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de Oliveira JCP, Cabanne GS, Santos FR. Phylogenomics of the gray-breasted sabrewing (Campylopterus largipennis) species complex in the Amazonia and Cerrado biomes. Genet Mol Biol 2024; 47:e20230331. [PMID: 39133262 PMCID: PMC11308382 DOI: 10.1590/1678-4685-gmb-2023-0331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/29/2024] [Indexed: 08/13/2024] Open
Abstract
The Neotropics are one of the most biodiverse regions of the world, where environmental dynamics, climate and geology resulted in a complex diversity of fauna and flora. In such complex and heterogeneous environments, widely distributed species require deep investigation about their biogeographic history. The gray-breasted sabrewing hummingbird Campylopterus largipennis is a species complex that occurs in forest and open ecosystems of South America, including also high-altitude grasslands. It has been recently split into four distinct species distributed in Amazonia (rainforest) and Cerrado (savanna) biomes with boundaries marked by ecological barriers. Here, we investigated the evolutionary dynamics of population lineages within this neotropical taxon to elucidate its biogeographical history and current lineage diversity. We used a reduced-representation sequencing approach to perform fine-scale population genomic analyses of samples distributed throughout Amazonia and Cerrado localities, representing all four recently recognized species. We found a deep genetic structure separating species from both biomes, and a more recent divergence between species within each biome and from distinct habitats. The population dynamics through time was shown to be concordant with known vicariant events, isolation by distance, and altitudinal breaks, where the Amazon River and the Espinhaço Mountain Range worked as important barriers associated to speciation.
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Affiliation(s)
- Jean Carlo Pedroso de Oliveira
- Universidade Federal de Minas Gerais, Instituto de Ciências
Biológicas, Departamento de Genética, Ecologia e Evolução, Belo Horizonte, MG,
Brazil
| | - Gustavo Sebastián Cabanne
- División de Ornitología, Museo Argentino de Ciencias Naturales
“Bernardino Rivadavia” (MACN - CONICET), Buenos Aires, Argentina
| | - Fabrício Rodrigues Santos
- Universidade Federal de Minas Gerais, Instituto de Ciências
Biológicas, Departamento de Genética, Ecologia e Evolução, Belo Horizonte, MG,
Brazil
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Guillory WX, de Medeiros Magalhães F, Coelho FEA, Bonatelli IAS, Palma-Silva C, Moraes EM, Garda AA, Burbrink FT, Gehara M. Geoclimatic drivers of diversification in the largest arid and semi-arid environment of the Neotropics: Perspectives from phylogeography. Mol Ecol 2024; 33:e17431. [PMID: 38877815 DOI: 10.1111/mec.17431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/16/2024]
Abstract
The South American Dry Diagonal, also called the Diagonal of Open Formations, is a large region of seasonally dry vegetation extending from northeastern Brazil to northern Argentina, comprising the Caatinga, Cerrado, and Chaco subregions. A growing body of phylogeography literature has determined that a complex history of climatic changes coupled with more ancient geological events has produced a diverse and endemic-rich Dry Diagonal biota. However, the exact drivers are still under investigation, and their relative strengths and effects are controversial. Pleistocene climatic fluctuations structured lineages via vegetation shifts, refugium formation, and corridors between the Amazon and Atlantic forests. In some taxa, older geological events, such as the reconfiguration of the São Francisco River, uplift of the Central Brazilian Plateau, or the Miocene inundation of the Chaco by marine incursions, were more important. Here, we review the Dry Diagonal phylogeography literature, discussing each hypothesized driver of diversification and assessing degree of support. Few studies statistically test these hypotheses, with most support drawn from associating encountered phylogeographic patterns such as population structure with the timing of ancient geoclimatic events. Across statistical studies, most hypotheses are well supported, with the exception of the Pleistocene Arc Hypothesis. However, taxonomic and regional biases persist, such as a proportional overabundance of herpetofauna studies, and the under-representation of Chaco studies. Overall, both Pleistocene climate change and Neogene geological events shaped the evolution of the Dry Diagonal biota, though the precise effects are regionally and taxonomically varied. We encourage further use of model-based analyses to test evolutionary scenarios, as well as interdisciplinary collaborations to progress the field beyond its current focus on the traditional set of geoclimatic hypotheses.
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Affiliation(s)
- Wilson X Guillory
- Department of Earth and Environmental Sciences, Rutgers University Newark, Newark, New Jersey, USA
- Department of Biological Sciences, Rutgers University Newark, Newark, New Jersey, USA
| | | | | | - Isabel A S Bonatelli
- Departamento de Ecologia e Biologia Evolutiva, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
| | - Clarisse Palma-Silva
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, Campinas, São Paulo, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, São Paulo, Brazil
| | - Adrian Antonio Garda
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, New York City, New York, USA
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University Newark, Newark, New Jersey, USA
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Lopes JC, Fonseca LHM, Johnson DM, Luebert F, Murray N, Nge FJ, Rodrigues-Vaz C, Soulé V, Onstein RE, Lohmann LG, Couvreur TLP. Dispersal from Africa to the Neotropics was followed by multiple transitions across Neotropical biomes facilitated by frugivores. ANNALS OF BOTANY 2024; 133:659-676. [PMID: 37968940 PMCID: PMC11082516 DOI: 10.1093/aob/mcad175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/10/2023] [Indexed: 11/17/2023]
Abstract
BACKGROUND AND AIM Plant disjunctions have fascinated biogeographers and ecologists for a long time. We use tribe Bocageeae (Annonaceae), a predominantly Neotropical plant group distributed across several present-day Neotropical biomes and with an African-American disjunction, to investigate long-distance dispersal mediated by frugivorous animals at both intercontinental and intracontinental scales. METHODS We reconstructed a species-level phylogeny of tribe Bocageeae with a dataset composed of 116 nuclear markers. We sampled 70 % of Bocageeae species, covering their geographical range and representing all eight genera. We estimated divergence times using BEAST, inferred ancestral range distributions and reconstructed ancestral states for fruit traits related to long-distance dispersal in a Bayesian framework. KEY RESULTS The ancestral Bocageeae date to the Early Eocene and were inferred to occur in Africa and proto-Amazonia. Their ancestral fruits were large and dehiscent. The first lineage split gave rise to an exclusively Neotropical clade during the Middle Eocene, in proto-Amazonia. Range exchange between the Amazon and the Atlantic Forest occurred at least once during the Miocene, and from Amazonia to Central America and Mexico during the Early Miocene. Transitions in different sets of fruit morphologies were inferred to be related to dispersal events across South American regions/biomes. CONCLUSIONS In Bocageeae, mammals might have been responsible for long-distance dispersal through the Boreotropics. In the Neotropics, proto-Amazonia is proposed to be the source for dispersal to other tropical American biomes. Long-distance dispersal might have happened via a wide range of dispersal guilds, depending on frugivore radiations, diversity and abundance in particular time periods and places. Hence, inter- and intracontinental dispersal might not rely on a single dispersal syndrome or guild, but more on the availability of frugivorous lineages for seed dispersal.
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Affiliation(s)
- Jenifer C Lopes
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA, USA
| | | | - David M Johnson
- Department of Biological Sciences, Ohio Wesleyan University, Delaware, OH, USA
| | - Federico Luebert
- Departamento de Ciencias Ambientales y Recursos Naturales Renovables Universidad de Chile, Santiago, Chile
- Departmento de Silvicultura y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
| | - Nancy Murray
- Department of Biological Sciences, Ohio Wesleyan University, Delaware, OH, USA
| | - Francis J Nge
- IRD, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Carlos Rodrigues-Vaz
- IRD, UMR DIADE, Université de Montpellier, Montpellier, France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle-CNRS-SU-EPHE-UA, Paris, France
| | - Vincent Soulé
- IRD, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Renske E Onstein
- Naturalis Biodiversity Center, Leiden, The Netherlands
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Lúcia G Lohmann
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- University and Jepson Herbaria, and Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Thomas L P Couvreur
- IRD, UMR DIADE, Université de Montpellier, Montpellier, France
- Naturalis Biodiversity Center, Leiden, The Netherlands
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Dalapicolla J, Weir JT, Vilaça ST, Quaresma TF, Schneider MPC, Vasconcelos ATR, Aleixo A. Whole genomes show contrasting trends of population size changes and genomic diversity for an Amazonian endemic passerine over the late quaternary. Ecol Evol 2024; 14:e11250. [PMID: 38660467 PMCID: PMC11040105 DOI: 10.1002/ece3.11250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/16/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
The "Amazon tipping point" is a global change scenario resulting in replacement of upland terra-firme forests by large-scale "savannization" of mostly southern and eastern Amazon. Reduced rainfall accompanying the Last Glacial Maximum (LGM) has been proposed to have acted as such a tipping point in the past, with the prediction that terra-firme inhabiting species should have experienced reductions in population size as drier habitats expanded. Here, we use whole-genomes of an Amazonian endemic organism (Scale-backed antbirds - Willisornis spp.) sampled from nine populations across the region to test this historical demography scenario. Populations from southeastern Amazonia and close to the Amazon-Cerrado ecotone exhibited a wide range of demographic patterns, while most of those from northern and western Amazonia experienced uniform expansions between 400 kya and 80-60 kya, with gradual declines toward 20 kya. Southeastern populations of Willisornis were the last to diversify and showed smaller heterozygosity and higher runs of homozygosity values than western and northern populations. These patterns support historical population declines throughout the Amazon that affected more strongly lineages in the southern and eastern areas, where historical "tipping point" conditions existed due to the widespread replacement of humid forest by drier and open vegetation during the LGM.
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Affiliation(s)
- Jeronymo Dalapicolla
- Instituto Tecnológico ValeBelémParáBrazil
- Departamento de Sistemática e EcologiaUniversidade Federal da Paraíba, João PessoaParaíbaBrazil
| | - Jason T. Weir
- Department of Biological SciencesUniversity of Toronto ScarboroughTorontoOntarioCanada
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
- Department of Natural History, Royal Ontario MuseumTorontoOntarioCanada
| | | | | | - Maria P. C. Schneider
- Laboratório de Genômica e BiotecnologiaInstituto de Ciências Biológicas, UFPABelémBrazil
| | - Ana Tereza R. Vasconcelos
- Laboratório de BioinformáticaLaboratório Nacional de Computação Científica, PetrópolisRio de JaneiroBrazil
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Wacker KS, Winger BM. An Elevational Phylogeographic Diversity Gradient in Neotropical Birds Is Decoupled from Speciation Rates. Am Nat 2024; 203:362-381. [PMID: 38358813 DOI: 10.1086/728598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
AbstractA key question about macroevolutionary speciation rates is whether they are controlled by microevolutionary processes operating at the population level. For example, does spatial variation in population genetic differentiation underlie geographical gradients in speciation rates? Previous work suggests that speciation rates increase with elevation in Neotropical birds, but underlying population-level gradients remain unexplored. Here, we characterize elevational phylogeographic diversity between montane and lowland birds in the megadiverse Andes-Amazonian system and assess its relationship to speciation rates to evaluate the link between population-level differentiation and species-level diversification. We aggregated and georeferenced nearly 7,000 mitochondrial DNA sequences across 103 species or species complexes in the Andes and Amazonia and used these sequences to describe phylogeographic differentiation across both regions. Our results show increased levels of both discrete and continuous metrics of population structure in the Andean mountains compared with the Amazonian lowlands. However, higher levels of population differentiation do not predict higher rates of speciation in our dataset. Multiple potential factors may lead to our observed decoupling of initial population divergence and speciation rates, including the ephemerality of incipient species and the multifaceted nature of the speciation process, as well as methodological challenges associated with estimating rates of population differentiation and speciation.
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Magalhães RF, K S Ramos E, Bandeira LN, Ferreira JS, Werneck FP, Anciães M, Bruschi DP. Integrative species delimitation uncovers hidden diversity within the Pithecopus hypochondrialis species complex (Hylidae, Phyllomedusinae) and its phylogeography reveals Plio-Pleistocene connectivity among Neotropical savannas. Mol Phylogenet Evol 2024; 190:107959. [PMID: 37918682 DOI: 10.1016/j.ympev.2023.107959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023]
Abstract
Despite their limited vagility and pronounced habitat heterogeneity in the tropics, many anuran species have unexpectedly extensive geographic ranges. One prominent example of this phenomenon is Pithecopus hypochondrialis, which is found in the Cerrado, Guianan savanna, and Llanos domains, as well as isolated tracts of savanna and open habitat within the Amazon Forest. The present study employs an integrative species delimitation approach to test the hypothesis that P. hypochondrialis is in fact a species complex. We also reconstruct the relationships among the lineages delimited here and other Pithecopus species. In this study, we employ Ecological Niche Modelling (ENM) and spatiotemporal phylogeographic reconstruction approaches to evaluate a multitude of scenarios of connectivity across the Neotropical savannas. We identified three divergent lineages, two of which have been described previously. The lineages were allocated to a lowland Pithecopus clade, although the relationships among these lineages are weakly supported. Both the ENM and the phylogeographic reconstruction highlight the occurrence of periods of connectivity among the Neotropical savannas over the course of the Pliocene and Pleistocene epochs. These processes extended from eastern Amazonia to the northern coast of Brazil. The findings of the present study highlight the presence of hidden diversity within P. hypochondrialis, and reinforce the need for a comprehensive taxonomic review. These findings also indicate intricate and highly dynamic patterns of connectivity across the Neotropical savannas that date back to the Pliocene.
