Island endemic amphibians in the Neotropics. Mol Phylogenet Evol 160:107113

    PubMed  Google Scholar 

  • De Queiroz K (2007) Species concepts and species delimitation. Syst Biol 56(6):879–886

    PubMed  Google Scholar 

  • Domingos FM, Colli GR, Lemmon A et al (2017) In the shadows: phylogenomics and coalescent species delimitation unveil cryptic diversity in a Cerrado endemic lizard (Squamata: Tropidurus). Mol Phylogenet Evol 107:455–465

    PubMed  Google Scholar 

  • Edwards SV, Shultz AJ, Campbell-Staton SC (2015) Next-generation sequencing and the expanding domain of phylogeography. Folia Zool 64(3):187–206

    Google Scholar 

  • Edwards SV, Robin VV, Ferrand N et al (2022) The evolution of comparative phylogeography: putting the geography (and more) into comparative population genomics. Genome Biol Evol 14(1):evab176

    PubMed  Google Scholar 

  • Elith J, Leathwick J (2009) Species distribution models: ecological explanation and prediction across space and time. Ann Rev Ecol Evol Syst 40:677–697

    Google Scholar 

  • Endler JA (1977) Geographic variation, speciation, and clines. Princeton University Press, Princeton

    Google Scholar 

  • Feduccia A (2003) ‘Big bang’ for tertiary birds? Trends Ecol Evol 18(4):172–176

    Google Scholar 

  • Fegies AC, Carmignotto AP, Perez MF et al (2021) Molecular phylogeny of Cryptonanus (Didelphidae: Thylamyini): evidence for a recent and complex diversification in south American open biomes. Mol Phylogenet Evol 162:107213

    PubMed  Google Scholar 

  • Flagel L, Brandvain Y, Schrider DR (2019) The unreasonable effectiveness of convolutional neural networks in population genetic inference. Mol Biol Evol 36(2):220–238

    CAS  PubMed  Google Scholar 

  • Fonseca EM, Colli GR, Werneck FP et al (2021) Phylogeographic model selection using convolutional neural networks. Mol Ecol Resour 21(8):2661–2675

    Google Scholar 

  • Forester BR, Lasky JR, Wagner HH et al (2018) Comparing methods for detecting multilocus adaptation with multivariate genotype–environment associations. Mol Ecol 27(9):2215–2233

    CAS  PubMed  Google Scholar 

  • Fouquet A, Noonan BP, Rodrigues MT et al (2012) Multiple quaternary refugia in the eastern Guiana shield revealed by comparative phylogeography of 12 frog species. Syst Biol 61(3):461–489

    PubMed  Google Scholar 

  • Franco FF, Jojima CL, Perez MF et al (2017) The xeric side of the Brazilian Atlantic Forest: the forces shaping phylogeographic structure of cacti. Ecol Evol 22:9281–9293

    Google Scholar 

  • Frazão A, Silva HRD, Russo CADM (2015) The Gondwana breakup and the history of the Atlantic and Indian oceans unveils two new clades for early neobatrachian diversification. PLoS One 10(11):e0143926

    PubMed  PubMed Central  Google Scholar 

  • French CM, Deutsch MS, Chávez G et al (2019) Speciation with introgression: phylogeography and systematics of the Ameerega petersi group (Dendrobatidae). Mol Phylogenet Evol 138:31–42

    PubMed  Google Scholar 

  • Garrick RC, Bonatelli IA, Hyseni C et al (2015) The evolution of phylogeographic data sets. Mol Ecol 24:1164–1171

    CAS  PubMed  Google Scholar 

  • Gates DM (1993) Climate change and its biological consequences. Sinauer Associates, Sunderland

    Google Scholar 

  • Gehara M, Garda AA, Werneck FP et al (2017) Estimating synchronous demographic changes across populations using hABC and its application for a herpetological community from northeastern Brazil. Mol Ecol 26(18):4756–4771

    PubMed  Google Scholar 

  • Guillory WX, Muell MR, Summers K et al (2019) Phylogenomic reconstruction of the neotropical poison frogs (Dendrobatidae) and their conservation. Diversity 11(8):126

    CAS  Google Scholar 

  • Haffer J (1969) Speciation in Amazonian forest birds. Science 165:131–137

    CAS  PubMed  Google Scholar 

  • Hamdan B, Guedes TB, Carrasco PA et al (2020) A complex biogeographic history of diversification in Neotropical lancehead pitvipers (Serpentes, Viperidae). Zool Scr 49(2):145–158

    Google Scholar 

  • Hewitt GM (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biol J Linn Soc 58:247–276

    Google Scholar 

  • Hey J, Nielsen R (2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 67(2):747–760

    Google Scholar 

  • Hickerson MJ, Meyer CP (2008) Testing comparative phylogeographic models of marine vicariance and dispersal using a hierarchical Bayesian approach. BMC Evol Biol 8(1):1–8

    Google Scholar 

  • Hickerson MJ, Carstens BC, Cavender-Bares J (2010) Phylogeography’s past, present, and future: 10 years after Avise, 2000. Mol Phylogenet Evol 54:291–301

    CAS  PubMed  Google Scholar 

  • Hoorn C, Wesselingh F (2010) Amazonia: landscape and species evolution. A look into the past. Wiley-Blackwell, Chichester

    Google Scholar 

  • Hoorn C, Wesselingh FP, ter Steege H et al (2010) Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science 330:927–931

    CAS  PubMed  Google Scholar 

  • Hubert N, Renno J-F (2006) Historical biogeography of south American freshwater fishes. J Biogeogr 33:1414–1436

    Google Scholar 

  • Hubert N, Duponchelle F, Nunez J et al (2007) Phylogeography of the piranha genera Serrasalmus and Pygocentrus: implications for the diversification of the Neotropical ichthyofauna. Mol Ecol 16:2115–2136

    CAS  PubMed  Google Scholar 

  • Hughes CE, Pennington RT, Antonelli A (2013) Neotropical plant evolution: assembling the big picture. Bot J Linn Soc 171(1):1–18

    Google Scholar 

  • Jenkins CN, Pimm SL, Joppa LN (2013) Global patterns of terrestrial vertebrate diversity and conservation. PNAS 110(28):E2602–E2610

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kingman JF (1982) The coalescent. Stoch Process Appl 13(3):235–248

    Google Scholar 

  • Kirschner P, Perez MF, Záveská E et al (2022) Congruent evolutionary responses of European steppe biota to late quaternary climate change. Nat Commun 13:1921

    CAS  PubMed  PubMed Central  Google Scholar 

  • Knowles LL (2009) Statistical phylogeography. Ann Rev Ecol Evol Syst 40:593–612

    Google Scholar 

  • Knowles LL, Maddison WP (2002) Statistical phylogeography. Mol Ecol 11(12):2623–2635

    PubMed  Google Scholar 

  • Kopuchian C, Campagna L, Lijtmaer DA (2020) A test of the riverine barrier hypothesis in the largest subtropical river basin in the Neotropics. Mol Ecol 29(12):2137–2149

    PubMed  Google Scholar 

  • Lanna FM, Colli GR, Burbrink FT et al (2022) Identifying traits that enable lizard adaptation to different habitats. J Biogeogr 49(1):104–116

    Google Scholar 

  • Leite RN, Rogers DS (2013) Revisiting Amazonian phylogeography: insights into diversification hypotheses and novel perspectives. Org Divers Evol 13(4):639–664

    Google Scholar 

  • Li J, Huang JP, Sukumaran J et al (2018) Microevolutionary processes impact macroevolutionary patterns. BMC Evol Biol 18(1):1–8

    Google Scholar 

  • Lieberman BS, Eldredge N (1996) Trilobite biogeography in the middle Devonian: geological process and analytical methods. Paleobiology 22:66–79

    Google Scholar 

  • López-Fernández H, Arbour JH, Winemiller KO et al (2012) Testing for ancient adaptive radiations in Neotropical cichlid fishes. Evolution 67(5):1321–1337

    Google Scholar 

  • Lötters S, Van der Meijden A, Rödder D et al (2010) Reinforcing and expanding the predictions of the disturbance vicariance hypothesis in Amazonian harlequin frogs: a molecular phylogenetic and climate envelope modelling approach. Biodivers Conserv 19:2125–2146