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Affiliation(s)
- Rafael F Magalhães
- Department of Natural Sciences, Universidade Federal de São João del-Rei, Campus Dom Bosco, Praça Dom Helvécio, 70, São João del-Rei, MG 36301-160, Brazil; Postgraduate Programme in Zoology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627, Belo Horizonte, MG 31270-010, Brazil.
| | - Elisa K S Ramos
- Faculty of Philosophy and Natural Sciences, Department of Environmental Sciences, University of Basel, Bernoullistrasse 30, Basel 4056, Switzerland.
| | - Lucas N Bandeira
- Postgraduate Programme in Ecology, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil.
| | - Johnny S Ferreira
- Postgraduate Programme in Genetics, Department of Genetics, Biological Sciences Sector, Universidade Federal do Paraná, Caixa Postal 19071, Curitiba, PR 81531-980, Brazil.
| | - Fernanda P Werneck
- Postgraduate Programme in Ecology, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil; Scientific Biological Collections Program, Biodiversity Coordination, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil.
| | - Marina Anciães
- Postgraduate Programme in Ecology, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil; Scientific Biological Collections Program, Biodiversity Coordination, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil.
| | - Daniel P Bruschi
- Postgraduate Programme in Genetics, Department of Genetics, Biological Sciences Sector, Universidade Federal do Paraná, Caixa Postal 19071, Curitiba, PR 81531-980, Brazil.
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de Carvalho DL, Silva SM, Sousa-Neves T, Gonçalves GSR, Silva DP, Santos MPD. Predicting the future of threatened birds from a Neotropical ecotone area. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 196:61. [PMID: 38110623 DOI: 10.1007/s10661-023-12174-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 11/22/2023] [Indexed: 12/20/2023]
Abstract
Climate change affects ecosystems in different ways. These effects are particularly worrying in the Neotropical region, where species are most vulnerable to these changes because they live closer to their thermal safety limits. Thus, establishing conservation priorities, particularly for the definition of protected areas (PAs), is a priority. However, some PA systems within the Neotropics are ineffective even under the present environmental conditions. Here, we test the effectiveness of a PA system, within an ecotone in northern Brazil, in protecting 24 endangered bird species under current and future (RCP8.5) climatic scenarios. We used species distribution modeling and dispersal corridor modeling to describe the priority areas for conservation of these species. Our results indicate that several threatened bird taxa are and will potentially be protected (i.e., occur within PAs). Nonetheless, the amount of protected area is insufficient to maintain the species in the ecotone. Moreover, most taxa will probably present drastic declines in their range sizes; some are even predicted to go globally extinct soon. Thus, we highlight the location of a potentially effective system of dispersal corridors that connects PAs in the ecotone. We reinforce the need to implement public policies and raise public awareness to maintain PAs and mitigate anthropogenic effects within them, corridors, and adjacent areas, aiming to conserve the richness and diversity of these already threatened species.
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Affiliation(s)
- Dorinny Lisboa de Carvalho
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará, Museu Paraense Emílio Goeldi, Av. Augusto Corrêa 01, Guamá, Belém, PA, CEP 66075-110, Brazil.
| | - Sofia Marques Silva
- Coordenação em Zoologia, Museu Paraense Emílio Goeldi, Av. Perimetral, 1901, Terra Firme, Belém, PA, CEP 66077 830, Brazil
| | - Tiago Sousa-Neves
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará, Museu Paraense Emílio Goeldi, Av. Augusto Corrêa 01, Guamá, Belém, PA, CEP 66075-110, Brazil
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Rua Padre Armando Quintas, 07, 4485-661, Vairão, Portugal
| | - Gabriela Silva Ribeiro Gonçalves
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará, Museu Paraense Emílio Goeldi, Av. Augusto Corrêa 01, Guamá, Belém, PA, CEP 66075-110, Brazil
| | - Daniel Paiva Silva
- COBIMA Lab, Departamento de Ciências Biológicas, Instituto Federal Goiano, IF Goiano, Rodovia Geraldo Silva Nascimento, KM 2,5 Zona Rural, Urutaí, GO, CEP 75790-000, Brazil
| | - Marcos Pérsio Dantas Santos
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará, Museu Paraense Emílio Goeldi, Av. Augusto Corrêa 01, Guamá, Belém, PA, CEP 66075-110, Brazil
- Instituto de Ciências Biológicas, Faculdade de Ciências Biológicas, Universidade Federal do Pará, Av. Augusto Corrêa 01, Guamá, Belém, PA, CEP 66075-110, Brazil
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8
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Bocalini F, Bolívar-Leguizamón SD, Silveira LF, Bravo GA. Amazonian colonization from the Atlantic Forest: New perspectives on the connections of South American tropical forests. Mol Ecol 2023; 32:6874-6895. [PMID: 37902123 DOI: 10.1111/mec.17180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/31/2023]
Abstract
An open and dry vegetation belt separates Amazonia (AM) and the Atlantic Forest (AF). Evidence from palaeoclimatic and phylogenetic studies suggests past connections between these forests during cycles of increased humidity through the formation of forest corridors. The distinctive northern AF avifauna is known to have affinities both with AM and the southern AF. Still, the extent of how these two regions contributed to the assemblage of this avifauna remains poorly understood. Using historical demographic analyses and comparative phylogeography based on sub-genomic genetic sampling, we assessed how past connections between AM and AF led to shared vicariance and colonization events in four avian AF endemic taxa. Our results supported the occurrence of humid forest corridors promoting the contact between AF and AM populations and suggested two vicariant events and two colonization events from AF to AM. Population divergences were mostly non-synchronous and occurred multiple times during the Pleistocene. Historical gene flow was prevalent across study groups, supporting migration flows after the initial separation between AM and AF - a pattern previously unknown in birds between these regions. Idiosyncratic histories and divergent demographic syndromes suggest that organisms' responses to climate-driven habitat shifts broadly depend on their ecological attributes. This study strengthened our knowledge of past connections between AM and AF and provided demographic scenarios amenable for testing in other groups of co-distributed organisms.
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Affiliation(s)
| | - Sergio D Bolívar-Leguizamón
- Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Ciências Biológicas, Escola Superior de Agricultura 'Luiz de Queiroz' - ESALQ - Universidade de São Paulo, Piracicaba, Brazil
| | - Luís F Silveira
- Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil
| | - Gustavo A Bravo
- Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil
- Department of Organismic and Evolutionary Biology & Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
- Colecciones Ornitológicas, Centro de Colecciones y Gestión de Especies, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Boyacá, Colombia
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9
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Nunes SPDQ, França MC, Cohen MCL, Pessenda LCR, Rodrigues ESF, Magalhães EAS, Silva FAB. Assessment the Impacts of Sea-Level Changes on Mangroves of Ceará-Mirim Estuary, Northeastern Brazil, during the Holocene and Anthropocene. PLANTS (BASEL, SWITZERLAND) 2023; 12:1721. [PMID: 37111944 PMCID: PMC10141466 DOI: 10.3390/plants12081721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/16/2023] [Accepted: 04/17/2023] [Indexed: 06/19/2023]
Abstract
Predictions of the effects of modern Relative Sea-Level (RSL) rise on mangroves should be based on decadal-millennial mangrove dynamics and the particularities of each depositional environment under past RSL changes. This work identified inland and seaward mangrove migrations along the Ceará-Mirim estuary (Rio Grande do Norte, northeastern Brazil) during the mid-late Holocene and Anthropocene based on sedimentary features, palynological, and geochemical (δ13C, δ15N, C/N) data integrated with spatial-temporal analysis based on satellite images. The data indicated three phases for the mangrove development: (1°) mangrove expansion on tidal flats with estuarine organic matter between >4420 and ~2870 cal yrs BP, under the influence of the mid-Holocene sea-level highstand; (2°) mangrove contraction with an increased contribution of C3 terrestrial plants between ~2870 and ~84 cal yrs BP due to an RSL fall, and (3°) mangrove expansion onto the highest tidal flats since ~84 cal yr BP due to a relative sea-level rise. However, significant mangrove areas were converted to fish farming before 1984 CE. Spatial-temporal analysis also indicated a mangrove expansion since 1984 CE due to mangrove recolonization of shrimp farming areas previously deforested for pisciculture. This work mainly evidenced a trend of mangrove expansion due to RSL rise preceding the effects of anthropogenic emissions of CO2 in the atmosphere and the resilience of these forests in the face of anthropogenic interventions.
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Affiliation(s)
- Sérgio. P. D. Q. Nunes
- Laboratory of Coastal Dynamics, Graduate Program of Geology and Geochemistry, Federal University of Pará, Belém 66075-110, PA, Brazil
| | - Marlon C. França
- Laboratory of Coastal Dynamics, Graduate Program of Geology and Geochemistry, Federal University of Pará, Belém 66075-110, PA, Brazil
- Federal Institute of Espírito Santo, Piúma 29285-000, ES, Brazil
| | - Marcelo C. L. Cohen
- Laboratory of Coastal Dynamics, Graduate Program of Geology and Geochemistry, Federal University of Pará, Belém 66075-110, PA, Brazil
- Department of Oceanography and Coastal Sciences, College of the Coast and Environment, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Luiz C. R. Pessenda
- CENA/14C Laboratory, University of São Paulo, Av. Centenário 303, Piracicaba 13400-000, SP, Brazil
| | - Erika S. F. Rodrigues
- Laboratory of Coastal Dynamics, Graduate Program of Geology and Geochemistry, Federal University of Pará, Belém 66075-110, PA, Brazil
| | - Evandro A. S. Magalhães
- CENA/14C Laboratory, University of São Paulo, Av. Centenário 303, Piracicaba 13400-000, SP, Brazil
| | - Fernando A. B. Silva
- Laboratory of Coastal Dynamics, Graduate Program of Geology and Geochemistry, Federal University of Pará, Belém 66075-110, PA, Brazil
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Fisher GB, Luna LV, Amidon WH, Burbank DW, de Boer B, Stap LB, Bookhagen B, Godard V, Oskin ME, Alonso RN, Tuenter E, Lourens LJ. Milankovitch-paced erosion in the southern Central Andes. Nat Commun 2023; 14:424. [PMID: 36702814 PMCID: PMC9880006 DOI: 10.1038/s41467-023-36022-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/11/2023] [Indexed: 01/27/2023] Open
Abstract
It has long been hypothesized that climate can modify both the pattern and magnitude of erosion in mountainous landscapes, thereby controlling morphology, rates of deformation, and potentially modulating global carbon and nutrient cycles through weathering feedbacks. Although conceptually appealing, geologic evidence for a direct climatic control on erosion has remained ambiguous owing to a lack of high-resolution, long-term terrestrial records and suitable field sites. Here we provide direct terrestrial field evidence for long-term synchrony between erosion rates and Milankovitch-driven, 400-kyr eccentricity cycles using a Plio-Pleistocene cosmogenic radionuclide paleo-erosion rate record from the southern Central Andes. The observed climate-erosion coupling across multiple orbital cycles, when combined with results from the intermediate complexity climate model CLIMBER-2, are consistent with the hypothesis that relatively modest fluctuations in precipitation can cause synchronous and nonlinear responses in erosion rates as landscapes adjust to ever-evolving hydrologic boundary conditions imposed by oscillating climate regimes.