    Google Scholar 

  • Löwenberg-Neto P (2014) Neotropical region: a shapefile of Morrone’s (2014) biogeographical regionalisation. Zootaxa 3802(2):300–300

    Google Scholar 

  • Lundberg JG, Marshall LG, Guerrero J et al (1998) The stage for Neotropical fish diversification: a history of tropical south American Rivers. In: Malabarba LR, Reis RE, Vari RP, Lucena ZMS, Lucena CAS (eds) Phylogeny and classification of Neotropical fishes. Edipucrs, Porto Alegre, pp 13–48

    Google Scholar 

  • Machado CB, PMJr G, Carnaval AC (2018) Bayesian analyses detect a history of both vicariance and geodispersal in Neotropical freshwater fishes. J Biogeogr 45(6):1313–1325

    Google Scholar 

  • Machado AF, Nunes MS, Silva CR et al (2019) Integrating phylogeography and ecological niche modelling to test diversification hypotheses using a Neotropical rodent. Evol Ecol 33:111–148

    Google Scholar 

  • Macqueen P (2012) Last chance to see: the role of phylogeography in the preservation of tropical biodiversity. Trop Conserv Sci 5(4):417–425

    Google Scholar 

  • Marshall LG, Webb SD, Sepkoski JJJ et al (1982) Mammalian evolution and the great American interchange. Science 215(4538):1351–1357

    CAS  PubMed  Google Scholar 

  • Marske KA (2016) Phylogeography. In: Kliman RM (ed) Encyclopedia of evolutionary biology, volume 3. Elsevier Academic Press, Amsterdam, pp 291–296

    Google Scholar 

  • Mascarenhas R, Miyaki CY, Dobrovolski R et al (2019) Late Pleistocene climate change shapes population divergence of an Atlantic Forest passerine: a model-based phylogeographic hypothesis test. J Ornithol 160:733–748

    Google Scholar 

  • Mayden RL (1997) A hierarchy of species concepts: the denouement in the saga of the species problem. In: Claridge MF, Dawah HA, Wilson MR (eds) Species: the units of biodiversity. Chapman and Hall, London, pp 381–424

    Google Scholar 

  • McGill BJ, Chase JM, Hortal J et al (2019) Unifying macroecology and macroevolution to answer fundamental questions about biodiversity. Glob Ecol Biogeogr 28(12):1925–1936

    Google Scholar 

  • McLoughlin S (2001) The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism. Aust J Bot 49(3):271–300

    Google Scholar 

  • Melo BF, Albert JS, Dagosta FCP et al (2021) Biogeography of curimatid fishes reveals multiple lowland-upland river transitions and differential diversification in the Neotropics (Teleostei, Curimatidae). Ecol Evol 11:15815–15832

    PubMed  PubMed Central  Google Scholar 

  • Meseguer AS, Michel A, Fabre P et al (2021) The origins and drivers of Neotropical diversity. https://doi.org/10.1101/2021.02.24.432517

  • Miño CI, Avelar LH, da Silva FM et al (2017) Genetic differentiation and historical demography of wood stork populations in Brazilian wetlands: implications for the conservation of the species and associated ecosystems. Aquat Conserv 27(6):1313–1324

    Google Scholar 

  • Miranda F, Bertassoni A, Abba AM (2014) Myrmecophaga tridactyla. The IUCN Red List of Threatened Species http://www.iucnredlist.org. Accessed 08 Sept 2022

  • Miranda LS, Prestes BO, Aleixo A (2021) Molecular systematics and phylogeography of a widespread Neotropical avian lineage: evidence for cryptic speciation with protracted gene flow throughout the late quaternary. Biol J Linn Soc 132(2):431–450

    Google Scholar 

  • Mondin LADC, Machado CB, Resende EKD et al (2018) Genetic pattern and demographic history of Salminus brasiliensis: population expansion in the Pantanal region during the Pleistocene. Front Genet 9:1

    PubMed  PubMed Central  Google Scholar 

  • Moritz C (1994) Defining evolutionarily significant units for conservation. Trends Ecol Evol 9:373–375

    CAS  PubMed  Google Scholar 

  • Moritz C, Patton JL, Schneider CJ et al (2000) Diversification of rainforest faunas: an integrated molecular approach. Ann Rev Ecol Syst 31:533–563

    Google Scholar 

  • Morrone JJ (2014) Biogeographical regionalisation of the Neotropical region. Zootaxa 3782(1):1–110

    PubMed  Google Scholar 

  • Morrone JJ (2017) Neotropical biogeography: regionalization and evolution. CRC Press

    Google Scholar 

  • Myers N, Mittermeier RA, Mittermeier CG et al (2000) Biodiversity hotspots for conservation priorities. Nature 403:853–858

    CAS  PubMed  Google Scholar 

  • Nazareno AG, Dick CW, Lohmann LG (2019) A biogeographic barrier test reveals a strong genetic structure for a canopy-emergent Amazon tree species. Sci Rep 9:18602

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nores M (2020) Avian diversity in humid tropical and subtropical south American forests, with a discussion about their related climatic and geological underpinnings. In: Rull V, Carnaval C (eds) Neotropical diversification: patterns and processes. Springer, Berlin, pp 145–188

    Google Scholar 

  • Oaks JR (2019) Full Bayesian comparative phylogeography from genomic data. Syst Biol 68(3):371–395

    CAS  PubMed  Google Scholar 

  • Ochoa LE, Melo BF, García-Melo JE et al (2020) Species delimitation reveals an underestimated diversity of Andean catfishes of the family Astroblepidae (Teleostei: Siluriformes). Neotrop Ichthyol 18(4):1–19

    Google Scholar 

  • Oliveira EA, Perez MF, Bertollo LA et al (2020) Historical demography and climate driven distributional changes in a widespread Neotropical freshwater species with high economic importance. Ecography 43(9):1291–1304

    Google Scholar 

  • Olson DM, Dinerstein E, Wikramanayake ED et al (2001) Terrestrial ecoregions of the world: a new map of life on earth: a new global map of terrestrial ecoregions provides an innovative tool for conserving biodiversity. Bioscience 51:933–938

    Google Scholar 

  • Pelletier TA, Carstens BC, Tank DC et al (2018) Predicting plant conservation priorities on a global scale. Proc Natl Acad Sci U S A 115(51):13027–13032

    CAS  PubMed  PubMed Central  Google Scholar 

  • Peres EA, Sobral-Souza T, Perez MF et al (2015) Pleistocene niche stability and lineage diversification in the subtropical spider Araneus omnicolor (Araneidae). PLoS One 10(4):e0121543

    PubMed  PubMed Central  Google Scholar 

  • Perez MF, Bonatelli IA, Moraes EM et al (2016a) Model-based analysis supports interglacial refugia over long-dispersal events in the diversification of two south American cactus species. Heredity 116(6):550–557

    CAS  PubMed  PubMed Central  Google Scholar 

  • Perez MF, Carstens BC, Rodrigues GL et al (2016b) Anonymous nuclear markers reveal taxonomic incongruence and long-term disjunction in a cactus species complex with continental-Island distribution in South America. Mol Phylogenet Evol 95:11–19

    PubMed  Google Scholar 

  • Perez MF, Franco FF, Bombonato JR et al (2018) Assessing population structure in the face of isolation by distance: are we neglecting the problem? Divers Distrib 24(12):1883–1889

    Google Scholar 

  • Perez MF, Bonatelli IA, Romeiro-Brito M et al (2022) Coalescent-based species delimitation meets deep learning: insights from a highly fragmented cactus system. Mol Ecol Resour 22(3):1016–1028

    PubMed  Google Scholar 

  • Pie MR, Bornschein MR, Ribeiro LF et al (2019) Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest. Mol Phylogenet Evol 141:106627

    CAS  PubMed  Google Scholar 

  • Pinheiro F, Dantas-Queiroz MV, Palma-Silva C (2018) Plant species complexes as models to understand speciation and evolution: a review of south American studies. Crit Rev Plant Sci 37(1):54–80

    Google Scholar 

  • Posadas P, Crisci JV, Katinas L et al (2006) Historical biogeography: a review of its basic concepts and critical issues. J Arid Environ 66:389–403

    Google Scholar 

  • Prado DE, Gibbs PE (1993) Patterns of species distributions in the dry seasonal forests of South America. Ann Missouri Bot Gard 1:902–927