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Affiliation(s)
- G. Burch Fisher
- grid.89336.370000 0004 1936 9924Jackson School of Geosciences, University of Texas at Austin, Austin, TX 78712 USA ,grid.133342.40000 0004 1936 9676Earth Research Institute, University of California, Santa Barbara, CA 93106 USA
| | - Lisa V. Luna
- grid.11348.3f0000 0001 0942 1117Institute of Environmental Science and Geography, University of Potsdam, Potsdam, Germany
| | - William H. Amidon
- grid.260002.60000 0000 9743 9925Department of Earth and Climate Sciences, Middlebury College, Middlebury, VT 05753 USA
| | - Douglas W. Burbank
- grid.133342.40000 0004 1936 9676Earth Research Institute, University of California, Santa Barbara, CA 93106 USA
| | - Bas de Boer
- grid.12380.380000 0004 1754 9227Earth and Climate Cluster, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Lennert B. Stap
- grid.5477.10000000120346234Institute for Marine and Atmospheric Research, Utrecht University, Utrecht, the Netherlands
| | - Bodo Bookhagen
- grid.11348.3f0000 0001 0942 1117Institute of Geoscience, University of Potsdam, Potsdam, Germany
| | - Vincent Godard
- grid.498067.40000 0001 0845 4216Aix-Marseille Univ., CNRS, IRD, INRAE, CEREGE, Aix-en-Provence, France ,grid.440891.00000 0001 1931 4817Institut Universitaire de France, Paris, France
| | - Michael E. Oskin
- grid.27860.3b0000 0004 1936 9684Department of Earth and Planetary Sciences, University of California, Davis, CA USA
| | - Ricardo N. Alonso
- grid.10821.3a0000 0004 0490 9553Universidad Nacional de Salta, Salta, Argentina
| | - Erik Tuenter
- grid.8653.80000000122851082Royal Netherlands Meteorological Institute (KNMI), De Bilt, the Netherlands
| | - Lucas J. Lourens
- grid.5477.10000000120346234Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, the Netherlands
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11
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Fang J, Tan X, Yang Z, Shen W, Peñuelas J. Contrasting terpene emissions from canopy and understory vegetation in response to increases in nitrogen deposition and seasonal changes in precipitation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120800. [PMID: 36473640 DOI: 10.1016/j.envpol.2022.120800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Given global change and shifts in climate are expected to increase BVOC emissions, the quantification of links between environmental conditions, plant physiology, and terpene emission dynamics is required to improve model predictions of ecosystem responses to increasing nitrogen deposition and changes in precipitation regimes. Here, we conducted a two-factor field experiment in sub-tropical forest plots to determine effects of N addition (N), precipitation change (PC), and NP (N and PC combined treatment) on wet and dry season terpene emissions and leaf photosynthetic parameters from canopy and understory species. Changes of β-ocimene and sabinene under PC and NP in the wet season (0.4-5.6-fold change) were the largest contributor to changes in total terpene emissions. In the dry season, the standardized total terpene emission rate was enhanced by 144.9% under N addition and 185.7% under PC for the understory species, while the total terpene emission rate was lower under NP than N addition and PC, indicating that N addition tended to moderate increases in PC-induced understory total terpene emissions. In the wet season, the total terpene emission rate under N and PC was close to ambient conditions for the canopy species, while the total terpene emission rate was enhanced by 54.6% under NP, indicating that N and PC combined treatment had an additive effect on canopy total terpene emissions. Total terpene emission rates increased with rates of net leaf photosynthesis (Pn) and transpiration (Tr) and there was a decoupling between terpene emission rates and Pn under NP, indicating that complex effects between PC and N decreased the regularity of single-factor effects. We recommend that N and PC interaction effects are included in models for the prediction of terpene emissions, particularly from canopy vegetation during the wet season as a major source of forest ecosystem terpene emissions.
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Affiliation(s)
- Jianbo Fang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangping Tan
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Ziyin Yang
- University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Weijun Shen
- Guangxi Key Laboratory of Forest Ecology and Conservation, State Key Laboratory for Conservation and Utilization of Agro-bioresources, College of Forestry, Guangxi University, Nanning, Guangxi, 530004, China.
| | - Josep Peñuelas
- CREAF, Campus Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, 08193, Catalonia, Spain; CSIC, Global Ecology Unit CREAF - CSIC-UAB, Bellaterra, Barcelona, 08193, Catalonia, Spain
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12
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Luna LW, Naka LN, Thom G, Knowles LL, Sawakuchi AO, Aleixo A, Ribas CC. Late Pleistocene landscape changes and habitat specialization as promoters of population genomic divergence in Amazonian floodplain birds. Mol Ecol 2023; 32:214-228. [PMID: 36261866 DOI: 10.1111/mec.16741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/28/2022] [Accepted: 10/06/2022] [Indexed: 12/29/2022]
Abstract
Although vicariant processes are expected to leave similar genomic signatures among codistributed taxa, ecological traits such as habitat and stratum can influence genetic divergence within species. Here, we combined landscape history and habitat specialization to understand the historical and ecological factors responsible for current levels of genetic divergence in three species of birds specialized in seasonally flooded habitats in muddy rivers and which are widespread in the Amazon basin but have isolated populations in the Rio Branco. Populations of the white-bellied spinetail (Mazaria propinqua), lesser wagtail-tyrant (Stigmatura napensis) and bicolored conebill (Conirostrum bicolor) are currently isolated in the Rio Branco by the black-waters of the lower Rio Negro, offering a unique opportunity to test the effect of river colour as a barrier to gene flow. We used ultraconserved elements (UCEs) to test alternative hypotheses of population history in a comparative phylogeographical approach by modelling genetic structure, demographic history and testing for shared divergence time among codistributed taxa. Our analyses revealed that (i) all three populations from the Rio Branco floodplains are genetically distinct from other populations along the Amazon River floodplains; (ii) these divergences are the result of at least two distinct events, consistent with species habitat specialization; and (iii) the most likely model of population evolution includes lower population connectivity during the Late Pleistocene transition (~250,000 years ago), with gene flow being completely disrupted after the Last Glacial Maximum (~21,000 years ago). Our findings highlight how landscape evolution modulates population connectivity in habitat specialist species and how organisms can have different responses to the same historical processes of environmental change, depending on their habitat affinity.
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Affiliation(s)
- Leilton Willians Luna
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA.,Department of Zoology, Universidade Federal do Pará/Emílio Goeldi Museum, Belém, Brazil
| | - Luciano Nicolas Naka
- Laboratory of Avian Ecology and Evolution, Department of Zoology, Universidade Federal do Pernambuco, Recife, Brazil
| | - Gregory Thom
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Laura Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Alexandre Aleixo
- Department of Zoology, Universidade Federal do Pará/Emílio Goeldi Museum, Belém, Brazil.,Instituto Tecnológico Vale, Belém, Brazil.,Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
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13
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Antiphase response of the Indonesian-Australian monsoon to millennial-scale events of the last glacial period. Sci Rep 2022; 12:20214. [PMID: 36424387 PMCID: PMC9691635 DOI: 10.1038/s41598-022-21843-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 10/04/2022] [Indexed: 11/27/2022] Open
Abstract
Antiphase behaviour of monsoon systems in alternate hemispheres is well established at yearly and orbital scales in response to alternating sensible heating of continental landmasses. At intermediate timescales without a sensible heating mechanism both in-phase and antiphase behaviours of northern and southern hemisphere monsoon systems are recorded at different places and timescales. At present, there is no continuous, high resolution, precisely dated record of millennial-scale variability of the Indonesian-Australian monsoon during the last glacial period with which to test theories of paleomonsoon behaviour. Here, we present an extension of the Liang Luar, Flores, speleothem δ18O record of past changes in southern hemisphere summer monsoon intensity back to 55.7 kyr BP. Negative δ18O excursions (stronger monsoon) occur during Heinrich events whereas positive excursions (weaker monsoon) occur during Dansgaard-Oeschger interstadials-a first order antiphase relationship with northern hemisphere summer monsoon records. An association of negative δ18O excursions with speleothem growth phases in Liang Luar suggests that these stronger monsoons are related to higher rainfall amounts. However, the response to millennial-scale variability is inconsistent, including a particularly weak response to Heinrich event 3. We suggest that additional drivers such as underlying orbital-scale variability and drip hydrology influence the δ18O response.
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14
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Ortiz DA, Hoskin CJ, Werneck FP, Réjaud A, Manzi S, Ron SR, Fouquet A. Historical biogeography highlights the role of Miocene landscape changes on the diversification of a clade of Amazonian tree frogs. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00588-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe diversification processes underlying why Amazonia hosts the most species-rich vertebrate fauna on earth remain poorly understood. We studied the spatio-temporal diversification of a tree frog clade distributed throughout Amazonia (Anura: Hylidae: Osteocephalus, Tepuihyla, and Dryaderces) and tested the hypothesis that Miocene mega wetlands located in western and central Amazonia impacted connectivity among major biogeographic areas during extensive periods. We assessed the group’s diversity through DNA-based (16S rRNA) species delimitation to identify Operational Taxonomic Units (OTUs) from 557 individuals. We then selected one terminal for each OTU (n = 50) and assembled a mitogenomic matrix (~14,100 bp; complete for 17 terminals) to reconstruct a Bayesian, time-calibrated phylogeny encompassing nearly all described species. Ancestral area reconstruction indicates that each genus was restricted to one of the major Amazonian biogeographic areas (western Amazonia, Guiana Shield and Brazilian Shield, respectively) between ~10 and 20 Mya, suggesting that they diverged and diversified in isolation during this period around the Pebas mega wetland. After 10 Mya and the transition to the modern configuration of the Amazon River watershed, most speciation within each genus continued to occur within each area. In Osteocephalus, only three species expanded widely across Amazonia (< 6 Mya), and all were pond-breeders. Species with other breeding modes remained mostly restricted to narrow ranges. The spectacular radiation of Osteocephalus was probably driven by climatic stability, habitat diversity and the acquisition of new reproductive modes along the Andean foothills and western Amazonia. Our findings add evidence to the importance of major hydrological changes during the Miocene on biotic diversification in Amazonia.
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15
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Abstract
The widely accepted “Milankovitch theory” explains insolation-induced waxing and waning of the ice sheets and their effect on the global climate on orbital timescales. In the past half century, however, the theory has often come under scrutiny, especially regarding its “100-ka problem.” Another drawback, but the one that has received less attention, is the “monsoon problem,” which pertains to the exclusion of monsoon dynamics in classic Milankovitch theory even though the monsoon prevails over the vast low-latitude (∼30° N to ∼30° S) region that covers half of the Earth’s surface and receives the bulk of solar radiation. In this review, we discuss the major issues with the current form of Milankovitch theory and the progress made at the research forefront. We suggest shifting the emphasis from the ultimate outcomes of the ice volume to the causal relationship between changes in northern high-latitude insolation and ice age termination events (or ice sheet melting rate) to help reconcile the classic “100-ka problem.” We discuss the discrepancies associated with the characterization of monsoon dynamics, particularly the so-called “sea-land precession-phase paradox” and the “Chinese 100-ka problem.” We suggest that many of these discrepancies are superficial and can be resolved by applying a holistic “monsoon system science” approach. Finally, we propose blending the conventional Kutzbach orbital monsoon hypothesis, which calls for summer insolation forcing of monsoons, with Milankovitch theory to formulate a combined “Milankovitch-Kutzbach hypothesis” that can potentially explain the dual nature of orbital hydrodynamics of the ice sheet and monsoon systems, as well as their interplays and respective relationships with the northern high-latitude insolation and inter-tropical insolation differential. Orbital-scale climate variations of Earth are dictated by ice sheet and monsoon Views of “monsoon system science” reinforce the Kutzbach monsoon hypothesis A unified Milankovitch-Kutzbach hypothesis better explains the orbital dual nature
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16
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Dong X, Kathayat G, Rasmussen SO, Svensson A, Severinghaus JP, Li H, Sinha A, Xu Y, Zhang H, Shi Z, Cai Y, Pérez-Mejías C, Baker J, Zhao J, Spötl C, Columbu A, Ning Y, Stríkis NM, Chen S, Wang X, Gupta AK, Dutt S, Zhang F, Cruz FW, An Z, Lawrence Edwards R, Cheng H. Coupled atmosphere-ice-ocean dynamics during Heinrich Stadial 2. Nat Commun 2022; 13:5867. [PMID: 36195764 PMCID: PMC9532435 DOI: 10.1038/s41467-022-33583-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/23/2022] [Indexed: 11/09/2022] Open
Abstract
Our understanding of climate dynamics during millennial-scale events is incomplete, partially due to the lack of their precise phase analyses under various boundary conditions. Here we present nine speleothem oxygen-isotope records from mid-to-low-latitude monsoon regimes with sub-centennial age precision and multi-annual resolution, spanning the Heinrich Stadial 2 (HS2) - a millennial-scale event that occurred at the Last Glacial Maximum. Our data suggests that the Greenland and Antarctic ice-core chronologies require +320- and +400-year adjustments, respectively, supported by extant volcanic evidence and radiocarbon ages. Our chronological framework shows a synchronous HS2 onset globally. Our records precisely characterize a centennial-scale abrupt "tropical atmospheric seesaw" superimposed on the conventional "bipolar seesaw" at the beginning of HS2, implying a unique response/feedback from low-latitude hydroclimate. Together with our observation of an early South American monsoon shift at the HS2 termination, we suggest a more active role of low-latitude hydroclimate dynamics underlying millennial events than previously thought.