    Google Scholar 

  • Prangle D, Everitt RG, Kypraios T (2018) A rare event approach to high-dimensional approximate Bayesian computation. Stat Comput 28(4):819–834

    Google Scholar 

  • Prates I, Xue AT, Brown JL et al (2016) Inferring responses to climate dynamics from historical demography in neotropical forest lizards. Proc Natl Acad Sci U S A 113(29):7978–7985

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ramirez JL, Santos CA, Machado CB et al (2020) Molecular phylogeny and species delimitation of the genus Schizodon (Characiformes, Anostomidae). Mol Phylogenet Evol 153:106959

    PubMed  Google Scholar 

  • Rannala B, Yang Z (2020) Species delimitation. In: Scornavacca C, Delsuc F, Galtier N (eds) Phylogenetics in the genomic era. Authors open access book: ffhal-02536468, p 5.5:1–18

    Google Scholar 

  • Raven PH, Gereau RE, Phillipson PB et al (2020) The distribution of biodiversity richness in the tropics. Sci Adv 6(37):eabc6228

    PubMed  Google Scholar 

  • Reguero MA, Goin FJ (2021) Paleogeography and biogeography of the Gondwanan final breakup and its terrestrial vertebrates: new insights from southern South America and the “double Noah’s Ark” Antarctic Peninsula. J S Am Earth Sci 108:103358

    Google Scholar 

  • Rheingantz ML, Trinca CS (2021) Lontra logicauda. IUCN 2021 IUCN red list of threatened species. http://www.iucnredlist.org. Accessed 07 Sept 2022

  • Rheingantz ML, Santiago-Plata VM, Trinca CS (2017) The Neotropical otter Lontra longicaudis: a comprehensive update on the current knowledge and conservation status of this semiaquatic carnivore. Mamm Rev 47(4):291–305

    Google Scholar 

  • Ribolli J, Zaniboni E, Scaranto BMS et al (2021) Cryptic diversity and diversification processes in three cis-Andean Rhamdia species (Siluriformes: Heptapteridae) revealed by DNA barcoding. Genet Mol Biol 44(3)

    Google Scholar 

  • Robert CP, Cornuet JM, Marin JM et al (2011) Lack of confidence in approximate Bayesian computation model choice. Proc Natl Acad Sci U S A 108(37):15112–15117

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rull V (2011) Neotropical biodiversity: timing and potential drivers. Trends Ecol Evol 26:508–513

    PubMed  Google Scholar 

  • Rull V (2020) Neotropical diversification: historical overview and conceptual insights. In: Rull V, Carnaval C (eds) Neotropical diversification: patterns and processes. Springer, Berlin, pp 13–49

    Google Scholar 

  • Rull V, Carnaval AC (eds) (2020) Neotropical diversification: patterns and processes. Springer, Berlin

    Google Scholar 

  • Sanchez T, Cury J, Charpiat G et al (2021) Deep learning for population size history inference: design, comparison and combination with approximate Bayesian computation. Mol Ecol Resour 21(8):2645–2660

    PubMed  Google Scholar 

  • Sánchez-Herrera M, Beatty CD, Nunes R et al (2020) An exploration of the complex biogeographical history of the Neotropical banner-wing damselflies (Odonata: Polythoridae). BMC Evol Biol 20(1):1–14

    Google Scholar 

  • Santos JC, Coloma LA, Summers K et al (2009) Amazonian amphibian diversity is primarily derived from late Miocene Andean lineages. PLoS Biol 7(3):e1000056

    PubMed  PubMed Central  Google Scholar 

  • Satler JD, Carstens BC, Hedin M (2013) Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus). Syst Biol 62(6):805–823

    PubMed  Google Scholar 

  • Schrider DR, Kern AD (2018) Supervised machine learning for population genetics: a new paradigm. Trends Genet 34(4):301–312

    CAS  PubMed  PubMed Central  Google Scholar 

  • Singhal S, Colli GR, Grundler MR et al (2022) No link between population isolation and speciation rate in squamate reptiles. Proc Natl Acad Sci U S A 119(4):e2113388119

    PubMed  PubMed Central  Google Scholar 

  • Smith TB, Wayne RK, Girman DJ et al (1997) A role for ecotones in generating rainforest biodiversity. Science 276:1855–1857