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Affiliation(s)
- Xiyu Dong
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Gayatri Kathayat
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an, 710049, China.
| | - Sune O Rasmussen
- Physics of Ice, Climate and Earth, Niels Bohr Institute, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Anders Svensson
- Physics of Ice, Climate and Earth, Niels Bohr Institute, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Jeffrey P Severinghaus
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
| | - Hanying Li
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Ashish Sinha
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an, 710049, China.,Department of Earth Science, California State University, Carson, CA, 90747, USA
| | - Yao Xu
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Haiwei Zhang
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Zhengguo Shi
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an, 710049, China.,State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, 710061, China.,Center for Excellence in Quaternary Science and Global Change, Chinese Academy of Sciences, Xi'an, 710061, China
| | - Yanjun Cai
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Carlos Pérez-Mejías
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Jonathan Baker
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Jingyao Zhao
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Christoph Spötl
- Institute of Geology, University of Innsbruck, 6020, Innsbruck, Austria
| | - Andrea Columbu
- Department of Earth Sciences, University of Pisa, Via Santa Maria 53, 56126, Pisa (PI), Italy
| | - Youfeng Ning
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Nicolás M Stríkis
- Department of Geochemistry, Universidade Federal Fluminense, Niterói, 24020-141, Brazil
| | - Shitao Chen
- School of Geography, Nanjing Normal University, Nanjing, 210023, China.,Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Ministry of Education, Nanjing, 210023, China.,Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, 210023, China
| | - Xianfeng Wang
- Earth Observatory of Singapore and Asian School of the Environment, Nanyang Technological University, Singapore, 639798, Singapore
| | - Anil K Gupta
- Department of Geology and Geophysics, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Som Dutt
- Wadia Institute of Himalayan Geology, Dehradun, 248001, India
| | - Fan Zhang
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Francisco W Cruz
- Instituto de Geociências, Universidade de São Paulo, São Paulo, 05508-090, Brazil
| | - Zhisheng An
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, 710061, China
| | - R Lawrence Edwards
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Hai Cheng
- Institute of Global Environmental Change, Xi'an Jiaotong University, Xi'an, 710049, China. .,State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, 710061, China. .,Key Laboratory of Karst Dynamics, MLR, Institute of Karst Geology, CAGS, Guilin, 541004, China.
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17
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Pereira AG, da Silva Ferreira MF, da Silveira TC, Soler-Guilhen JH, Canal GB, Alves LB, de Almeida FAN, Gaiotto FA, Ferreira A. Patterns of genetic diversity and structure of a threatened palm species (Euterpe edulis Arecaceae) from the Brazilian Atlantic Forest. Heredity (Edinb) 2022; 129:161-168. [PMID: 35697755 PMCID: PMC9411632 DOI: 10.1038/s41437-022-00549-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/25/2022] [Accepted: 06/01/2022] [Indexed: 11/08/2022] Open
Abstract
The detection of distribution patterns of genetic diversity of plant and animal species has contributed to the understanding of biodiversity and evolutionary history of the Atlantic Forest. We used microsatellite markers to access the genetic diversity and structure of 26 populations and 527 adult individuals of Euterpe edulis, a native palm which is an important food resource for fauna and is intensively exploited due to economic reasons. We found high genetic diversity and inbreeding in all populations analyzed. We report highest rates of inbreeding for this species, which could reflect the anthropic impacts of selective cutting, fragmentation, and change in foraging behavior from pollinators and less availability and mobility of large dispersers. We detected by STRUCTURE, two genetic groups, Northern and Southern, which divide the Brazilian Atlantic Forest geographically. These groups have low genetic admixtures, but we found a region of lineage hybridization in the contact zone with low recent gene flow. Distribution pattern of this species corroborates results from previous studies reporting the Last Glacial Maximum (LGM) have shaped the structuring of the species through movements of forests' expansion and contraction. The STRUCTURE analysis of each group revealed the presence of genetic subgroups with low rates of recurrent gene flow. Southern subgroups have higher rates of admixtures than the Northern subgroups, revealing greater historical connectivity of forests in this region.
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Affiliation(s)
| | | | | | | | | | | | | | - Fernanda Amato Gaiotto
- Department of Biological Sciences, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - Adésio Ferreira
- Department of Agronomy, Universidade Federal do Espírito Santo, Alegre, Brazil
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18
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Sawakuchi AO, Schultz ED, Pupim FN, Bertassoli DJ, Souza DF, Cunha DF, Mazoca CE, Ferreira MP, Grohmann CH, Wahnfried ID, Chiessi CM, Cruz FW, Almeida RP, Ribas CC. Rainfall and sea level drove the expansion of seasonally flooded habitats and associated bird populations across Amazonia. Nat Commun 2022; 13:4945. [PMID: 35999209 PMCID: PMC9399099 DOI: 10.1038/s41467-022-32561-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/05/2022] [Indexed: 01/27/2023] Open
Abstract
Spatial arrangement of distinct Amazonian environments through time and its effect on specialized biota remain poorly known, fueling long-lasting debates about drivers of biotic diversification. We address the late Quaternary sediment deposition that assembled the world's largest seasonally flooded ecosystems. Genome sequencing was used to reconstruct the demographic history of bird species specialized in either early successional vegetation or mature floodplain forests. Sediment deposition that built seasonally flooded habitats accelerated throughout the Holocene (last 11,700 years) under sea level highstand and intensification of the South American Monsoon, at the same time as global increases in atmospheric methane concentration. Bird populations adapted to seasonally flooded habitats expanded due to enlargement of Amazonian river floodplains and archipelagos. Our findings suggest that the diversification of the biota specialized in seasonally flooded habitats is coupled to sedimentary budget changes of large rivers, which rely on combined effects of sea level and rainfall variations. This study found that millennial periods of higher rainfall combined with rising sea level enhanced sediment accumulation in Amazonian rivers valleys. This fuelled synchronous expansion of vegetation adapted to seasonally flooded substrates and its specialized bird populations, showing how global climate changes can affect specific Amazonian species.
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Affiliation(s)
- A O Sawakuchi
- Institute of Geosciences, University of São Paulo, Rua do Lago 562, São Paulo, SP, Brazil.
| | - E D Schultz
- Programa de Pós-Graduação em Biologia (Ecologia), Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Manaus, AM, Brazil.,Department of Ornithology, American Museum of Natural History, 200 Central Park West, New York, NY, USA
| | - F N Pupim
- Departamento de Ciências Ambientais, Universidade Federal de São Paulo (UNIFESP), Rua São Nicolau 210, Diadema, SP, Brazil
| | - D J Bertassoli
- School of Arts, Sciences and Humanities, University of São Paulo, Av. Arlindo Bettio 1000, São Paulo, SP, Brazil
| | - D F Souza
- Gerência de Hidrologia e Gestão Territorial, Serviço Geológico do Brasil (CPRM-SGB), Rua Costa 55, São Paulo, SP, Brazil
| | - D F Cunha
- Programa de Pós-Graduação em Geoquímica e Geotectônica, Institute of Geosciences, University of São Paulo, Rua do Lago 562, São Paulo, SP, Brazil
| | - C E Mazoca
- Institute of Geosciences, University of São Paulo, Rua do Lago 562, São Paulo, SP, Brazil
| | - M P Ferreira
- Programa de Pós-Graduação em Geoquímica e Geotectônica, Institute of Geosciences, University of São Paulo, Rua do Lago 562, São Paulo, SP, Brazil
| | - C H Grohmann
- Institute of Energy and Environment, University of São Paulo, Av. Prof. Luciano Gualberto 1289, São Paulo, SP, Brazil
| | - I D Wahnfried
- Departamento de Geociências, Universidade Federal do Amazonas, Av. Gen. Rodrigo Octávio Jordão Ramos 6200, Manaus, AM, Brazil
| | - C M Chiessi
- School of Arts, Sciences and Humanities, University of São Paulo, Av. Arlindo Bettio 1000, São Paulo, SP, Brazil
| | - F W Cruz
- Institute of Geosciences, University of São Paulo, Rua do Lago 562, São Paulo, SP, Brazil
| | - R P Almeida
- Institute of Geosciences, University of São Paulo, Rua do Lago 562, São Paulo, SP, Brazil
| | - C C Ribas
- Programa de Pós-Graduação em Biologia (Ecologia), Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Manaus, AM, Brazil.,Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Manaus, AM, Brazil
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19
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Cronemberger ÁA, Werneck FP, Ávila-Pires TCS. Phylogeography of a Typical Forest Heliothermic Lizard Reveals the Combined Influence of Rivers and Climate Dynamics on Diversification in Eastern Amazonia. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.777172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The formation of the Amazon drainage basin has been considered an important driver of speciation of several taxa, promoting vicariant events or reinforcement of barriers that restrict gene flow between opposite river margins. Several recent studies reported a set of miscellaneous events involving climatic fluctuations, geomorphological changes, and dispersal mechanisms as propellers of diversification of Amazonian rainforest taxa. Here, we show the results of dated phylogenetic, biogeographic, and populational analyses to investigate which events could better explain the current distribution of a heliothermic, active foraging lizard in the central and eastern portions of the Amazonian rainforest (besides a disjunct distribution in part of the Atlantic Forest). We sampled Kentropyx calcarata from most of its area of occurrence in Amazonia and used mitochondrial and nuclear markers to evaluate if the genetic structure agrees with evolutionary scenarios previously proposed for Amazonia. We performed phylogenetic and populational analyses to better understand the dynamics of this species in the Amazonia rainforest over time. Phylogenetic inference recovered ten K. calcarata structured lineages in eastern Amazonia, some of them limited by the Amazon River and its southern tributaries (Tapajós, Xingu, and Tocantins), although we detected occasional haplotype sharing across some of the river banks. According to molecular dating, K. calcarata diversified since Miocene–Pliocene, and some of the lineages presented signs of demographic expansion during the Pleistocene, supposedly triggered by climatic dynamics. The putative ancestral lineage of K. calcarata was distributed on the Guiana Shield, later spreading south and southeastward by dispersion. Our results indicate that Amazonian rivers acted as barriers to the dispersal of Kentropyx calcarata, but they were not the sole drivers of diversification.
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20
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Trivedi P, Batista BD, Bazany KE, Singh BK. Plant-microbiome interactions under a changing world: responses, consequences and perspectives. THE NEW PHYTOLOGIST 2022; 234:1951-1959. [PMID: 35118660 DOI: 10.1111/nph.18016] [Citation(s) in RCA: 112] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/19/2022] [Indexed: 05/07/2023]
Abstract
Climate change is increasing global temperatures and the frequency and severity of droughts in many regions. These anthropogenic stresses pose a significant threat to plant performance and crop production. The plant-associated microbiome modulates the impacts of biotic and abiotic stresses on plant fitness. However, climate change-induced alteration in composition and activities of plant microbiomes can affect host functions. Here, we highlight recent advancements in our understanding of the impact of climate change (warming and drought) on plant-microbiome interactions and on their ecological functions from genome to ecosystem scales. We identify knowledge gaps, propose new concepts and make recommendations for future research directions. It is proposed that in the short term (years to decades), the adaptation of plants to climate change is mainly driven by the plant microbiome, whereas in the long term (century to millennia), the adaptation of plants will be driven equally by eco-evolutionary interactions between the plant microbiome and its host. A better understanding of the response of the plant and its microbiome interactions to climate change and the ways in which microbiomes can mitigate the negative impacts will better inform predictions of climate change impacts on primary productivity and aid in developing management and policy tools to improve the resilience of plant systems.
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Affiliation(s)
- Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Bruna D Batista
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2751, Australia
| | - Kathryn E Bazany
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2751, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Richmond, NSW, 2751, Australia
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21
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Cavender-Bares J, Schneider FD, Santos MJ, Armstrong A, Carnaval A, Dahlin KM, Fatoyinbo L, Hurtt GC, Schimel D, Townsend PA, Ustin SL, Wang Z, Wilson AM. Integrating remote sensing with ecology and evolution to advance biodiversity conservation. Nat Ecol Evol 2022; 6:506-519. [PMID: 35332280 DOI: 10.1038/s41559-022-01702-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 02/10/2022] [Indexed: 12/31/2022]
Abstract
Remote sensing has transformed the monitoring of life on Earth by revealing spatial and temporal dimensions of biological diversity through structural, compositional and functional measurements of ecosystems. Yet, many aspects of Earth's biodiversity are not directly quantified by reflected or emitted photons. Inclusive integration of remote sensing with field-based ecology and evolution is needed to fully understand and preserve Earth's biodiversity. In this Perspective, we argue that multiple data types are necessary for almost all draft targets set by the Convention on Biological Diversity. We examine five key topics in biodiversity science that can be advanced by integrating remote sensing with in situ data collection from field sampling, experiments and laboratory studies to benefit conservation. Lowering the barriers for bringing these approaches together will require global-scale collaboration.
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Affiliation(s)
| | - Fabian D Schneider
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | | | - Amanda Armstrong
- Biospheric Sciences Laboratory, NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - Ana Carnaval
- Department of Biology, Ph.D. Program in Biology, City University of New York and The Graduate Center of CUNY, New York City, NY, USA
| | - Kyla M Dahlin
- Department of Geography, Environment, and Spatial Sciences, Michigan State University, East Lansing, MI, USA
| | - Lola Fatoyinbo
- Biospheric Sciences Laboratory, NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - George C Hurtt
- Department of Geographical Sciences, University of Maryland, College Park, MD, USA
| | - David Schimel
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Philip A Townsend
- Department of Forest and Wildlife Ecology, Univ. of Wisconsin-Madison, Madison, WI, USA
| | - Susan L Ustin
- Department of Land, Air and Water Resources and the John Muir Institute of the Environment, University of California, Davis, CA, USA
| | - Zhihui Wang
- Key Lab of Guangdong for Utilization of Remote Sensing and Geographical Information System, Guangdong Open Laboratory of Geospatial Information Technology and Application, Guangzhou Institute of Geography, Guangdong Academy of Sciences, Guangzhou, China
| | - Adam M Wilson
- Department of Geography, University at Buffalo, Buffalo, NY, USA
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22
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Bush MB, Rozas-Davila A, Raczka M, Nascimento M, Valencia B, Sales RK, McMichael CNH, Gosling WD. A palaeoecological perspective on the transformation of the tropical Andes by early human activity. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200497. [PMID: 35249394 PMCID: PMC8899620 DOI: 10.1098/rstb.2020.0497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Palaeoecological records suggest that humans have been in the Andes since at least 14 000 years ago. Early human impacts on Andean ecosystems included an increase in fire activity and the extinction of the Pleistocene megafauna. These changes in Andean ecosystems coincided with rapid climate change as species were migrating upslope in response to deglacial warming. Microrefugia probably played a vital role in the speed and genetic composition of that migration. The period from ca 14 500 to 12 500 years ago was when novel combinations of plant species appeared to form no-analogue assemblages in the Andes. By 12 000 years ago most areas in what are today the Andean grasslands were being burned and modified by human activity. As the vegetation of these highland settings has been modified by human activity for the entirety of the Holocene, they should be regarded as long-term manufactutred landscapes. The sharp tree lines separating Andean forests from grasslands that we see today were probably also created by repeated burning and owe their position more to human-induced fire than climatic constraints. In areas that were readly penetrated by humans on the forested slopes of the Andes, substantial modification and settlement had occurred by the mid-Holocene. In hard-to-reach areas, however, the amount of human modification may always have been minimal, and these slopes can be considered as being close to natural in their vegetation. This article is part of the theme issue 'Tropical forests in the deep human past'.
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Affiliation(s)
- M B Bush
- Institute for Global Ecology, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - A Rozas-Davila
- Institute for Global Ecology, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - M Raczka
- Department of Geography and Environmental Science, University of Reading, Whiteknights, Reading, Berkshire RG6 6AH, UK
| | - M Nascimento
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 904 Science Park, 1098 XH, Amsterdam, Netherlands
| | - B Valencia
- Facultad de Ciencias de la Tierra y Agua, Ciencias de la Tierra y Clima, Universidad Regional Amazónica Ikiam, Tena, Ecuador
| | - R K Sales
- Institute for Global Ecology, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - C N H McMichael
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 904 Science Park, 1098 XH, Amsterdam, Netherlands
| | - W D Gosling
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 904 Science Park, 1098 XH, Amsterdam, Netherlands
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23
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Coelho FEA, Camurugi F, Marques R, Magalhães FDM, Werneck FP, Garda AA. Historical connections between Atlantic Forest and Amazonia drove genetic and ecological diversity in Lithobates palmipes (Anura, Ranidae). SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2046657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Felipe Eduardo Alves Coelho
- Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Norte, Centro de Biociências, Avenida Senador Salgado Filho, S/N, Lagoa Nova, Natal 59078-900, RN, Brazil
| | - Felipe Camurugi
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Centro de Biociências, Avenida Senador Salgado Filho, S/N, Lagoa Nova, Natal 59078-900, RN, Brazil
| | - Ricardo Marques
- Programa de Pós-Graduação em Ciências Biológicas (Zoologia, Universidade Federal da Paraíba, Centro de Ciências Exatas e da Natureza, Departamento de Sistemática e Ecologia, Campus I – Cidade Universitaria, S/N, Cidade Universitária, João Pessoa 58051-900, Paraíba, Brasil
| | - Felipe De Medeiros Magalhães
- Programa de Pós-Graduação em Ciências Biológicas (Zoologia, Universidade Federal da Paraíba, Centro de Ciências Exatas e da Natureza, Departamento de Sistemática e Ecologia, Campus I – Cidade Universitaria, S/N, Cidade Universitária, João Pessoa 58051-900, Paraíba, Brasil
- Earth and Environmental Sciences, Ecology and Evolution, Rutgers University-Newark, 195 University Ave, Newark 07102, New Jersey NJ, USA
| | - Fernanda P. Werneck
- Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo 2936, Aleixo, Manaus 69067-375, Amazonas, Brazil
| | - Adrian Antonio Garda
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Centro de Biociências, Avenida Senador Salgado Filho, S/N, Lagoa Nova, Natal 59078-900, RN, Brazil
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24
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Pereira EA, Ceron K, Silva HR, Santana DJ. The dispersal between Amazonia and Atlantic Forest during the Early Neogene revealed by the biogeography of the treefrog tribe Sphaenorhynchini (Anura, Hylidae). Ecol Evol 2022; 12:e8754. [PMID: 35386873 PMCID: PMC8975791 DOI: 10.1002/ece3.8754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 01/18/2022] [Accepted: 03/04/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Elvis Almeida Pereira
- Laboratório de Herpetologia Departamento de Biologia Animal Universidade Federal Rural do Rio de Janeiro Rio de Janeiro Brazil
- Mapinguari ‐ Laboratório de Biogeografia e Sistemática de Anfíbios e Répteis Universidade Federal de Mato Grosso do Sul Campo Grande Brazil
- Laboratório de Genética e Biodiversidade Universidade Federal do Oeste do Pará Santarém Brazil
| | - Karoline Ceron
- Mapinguari ‐ Laboratório de Biogeografia e Sistemática de Anfíbios e Répteis Universidade Federal de Mato Grosso do Sul Campo Grande Brazil
- Departamento de Biologia Animal Universidade Estadual de Campinas (UNICAMP) São Paulo Brazil
| | - Hélio Ricardo Silva
- Laboratório de Herpetologia Departamento de Biologia Animal Universidade Federal Rural do Rio de Janeiro Rio de Janeiro Brazil
| | - Diego José Santana
- Mapinguari ‐ Laboratório de Biogeografia e Sistemática de Anfíbios e Répteis Universidade Federal de Mato Grosso do Sul Campo Grande Brazil
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25
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Pirani RM, Tonini JFR, Thomaz AT, Napoli MF, Encarnação LC, Knowles LL, Werneck FP. Deep Genomic Divergence and Phenotypic Admixture of the Treefrog Dendropsophus elegans (Hylidae: Amphibia) Coincide With Riverine Boundaries at the Brazilian Atlantic Forest. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.765977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Atlantic Forest (AF) domain is one of the Earth’s biodiversity hotspots, known for its high levels of species diversity and endemism. Factors related to palaeoenvironmental dynamics, such as the establishment of vegetational refugia and river basins, have different impacts on biological communities and biodiversity patterns in this domain. Here, we sample genome-wide RADseq data from a widespread treefrog (Dendropsophus elegans), inhabiting natural and human-impacted ecosystems at the Brazilian AF to test the impact of riverine boundaries and climatic refugia on population structure and diversification. We estimate divergence times and migration rate across identified genetic breaks related to the rivers Doce, Paraíba do Sul, Ribeira de Iguape, and Paraguaçu, known to represent barriers to gene flow for other AF endemic species, and test the role of climatic refugia. Finally, we investigate the impact of spatio-temporal population history on morphological variation in this species. We recovered a phylogeographic history supporting three distinct clades separated into two geographically structured populations, corresponding to the north and south of AF. In addition, we identified an admixture zone between north and south populations in the latitude close to the Doce River. Our findings support a pattern of isolation-by-distance and the existence of a secondary contact zone between populations, which might have been promoted by gene flow during population expansion. Further, we found support for models considering migration parameters for all the tested rivers with different population divergence times. Based on the species history and the AF palaeoenvironmental dynamics, we corroborate the role of forest refugia impacting population structure for this species through recent range expansion after the Last Glacial Maximum (LGM). The Doce and Paraíba do Sul Rivers coincide with the main genetic breaks, suggesting they might also have played a role in the diversification processes. Finally, despite finding subtle correlations for phenotypic data among different populations, variation is not strongly detectable and does not seem associated with speciation-level processes that could warrant taxonomic changes. Such results can be explained by phenotypic plasticity of the evaluated traits and by recent divergence times, where there has been insufficient time and weak selective pressures to accumulate enough phenotypic differences.
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26
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27
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Smith RJ, Singarayer JS, Mayle FE. Response of Amazonian forests to mid-Holocene drought: A model-data comparison. GLOBAL CHANGE BIOLOGY 2022; 28:201-226. [PMID: 34651394 DOI: 10.1111/gcb.15929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 09/22/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
There is a major concern for the fate of Amazonia over the coming century in the face of anthropogenic climate change. A key area of uncertainty is the scale of rainforest dieback to be expected under a future, drier climate. In this study, we use the middle Holocene (ca. 6000 years before present) as an approximate analogue for a drier future, given that palaeoclimate data show much of Amazonia was significantly drier than present at this time. Here, we use an ensemble of climate and vegetation models to explore the sensitivity of Amazonian biomes to mid-Holocene climate change. For this, we employ three dynamic vegetation models (JULES, IBIS, and SDGVM) forced by the bias-corrected mid-Holocene climate simulations from seven models that participated in the Palaeoclimate Modelling Intercomparison Project 3 (PMIP3). These model outputs are compared with a multi-proxy palaeoecological dataset to gain a better understanding of where in Amazonia we have most confidence in the mid-Holocene vegetation simulations. A robust feature of all simulations and palaeodata is that the central Amazonian rainforest biome is unaffected by mid-Holocene drought. Greater divergence in mid-Holocene simulations exists in ecotonal eastern and southern Amazonia. Vegetation models driven with climate models that simulate a drier mid-Holocene (100-150 mm per year decrease) better capture the observed (palaeodata) tropical forest dieback in these areas. Based on the relationship between simulated rainfall decrease and vegetation change, we find indications that in southern Amazonia the rate of tropical forest dieback was ~125,000 km2 per 100 mm rainfall decrease in the mid-Holocene. This provides a baseline sensitivity of tropical forests to drought for this region (without human-driven changes to greenhouse gases, fire, and deforestation). We highlight the need for more palaeoecological and palaeoclimate data across lowland Amazonia to constrain model responses.
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Affiliation(s)
- Richard J Smith
- Department of Geography and Environmental Science, School of Archaeology, Geography and Environmental Science (SAGES), University of Reading, Whiteknights, Reading, UK
| | - Joy S Singarayer
- Department of Meteorology, University of Reading, Whiteknights, Reading, UK
| | - Francis E Mayle
- Department of Geography and Environmental Science, School of Archaeology, Geography and Environmental Science (SAGES), University of Reading, Whiteknights, Reading, UK
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28
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Miyaki CY, Cruz FW, Hickerson M, Michelangeli FA, Pinto-da-Rocha R, Thomas W, Carnaval AC. A multidisciplinary framework for biodiversity prediction in the Brazilian Atlantic Forest hotspot. BIOTA NEOTROPICA 2022. [DOI: 10.1590/1676-0611-bn-2022-1339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract: We briefly describe selected results from our thematic project focused on the biodiversity of the Atlantic Forest (“AF BIOTA”), which was jointly funded by FAPESP’s BIOTA Program, the U.S. National Science Foundation Dimensions of Biodiversity Program, and the National Aeronautics and Space Administration (NASA). As one of the five most important hotspots of biodiversity in the world, the Atlantic Forest (AF) holds less than 16% of its vegetation cover, yet, amongst the hotspots, it still harbors one of the highest numbers of species, including endemics. By gathering specialists across multiple disciplines (biology, geology, engineering), we aimed to understand how this megabiodiversity was built through time, informing biodiversity science and conservation. Among the results, we trained 18 Master’s and 26 Ph.D. students, published more than 400 peer-reviewed papers that improved our knowledge about the forest’s biologic and climatic diversity and dynamics through time, developed new analytical methods, produced outreach videos and articles, and provided data to help define biodiversity conservation policies.