    CAS  Google Scholar 

  • Smith BT, Harvey MG, Faircloth BC et al (2014) Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales. Syst Biol 63:83–95

    PubMed  Google Scholar 

  • Soares LMDS, Bates J, Carneiro LS et al (2019) Molecular systematics, biogeography and taxonomy of forest-falcons in the Micrastur ruficollis species complex (Aves: Falconidae). J Avian Biol 50(4)

    Google Scholar 

  • Solomon SE, Bacci M Jr, Martins J Jr et al (2008) Paleodistributions and comparative molecular phylogeography of leafcutter ants (Atta spp.) provide new insight into the origins of Amazonian diversity. PLoS One 3(7):e2738

    PubMed  PubMed Central  Google Scholar 

  • Souza FH, Perez MF, Bertollo LA et al (2019) Interspecific genetic differences and historical demography in south American arowanas (Osteoglossiformes, Osteoglossidae, Osteoglossum). Genes 10(9):693

    PubMed  PubMed Central  Google Scholar 

  • Souza FH, Sassi FD, Ferreira PH et al (2022) Integrating cytogenetics and population genomics: Allopatry and neo-sex chromosomes may have shaped the genetic divergence in the Erythrinus erythrinus species complex (Teleostei, Characiformes). Biology 11(2):315

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sullivan J, Smith ML, Espíndola A et al (2019) Integrating life history traits into predictive phylogeography. Mol Ecol 28(8):2062–2073

    PubMed  Google Scholar 

  • Tagliacollo VA, Roxo FF, Duke-Sylevester SM et al (2015) Biogeographical signature of river capture events in Amazonian lowlands. J Biogeogr 42(12):2349–2362

    Google Scholar 

  • Thom G, Xue AT, Sawakuchi AO et al (2020) Quaternary climate changes as speciation drivers in the Amazon floodplains. Sci Adv 6(11):eaax4718

    CAS  PubMed  PubMed Central  Google Scholar 

  • Torada L, Lorenzon L, Beddis A (2019) ImaGene: a convolutional neural network to quantify natural selection from genomic data. BMC Bioinf 20(9):1–2

    Google Scholar 

  • Trinca CS, de Thoisy B, Rosas F et al (2012) Phylogeography and demographic history of the Neotropical otter (Lontra longicaudis). J Hered 103(4):479–492

    PubMed  Google Scholar 

  • Turchetto-Zolet AC, Pinheiro F, Salgueiro F et al (2013) Phylogeographical patterns shed light on the evolutionary process in South America. Mol Ecol 22(5):1193–1213

    CAS  PubMed  Google Scholar 

  • Vila R, Bell CD, Macniven R et al (2011) Phylogeny and palaeoecology of Polyommatus blue butterflies show Beringia was a climate-regulated gateway to the New World. Proc R Soc Lond B Biol Sci 278(1719):2737–2744

    Google Scholar 

  • Wakeley J (2003) Inferences about the structure and history of populations: Coalescents and intraspecific phylogeography. In: Singh R, Uyenoyama M (eds) The evolution of population biology. Cambridge University Press, Cambridge, pp 193–215

    Google Scholar 

  • Wallace AR (1852) On the monkeys of the Amazon. Proc Zool Soc 20:107–110

    Google Scholar 

  • Zachos JC, Dickens GR, Zeebe RE (2008) An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics. Nature 451(7176):279–283

    CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil

    Carolina B. Machado & Manolo F. Perez

  2. Laboratório de Ecologia e Conservação Marinha, Universidade Federal do Sul da Bahia, Porto Seguro, Bahia, Brazil

    Carolina B. Machado

  3. Muséum National d’Histoire Naturelle, Institut de Systématique, Évolution, Biodiversité (ISYEB), Paris, Île-de-France, France

    Manolo F. Perez

Authors
  1. Carolina B. Machado
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Manolo F. Perez
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil

    Pedro M. Galetti Jr.

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Machado, C.B., Perez, M.F. (2023). Phylogeography for Neotropical Species Conservation: Lineages Through Time and Space. In: Galetti Jr., P.M. (eds) Conservation Genetics in the Neotropics. Springer, Cham. https://doi.org/10.1007/978-3-031-34854-9_6

Download citation

Publish with us

Policies and ethics

Search

Navigation