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29
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Rivera D, Prates I, Firneno TJ, Rodrigues MT, Caldwell JP, Fujita MK. Phylogenomics, introgression, and demographic history of South American true toads (Rhinella). Mol Ecol 2021; 31:978-992. [PMID: 34784086 DOI: 10.1111/mec.16280] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/24/2021] [Accepted: 11/11/2021] [Indexed: 11/28/2022]
Abstract
The effects of genetic introgression on species boundaries and how they affect species' integrity and persistence over evolutionary time have received increased attention. The increasing availability of genomic data has revealed contrasting patterns of gene flow across genomic regions, which impose challenges to inferences of evolutionary relationships and of patterns of genetic admixture across lineages. By characterizing patterns of variation across thousands of genomic loci in a widespread complex of true toads (Rhinella), we assess the true extent of genetic introgression across species thought to hybridize to extreme degrees based on natural history observations and multi-locus analyses. Comprehensive geographic sampling of five large-ranged Neotropical taxa revealed multiple distinct evolutionary lineages that span large geographic areas and, at times, distinct biomes. The inferred major clades and genetic clusters largely correspond to currently recognized taxa; however, we also found evidence of cryptic diversity within taxa. While previous phylogenetic studies revealed extensive mito-nuclear discordance, our genetic clustering analyses uncovered several admixed individuals within major genetic groups. Accordingly, historical demographic analyses supported that the evolutionary history of these toads involved cross-taxon gene flow both at ancient and recent times. Lastly, ABBA-BABA tests revealed widespread allele sharing across species boundaries, a pattern that can be confidently attributed to genetic introgression as opposed to incomplete lineage sorting. These results confirm previous assertions that the evolutionary history of Rhinella was characterized by various levels of hybridization even across environmentally heterogeneous regions, posing exciting questions about what factors prevent complete fusion of diverging yet highly interdependent evolutionary lineages.
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Affiliation(s)
- Danielle Rivera
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, TX, USA
| | - Ivan Prates
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Thomas J Firneno
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, TX, USA
| | - Miguel Trefaut Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Janalee P Caldwell
- Sam Noble Museum & Department of Biology, University of Oklahoma, Norman, Oklahoma, 73072-7029, USA
| | - Matthew K Fujita
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, TX, USA
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30
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Globally resolved surface temperatures since the Last Glacial Maximum. Nature 2021; 599:239-244. [PMID: 34759364 DOI: 10.1038/s41586-021-03984-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 09/01/2021] [Indexed: 11/08/2022]
Abstract
Climate changes across the past 24,000 years provide key insights into Earth system responses to external forcing. Climate model simulations1,2 and proxy data3-8 have independently allowed for study of this crucial interval; however, they have at times yielded disparate conclusions. Here, we leverage both types of information using paleoclimate data assimilation9,10 to produce the first proxy-constrained, full-field reanalysis of surface temperature change spanning the Last Glacial Maximum to present at 200-year resolution. We demonstrate that temperature variability across the past 24 thousand years was linked to two primary climatic mechanisms: radiative forcing from ice sheets and greenhouse gases; and a superposition of changes in the ocean overturning circulation and seasonal insolation. In contrast with previous proxy-based reconstructions6,7 our results show that global mean temperature has slightly but steadily warmed, by ~0.5 °C, since the early Holocene (around 9 thousand years ago). When compared with recent temperature changes11, our reanalysis indicates that both the rate and magnitude of modern warming are unusual relative to the changes of the past 24 thousand years.
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Estimation of Current and Future Suitable Areas for Tapirus pinchaque in Ecuador. SUSTAINABILITY 2021. [DOI: 10.3390/su132011486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
At present, climate change is a direct threat to biodiversity and its effects are evidenced by an increasingly accelerated loss of biodiversity. This study identified the main threats presently facing the Tapirus pinchaque species in Ecuador, generated predictive models regarding its distribution, and analyzed the protected areas as a conservation tool. The methodology was based on a literature review and the application of binary predictive models to achieve these objectives. The main results indicate that the T. pinchaque is seriously threatened, mainly by changes in land use. In addition, three models were selected that show current and future suitable areas for the conservation of the species. Its current distribution amounts to 67,805 km2, 33% (22,872 km2) of which is located in 31 of the 61 protected areas. Finally, it is important to take timely actions focused on biodiversity conservation, considering the importance of balance in ecosystems to the humans dependent thereof, and the results regarding the changes in the current and future distribution areas of the mountain tapir are a great contribution to be used as a management tool for its conservation.
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Pre-Columbian fire management and control of climate-driven floodwaters over 3,500 years in southwestern Amazonia. Proc Natl Acad Sci U S A 2021; 118:2022206118. [PMID: 34580203 DOI: 10.1073/pnas.2022206118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2021] [Indexed: 11/18/2022] Open
Abstract
In landscapes that support economic and cultural activities, human communities actively manage environments and environmental change at a variety of spatial scales that complicate the effects of continental-scale climate. Here, we demonstrate how hydrological conditions were modified by humans against the backdrop of Holocene climate change in southwestern Amazonia. Paleoecological investigations (phytoliths, charcoal, pollen, diatoms) of two sediment cores extracted from within the same permanent wetland, ∼22 km apart, show a 1,500-y difference in when the intensification of land use and management occurred, including raised field agriculture, fire regime, and agroforestry. Although rising precipitation is well known during the mid to late Holocene, human actions manipulated climate-driven hydrological changes on the landscape, revealing differing histories of human landscape domestication. Environmental factors are unable to account for local differences without the mediation of human communities that transformed the region to its current savanna/forest/wetland mosaic beginning at least 3,500 y ago. Regional environmental variables did not drive the choices made by farmers and fishers, who shaped these local contexts to better manage resource extraction. The savannas we observe today were created in the post-European period, where their fire regime and structural diversity were shaped by cattle ranching.
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Silva SM, Ribas CC, Aleixo A. Recent population differentiation in the habitat specialist Glossy Antshrike (Aves: Thamnophilidae) across Amazonian seasonally flooded forests. Ecol Evol 2021; 11:11826-11838. [PMID: 34522344 PMCID: PMC8427616 DOI: 10.1002/ece3.7951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 07/11/2021] [Accepted: 07/13/2021] [Indexed: 11/30/2022] Open
Abstract
We assessed population structure and the spatio-temporal pattern of diversification in the Glossy Antshrike Sakesphorus luctuosus (Aves, Thamnophilidae) to understand the processes shaping the evolutionary history of Amazonian floodplains and address unresolved taxonomic controversies surrounding its species limits. By targeting ultraconserved elements (UCEs) from 32 specimens of S. luctuosus, we identified independent lineages and estimated their differentiation, divergence times, and migration rates. We also estimated current and past demographic histories for each recovered lineage. We found evidence confirming that S. luctuosus consists of a single species, comprising at least four populations, with some highly admixed individuals and overall similar levels of migration between populations. We confirmed the differentiation of the Araguaia River basin population (S. l. araguayae) and gathered circumstantial evidence indicating that the taxon S. hagmanni may represent a highly introgressed population between three distinct phylogroups of S. luctuosus. Divergences between populations occurred during the last 1.2 mya. Signs of population expansions were detected for populations attributed to subspecies S. l. luctuosus, but not for the S. l. araguayae population. Our results support that S. luctuosus has had a complex population history, resulting from a high dependence on southeastern "clear water" seasonally flooded habitats and their availability through time. Spatial and demographic expansions toward the western "white water" flooded forests might be related to recent changes in connectivity and availability of these habitats. Our study reinforces the view that isolation due to absence of suitable habitat has been an important driver of population differentiation within Amazonian flooded forests, but also that differences between várzeas ("white water" floodplains, mostly in southwestern Amazonia) and igapós ("clear water" floodplains, especially located in the east) should be further explored as drivers of micro-evolution for terrestrial species.
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Affiliation(s)
- Sofia Marques Silva
- Research Centre in Biodiversity and Genetic ResourcesCIBIO/InBIOVairãoPortugal
- Department of ZoologyMuseu Paraense Emílio GoeldiBelémBrazil
| | | | - Alexandre Aleixo
- Department of ZoologyMuseu Paraense Emílio GoeldiBelémBrazil
- Finnish Museum of Natural HistoryUniversity of HelsinkiHelsinkiFinland
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Magalhães KX, da Silva RDF, Sawakuchi AO, Gonçalves AP, Gomes GFE, Muriel-Cunha J, Sabaj MH, de Sousa LM. Phylogeography of Baryancistrus xanthellus (Siluriformes: Loricariidae), a rheophilic catfish endemic to the Xingu River basin in eastern Amazonia. PLoS One 2021; 16:e0256677. [PMID: 34449827 PMCID: PMC8396747 DOI: 10.1371/journal.pone.0256677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 08/12/2021] [Indexed: 11/22/2022] Open
Abstract
Baryancistrus xanthellus (Loricariidae) is an endemic fish species from the Xingu River basin with its life history in the shallow rapid waters flowing over bedrock substrates. In order to investigate the genetic diversity and demographic history of B. xanthellus we analyzed sequence data for one mitochondrial gene (Cyt b) and introns 1 and 5 of nuclear genes Prolactin (Prl) and Ribosomal Protein L3 (RPL3). The analyses contain 358 specimens of B. xanthellus from 39 localities distributed throughout its range. The number of genetically diverged groups was estimated using Bayesian inference on Cyt b haplotypes. Haplotype networks, AMOVA and pairwise fixation index was used to evaluate population structure and gene flow. Historical demography was inferred through neutrality tests and the Extended Bayesian Skyline Plot (EBSP) method. Five longitudinally distributed Cyt b haplogroups for B. xanthellus were identified in the Xingu River and its major tributaries, the Bacajá and Iriri. The demographic analysis suggests that rapids habitats have expanded in the Iriri and Lower Xingu rivers since 200 ka (thousand years) ago. This expansion is possibly related to an increase in water discharge as a consequence of higher rainfall across eastern Amazonia. Conversely, this climate shift also would have promoted zones of sediment trapping and reduction of rocky habitats in the Xingu River channel upstream of the Iriri River mouth. Populations of B. xanthellus showed strong genetic structure along the free-flowing river channels of the Xingu and its major tributaries, the Bacajá and Iriri. The recent impoundment of the Middle Xingu channel for the Belo Monte hydroelectric dam may isolate populations at the downstream limit of the species distribution. Therefore, future conservation plans must consider the genetic diversity of B. xanthellus throughout its range.
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Affiliation(s)
- Keila Xavier Magalhães
- Laboratório de Ictiologia de Altamira, Universidade Federal do Pará, Altamira, Pará, Brazil
| | | | | | - Alany Pedrosa Gonçalves
- Instituto Nacional de Pesquisa da Amazônia, INPA, Programa de Pós-Graduação em Biologia de Água Doce e Pesca Interior, Manaus, Amazonas, Brazil
| | | | - Janice Muriel-Cunha
- Instituto de Estudos Costeiros, Campus Bragança, Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Mark H. Sabaj
- Department of Ichthyology, The Academy of Natural Sciences of Drexel University, Philadelphia, PA, United States of America
| | - Leandro Melo de Sousa
- Laboratório de Ictiologia de Altamira, Universidade Federal do Pará, Altamira, Pará, Brazil
- * E-mail:
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Martins LF, Choueri EL, Oliveira AFS, Domingos FMCB, Caetano GHO, Cavalcante VHGL, Leite RN, Fouquet A, Rodrigues MT, Carnaval AC, Colli GR, Werneck FP. Whiptail lizard lineage delimitation and population expansion as windows into the history of Amazonian open ecosystems. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1953185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Lidia F. Martins
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Erik L. Choueri
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Alan F. S. Oliveira
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | | | - Gabriel H. O. Caetano
- Mitrani Department of Desert Ecology, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 849900 Midreshet Ben-Gurion, Israel
| | | | - Rafael N. Leite
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Antoine Fouquet
- Laboratoire Evolution et Diversité Biologique (EDB), UMR5174, Bâtiment 4R1, 118 Route de Narbonne 31077, Toulouse, France
| | - Miguel T. Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ana C. Carnaval
- City College of New York and Biology Ph.D. Program, The Graduate Center City University of New York, New York, NY 10031, USA
| | - Guarino R. Colli
- Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Fernanda P. Werneck
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
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Conceição Oliveira L, Picanço Rodrigues D, Fortune Hopkins HC, Peter Lewis G, John Gilbert Hopkins M. Phylogeny and historical biogeography of the pantropical genus Parkia (Leguminosae, Caesalpinioideae, mimosoid clade). Mol Phylogenet Evol 2021; 163:107219. [PMID: 34146678 DOI: 10.1016/j.ympev.2021.107219] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/15/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
Parkia R.Br. (Leguminosae, Caesalpinioideae, mimosoid clade) is a pantropical genus with approximately 35 recognized species in three taxonomic sections (Parkia, Platyparkia and Sphaeroparkia), distributed widely in tropical forests and savannas in South and Central America, Africa-Madagascar and the Indo-Pacific region. In this study, phylogenetic analyses (Maximum Likelihood and Bayesian Inference), ancestral area and habitat estimations were performed using chloroplast (matK, trnL, psbA-trnH and rps16-trnQ) and nuclear (ITS/18S/26S) DNA sequences for the purpose of testing the monophyly of Parkia and inferring the geographic origin of the genus and times of divergence of the various lineages. This enabled investigation of factors that may have influenced its diversification in both hemispheres. Our results support the monophyly of the genus. A fossil-calibrated Bayesian analysis dated the Parkia crown node to the Miocene (at c. 18.85 Ma). Biogeographic analysis reconstructed an origin in the lowlands rainforests (terra firme) in Amazonia with subsequent radiation in the Neotropical region from the Miocene onwards, with dispersion events as far as Central America, and the Atlantic Forest and the cerrado of Brazil. A single dispersion from the Neotropics to the Paleotropics is hypothesised, with subsequent smaller radiations in Africa-Madagascar and the Indo-Pacific (crown ages 3.79 and 5.15 Ma respectively). Factors that may have influenced the radiation and speciation of Parkia include the elevation of the Andes (especially in the Miocene), and more recently the closing of the Panama gap in Neotropics, the climatic fluctuations of the Pleistocene influenced the diversification of species on both continents. The elevation of the Sunda Shelf in Indo-Pacific region during the last glacial maximum (LGM) appears to be the main driving force for speciation in that region. In Africa, the low number of species may be related to extinction processes.
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Affiliation(s)
- Lorena Conceição Oliveira
- Instituto Nacional de Pesquisas da Amazônia, Programa de Pós-Graduação em Botânica, Manaus, AM 69067-375, Brazil.
| | | | - Helen C Fortune Hopkins
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK; Royal Botanic Gardens, Kew, Comparative Plant and Fungal Biology Department, Richmond, Surrey, TW9 3AE, UK
| | - Gwilym Peter Lewis
- Royal Botanic Gardens, Kew, Comparative Plant and Fungal Biology Department, Richmond, Surrey, TW9 3AE, UK
| | - Michael John Gilbert Hopkins
- Instituto Nacional de Pesquisas da Amazônia, Programa de Pós-Graduação em Botânica, Manaus, AM 69067-375, Brazil
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Riley Peterson KN, Browne RA, Erwin TL. Carabid beetle (Coleoptera, Carabidae) richness, diversity, and community structure in the understory of temporarily flooded and non-flooded Amazonian forests of Ecuador. Zookeys 2021; 1044:831-876. [PMID: 34183894 PMCID: PMC8222208 DOI: 10.3897/zookeys.1044.62340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/09/2021] [Indexed: 11/17/2022] Open
Abstract
Although tropical regions harbor the greatest arthropod diversity on Earth, the majority of species are taxonomically and scientifically unknown. Furthermore, how they are organized into functional communities and distributed among habitats is mostly unstudied. Here we examine species richness, diversity, and community composition of carabid beetles (Coleoptera: Carabidae) and compare them between flooded (FP) and non-flooded terra firme (TF) forests in the Yasuní area of Ecuador. The forest understory was sampled using flight intercept traps (FITs) and systematic hand collections at night in June and July 2011 and 2012, and FITs in October and November 2011. A total of 1,255 Carabidae representing 20 tribes, 54 genera, and 143 morphospecies was collected. Mean number of individuals and mean species richness did not differ significantly between FP and TF; however, numbers of Cicindelini (tiger beetles) and Pentagonicini were higher in TF forest while numbers of Lachnophorini and Scaritini were higher in FP forest. Overall, FP had significantly higher rarefied richness but extrapolation of rarefaction curves using the Chao1 nonparametric diversity estimator show that this difference may decrease with additional sampling. The inverse Simpson index was significantly higher for FP than TF forest. Nonmetric multidimensional scaling (NMDS) ordination and dissimilarity coefficient values show that FP and TF forests maintain unique assemblages with minimal overlap in community composition. Given ongoing anthropogenic pressures, particularly petroleum extraction, and those resulting from climate change, a greater understanding of the richness, diversity and community assemblages of Yasuní rainforest are needed to better conserve the fauna of this megadiverse area of Amazonia.
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Affiliation(s)
- Kathryn N. Riley Peterson
- Department of Biology, Wake Forest University, Winston-Salem, NC, USAWake Forest UniversityWinston-SalemUnited States of America
- Department of Natural Sciences, Pfeiffer University, Misenheimer, NC, USAPfeiffer UniversityMisenheimerUnited States of America
| | - Robert A. Browne
- Department of Biology, Wake Forest University, Winston-Salem, NC, USAWake Forest UniversityWinston-SalemUnited States of America
| | - Terry L. Erwin
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USASmithsonian InstitutionWashingtonUnited States of America
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Attiná N, Núñez Bustos EO, Lijtmaer DA, Hebert PDN, Tubaro PL, Lavinia PD. Genetic variation in neotropical butterflies is associated with sampling scale, species distributions, and historical forest dynamics. Mol Ecol Resour 2021; 21:2333-2349. [PMID: 34097821 DOI: 10.1111/1755-0998.13441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 11/26/2022]
Abstract
Previous studies of butterfly diversification in the Neotropics have focused on Amazonia and the tropical Andes, while southern regions of the continent have received little attention. To address the gap in knowledge about the Lepidoptera of temperate South America, we analysed over 3000 specimens representing nearly 500 species from Argentina for a segment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Representing 42% of the country's butterfly fauna, collections targeted species from the Atlantic and Andean forests, and biodiversity hotspots that were previously connected but are now isolated. We assessed COI effectiveness for species discrimination and identification and how its performance was affected by geographic distances and taxon coverage. COI data also allowed to study patterns of genetic variation across Argentina, particularly between populations in the Atlantic and Andean forests. Our results show that COI discriminates species well, but that identification success is reduced on average by ~20% as spatial and taxonomic coverage rises. We also found that levels of genetic variation are associated with species' spatial distribution type, a pattern which might reflect differences in their dispersal and colonization abilities. In particular, intraspecific distance between populations in the Atlantic and Andean forests was significantly higher in species with disjunct distributions than in those with a continuous range. All splits between lineages in these forests dated to the Pleistocene, but divergence dates varied considerably, suggesting that historical connections between the Atlantic and Andean forests have differentially affected their shared butterfly fauna. Our study supports the fact that large-scale assessments of mitochondrial DNA variation are a powerful tool for evolutionary studies.
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Affiliation(s)
- Natalí Attiná
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Ezequiel O Núñez Bustos
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Darío A Lijtmaer
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Pablo L Tubaro
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Pablo D Lavinia
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina.,Universidad Nacional de Río Negro. CIT Río Negro (UNRN-CONICET). Sede Atlántica, Viedma, Río Negro, Viedma, Argentina
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Buainain N, Maximiano MFA, Ferreira M, Aleixo A, Faircloth BC, Brumfield RT, Cracraft J, Ribas CC. Multiple species and deep genomic divergences despite little phenotypic differentiation in an ancient Neotropical songbird, Tunchiornis ochraceiceps (Sclater, 1860) (Aves: Vireonidae). Mol Phylogenet Evol 2021; 162:107206. [PMID: 34015447 DOI: 10.1016/j.ympev.2021.107206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 05/04/2021] [Accepted: 05/11/2021] [Indexed: 11/20/2022]
Abstract
Several bird taxa have been recently described or elevated to full species and almost twice as many bird species than are currently recognized may exist. Defining species is one of the most basic and important issues in biological science because unknown or poorly defined species hamper subsequent studies. Here, we evaluate the species limits and evolutionary history of Tunchiornis ochraceiceps-a widespread forest songbird that occurs in the lowlands of Central America, Chocó and Amazonia-using an integrative approach that includes plumage coloration, morphometrics, vocalization and genomic data. The species has a relatively old crown age (~9 Ma) and comprises several lineages with little, if any, evidence of gene flow among them. We propose a taxonomic arrangement composed of four species, three with a plumage coloration diagnosis and one deeply divergent cryptic species. Most of the remaining lineages have variable but unfixed phenotypic characters despite their relatively old origin. This decoupling of genomic and phenotypic differentiation reveals a remarkable case of phenotypic conservatism, possibly due to strict habitat association. Lineages are geographically delimited by the main Amazonian rivers and the Andes, a pattern observed in studies of other understory upland forest Neotropical birds, although phylogenetic relationships and divergence times among populations are idiosyncratic.
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Affiliation(s)
- Nelson Buainain
- Instituto Nacional de Pesquisas da Amazônia (INPA), Programa de Pós-Graduação em Ecologia, Av. André Araújo, 2936, Petrópolis, Manaus, AM 69067-375, Brazil.
| | - Marina F A Maximiano
- Instituto Nacional de Pesquisas da Amazônia (INPA), Programa de Pós-Graduação em Ecologia, Av. André Araújo, 2936, Petrópolis, Manaus, AM 69067-375, Brazil
| | - Mateus Ferreira
- Centro de Estudos da Biodiversidade, Universidade Federal de Roraima, Av. Cap. Ene Garcez, 2413, Boa Vista, Roraima, RR 69304-000, Brazil
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Brant C Faircloth
- Louisiana State University, Department of Biological Sciences, Baton Rouge, LA 70803, USA; Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robb T Brumfield
- Louisiana State University, Department of Biological Sciences, Baton Rouge, LA 70803, USA; Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Joel Cracraft
- American Museum of Natural History, Department of Ornithology, New York, NY, USA
| | - Camila C Ribas
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo, 2936, Manaus, AM 69067-375, Brazil
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40
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Fonseca EM, Colli GR, Werneck FP, Carstens BC. Phylogeographic model selection using convolutional neural networks. Mol Ecol Resour 2021; 21:2661-2675. [PMID: 33973350 DOI: 10.1111/1755-0998.13427] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 04/02/2021] [Accepted: 04/28/2021] [Indexed: 11/26/2022]
Abstract
The discipline of phylogeography has evolved rapidly in terms of the analytical toolkit used to analyse large genomic data sets. Despite substantial advances, analytical tools that could potentially address the challenges posed by increased model complexity have not been fully explored. For example, deep learning techniques are underutilized for phylogeographic model selection. In non-model organisms, the lack of information about their ecology and evolution can lead to uncertainty about which demographic models are appropriate. Here, we assess the utility of convolutional neural networks (CNNs) for assessing demographic models in South American lizards in the genus Norops. Three demographic scenarios (constant, expansion, and bottleneck) were considered for each of four inferred population-level lineages, and we found that the overall model accuracy was higher than 98% for all lineages. We then evaluated a set of 26 models that accounted for evolutionary relationships, gene flow, and changes in effective population size among the four lineages, identifying a single model with an estimated overall accuracy of 87% when using CNNs. The inferred demography of the lizard system suggests that gene flow between non-sister populations and changes in effective population sizes through time, probably in response to Pleistocene climatic oscillations, have shaped genetic diversity in this system. Approximate Bayesian computation (ABC) was applied to provide a comparison to the performance of CNNs. ABC was unable to identify a single model among the larger set of 26 models in the subsequent analysis. Our results demonstrate that CNNs can be easily and usefully incorporated into the phylogeographer's toolkit.
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Affiliation(s)
- Emanuel M Fonseca
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Brazil
| | - Fernanda P Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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Fouquet A, Marinho P, Réjaud A, Carvalho TR, Caminer MA, Jansen M, Rainha RN, Rodrigues MT, Werneck FP, Lima AP, Hrbek T, Giaretta AA, Venegas PJ, Chávez G, Ron S. Systematics and biogeography of the Boana albopunctata species group (Anura, Hylidae), with the description of two new species from Amazonia. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1873869] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Antoine Fouquet
- Laboratoire Evolution et Diversité Biologique, UMR 5174, CNRS, IRD, Université Paul Sabatier, Bâtiment 4R1 31062 cedex 9, 118 Route de Narbonne, Toulouse, 31077, France
| | - Pedro Marinho
- Laboratório de Anuros Neotropicais, Instituto de Ciências Exatas e Naturais do Pontal, Universidade Federal de Uberlândia, Ituiutaba, MG, Brazil
| | - Alexandre Réjaud
- Laboratoire Evolution et Diversité Biologique, UMR 5174, CNRS, IRD, Université Paul Sabatier, Bâtiment 4R1 31062 cedex 9, 118 Route de Narbonne, Toulouse, 31077, France
| | - Thiago R. Carvalho
- Laboratório de Herpetologia, Departamento de Biodiversidade e Centro de Aquicultura, I.B., Universidade Estadual Paulista, Rio Claro, SP, Brazil
| | - Marcel A. Caminer
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Germany
| | - Martin Jansen
- Department of Terrestrial Zoology, Research Institute and Nature Museum Senckenberg, Frankfurt, Germany
| | - Raíssa N. Rainha
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, AM, Brazil
| | - Miguel T. Rodrigues
- Departamento de Zoologia, Universidade de São Paulo, Instituto de Biociências, São Paulo, SP, Brazil
| | - Fernanda P. Werneck
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, AM, Brazil
| | - Albertina P. Lima
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, AM, Brazil
| | - Tomas Hrbek
- Departamento de Genética, Universidade Federal do Amazonas, Manaus, AM, Brazil
| | - Ariovaldo A. Giaretta
- Laboratório de Anuros Neotropicais, Instituto de Ciências Exatas e Naturais do Pontal, Universidade Federal de Uberlândia, Ituiutaba, MG, Brazil
| | | | | | - Santiago Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
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Leme Pablos J, Kristina Silva A, Seraphim N, de Moraes Magaldi L, Pereira de Souza A, Victor Lucci Freitas A, Lucas Silva-Brandão K. North-south and climate-landscape-associated pattern of population structure for the Atlantic Forest White Morpho butterflies. Mol Phylogenet Evol 2021; 161:107157. [PMID: 33753193 DOI: 10.1016/j.ympev.2021.107157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 01/25/2021] [Accepted: 03/15/2021] [Indexed: 11/18/2022]
Abstract
Atlantic Forest White Morpho butterflies, currently classified as Morpho epistrophus and M. iphitus, are endemic to the Atlantic Forest, where they are widely distributed throughout heterogeneous environmental conditions. Studies with endemic butterflies allow to elucidate questions on both patterns of diversity distribution and current and past processes acting on insect groups in this biodiversity hotspot. In the present study, we characterized one mtDNA marker (COI sequences) and developed 11 polymorphic loci of microsatellite for 22 sampling locations distributed throughout the entire Atlantic Forest domain. We investigated both the taxonomic limits of taxa classified as White Morpho and the structure and distribution of the genetic diversity throughout their populations. Genetic markers and distribution data failed to identify species diversification, population structure, or isolation among subpopulations attributed to different taxa proposed for the White Morpho, suggesting that the current distinction between two species is unreasonable. The Bayesian coalescent tree based on COI sequences also failed to recover monophyletic clades for the putative species, and pointed instead to a north-south oriented pattern of genetic structure, with the northern clade coalescing later than the southern clade. Northern samples also showed more intragroup structure than southern samples based on mtDNA data. Clustering tests based on microsatellites indicated the existence of three genetic clusters, with turnover between the states of Paraná and São Paulo. The north-south pattern found for the White Morpho populations is showed for the first time to a endemic AF insect and coincides with the two different bioclimatic domains previously described for vertebrates and plants. Population structure observed for these butterflies is related to climate- and landscape-associated variables, mainly precipitation and elevation.
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Affiliation(s)
- Julia Leme Pablos
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Biologia Animal, Rua Monteiro Lobato, 255, 13083-862 Campinas, SP, Brazil
| | - Ana Kristina Silva
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Biologia Animal, Rua Monteiro Lobato, 255, 13083-862 Campinas, SP, Brazil
| | - Noemy Seraphim
- Instituto Federal de Educação, Ciência e Tecnologia de São Paulo, Campus Campinas, Rua Heitor Lacerda Guedes, 1000, 13059-581 Campinas, SP, Brazil
| | - Luiza de Moraes Magaldi
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Biologia Animal, Rua Monteiro Lobato, 255, 13083-862 Campinas, SP, Brazil
| | - Anete Pereira de Souza
- Universidade Estadual de Campinas, Centro de Biologia Molecular e Engenharia Genética, Av. Candido Rondom, 400, 13083-875 Campinas, SP, Brazil
| | - André Victor Lucci Freitas
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Biologia Animal, Rua Monteiro Lobato, 255, 13083-862 Campinas, SP, Brazil
| | - Karina Lucas Silva-Brandão
- Universidade Estadual de Campinas, Centro de Biologia Molecular e Engenharia Genética, Av. Candido Rondom, 400, 13083-875 Campinas, SP, Brazil; Universidade Federal do ABC, Centro de Ciências Naturais e Humanas, Av. dos Estados, 5001, 09210-580 Santo André, SP, Brazil.
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Martínez Cortizas A, Horák-Terra I, Pérez-Rodríguez M, Bindler R, Cooke CA, Kylander M. Structural equation modeling of long-term controls on mercury and bromine accumulation in Pinheiro mire (Minas Gerais, Brazil). THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 757:143940. [PMID: 33321335 DOI: 10.1016/j.scitotenv.2020.143940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/08/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
The application of statistical modeling is still infrequent in mercury research in peat, despite the ongoing debate on the weight of the diverse factors (climate, peat decomposition, vegetation changes, etc.) that may affect mercury accumulation. One of the few exceptions is the Hg record of Pinheiro mire (souheast Brazil). Previous studies on this mire modeled mercury using principal components regression and partial least squares. These methods assume independence between factors, which is seldom the case in natural systems, thus hampering the identification of mediating effects and interactions. To overcome these limitations, in this reserach we use structural equation modeling (PLS-SEM) to model mercury and bromine peat records - bromine has been used in some investigations to normalize mercury accumuation. The mercury model explained 83% of the variance and suggested a complex control: increased peat decomposition, dust deposition and humid climates enhanced mercury accumulation, while increased mineral fluxes resulted in a decrease in mercury accumulation. The bromine model explained 90% of the variation in concentrations: increased dust deposition and peat decomposition promoted bromine accumulation, while time (i.e. peat age) promoted bromine depletion. Thus, although mercury and bromine are both organically bound elements with relevant atmospheric cycles the weights of the factors involved in their accumulation differed significantly. Our results suggest caution when using bromine to normalize mercury accumulation. PLS-SEM results indicate a large time dependence of peat decomposition, catchment mineral fluxes, long-term climate change, and atmospheric deposition; while atmospheric dust, mineral fluxes and peat decomposition showed high to moderate climate dependency. In particular, they also point to a relevant role of autogenic processes (i.e. the build up and expansion of the mire within the catchment), which controlled local mineral fluxes; an aspect that has seldom been considered.
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Affiliation(s)
- Antonio Martínez Cortizas
- Ecopast (GI-1553), Facultade de Bioloxía, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
| | - Ingrid Horák-Terra
- Instituto de Ciências Agrárias, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil
| | - Marta Pérez-Rodríguez
- Institut für Geoökologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Richard Bindler
- Department of Ecology and Environmental Science, University of Umea, Umea, Sweden
| | - Colin A Cooke
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - Malin Kylander
- Department of Geological Sciences, Stockholm University, Stockholm, Sweden
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44
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Ritter CD, Coelho LA, Capurucho JM, Borges SH, Cornelius C, Ribas CC. Sister species, different histories: comparative phylogeography of two bird species associated with Amazonian open vegetation. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Although the expansion of open vegetation within Amazonia was the basis for the Forest Refugia hypothesis, studies of Amazonian biota diversification have focussed mostly on forest taxa. Here we compare the phylogeographic patterns and population history of two sister species associated with Amazonian open-vegetation patches, Elaenia cristata and Elaenia ruficeps (Aves: Tyrannidae). We sampled individuals across Amazonia for both species, and in the central Brazilian savannas (Cerrado) for E. cristata. We sequenced one mitochondrial (ND2) and two nuclear (BFib7 and ACO) markers. We tested for population structure, estimated migration rates and elucidated the historical demography of each species. The Amazon River is the strongest barrier for E. ruficeps and the Branco River is a secondary barrier. For the more broadly distributed E. cristata, there was no discernible population structure. Both species attained their current genetic diversity recently and E. cristata has undergone demographic expansion since the Last Glacial Maximum, The results suggest distinct effects of recent landscape change on population history for the two species. E. ruficeps, which only occurs in Amazonian white sand habitats, has been more isolated in open-vegetation patches than E. cristata, which occupies Amazonian savannas, and extends into the Central Brazilian Cerrado.
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Affiliation(s)
- Camila D Ritter
- Department of Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstrasse 5, S05 R04 H83, Essen, Germany
- Coordenação de Biodiversidade e Coleções Zoológicas, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Manaus, AM, Brazil
| | - Laís A Coelho
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, MC-5557, 1200 Amsterdam Avenue, New York, NY, USA
| | - João Mg Capurucho
- Department of Biological Sciences, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL, USA
| | - Sergio H Borges
- Universidade Federal do Amazonas, Av. Rodrigo Otávio Jordão Ramos 3000, Bloco E, Setor Sul, Manaus, AM, Brazil
| | - Cíntia Cornelius
- Universidade Federal do Amazonas, Av. Rodrigo Otávio Jordão Ramos 3000, Bloco E, Setor Sul, Manaus, AM, Brazil
| | - Camila C Ribas
- Coordenação de Biodiversidade e Coleções Zoológicas, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Manaus, AM, Brazil
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45
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Capurucho JMG, Ashley MV, Tsuru BR, Cooper JC, Bates JM. Dispersal ability correlates with range size in Amazonian habitat-restricted birds. Proc Biol Sci 2020; 287:20201450. [PMID: 33203330 DOI: 10.1098/rspb.2020.1450] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Understanding how species attain their geographical distributions and identifying traits correlated with range size are important objectives in biogeography, evolutionary biology and biodiversity conservation. Despite much effort, results have been varied and general trends have been slow to emerge. Studying species pools that occupy specific habitats, rather than clades or large groupings of species occupying diverse habitats, may better identify ranges size correlates and be more informative for conservation programmes in a rapidly changing world. We evaluated correlations between a set of organismal traits and range size in bird species from Amazonian white-sand ecosystems. We assessed if results are consistent when using different data sources for phylogenetic and range hypotheses. We found that dispersal ability, as measured by the hand-wing index, was correlated with range size in both white-sand birds and their non-white-sand sister taxa. White-sand birds had smaller ranges on average than their sister taxa. The results were similar and robust to the different data sources. Our results suggest that the patchiness of white-sand ecosystems limits species' ability to reach new habitat islands and establish new populations.
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Affiliation(s)
- João M G Capurucho
- Department of Biological Sciences, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, USA.,Life Sciences Section, Negaunee Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - Mary V Ashley
- Department of Biological Sciences, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, USA
| | - Brian R Tsuru
- Life Sciences Section, Negaunee Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - Jacob C Cooper
- Life Sciences Section, Negaunee Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA.,Committee on Evolutionary Biology, The University of Chicago, 1025 E 57th Street, Chicago, IL 60637, USA
| | - John M Bates
- Life Sciences Section, Negaunee Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
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46
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Deininger M, McDermott F, Cruz FW, Bernal JP, Mudelsee M, Vonhof H, Millo C, Spötl C, Treble PC, Pickering R, Scholz D. Inter-hemispheric synchroneity of Holocene precipitation anomalies controlled by Earth's latitudinal insolation gradients. Nat Commun 2020; 11:5447. [PMID: 33116129 PMCID: PMC7595035 DOI: 10.1038/s41467-020-19021-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/23/2020] [Indexed: 11/09/2022] Open
Abstract
Atmospheric circulation is a fundamental component of Earth’s climate system, transporting energy poleward to partially offset the latitudinal imbalance in insolation. Changes in the latitudinal distribution of insolation thus force variations in atmospheric circulation, in turn altering regional hydroclimates. Here we demonstrate that regional hydroclimates controlled by the Northern Hemisphere mid-latitude storm tracks and the African and South American Monsoons changed synchronously during the last 10 kyrs. We argue that these regional hydroclimate variations are connected and reflect the adjustment of the atmospheric poleward energy transport to the evolving differential heating of the Northern and Southern Hemispheres. These results indicate that changes in latitudinal insolation gradients and associated variations in latitudinal temperature gradients exert important control on atmospheric circulation and regional hydroclimates. Since the current episode of global warming strongly affects latitudinal temperature gradients through Arctic amplification, our results can inform projections of likely inter-hemispheric precipitation changes in the future. Solar insolation is not equally distributed on the Earth’s surface and such imbalances influence the atmospheric circulation. Here, the authors show that latitudinal insolation gradients synchronized the hydroclimate in the Northern mid-latitudes and the African and South American Monsoons throughout the Holocene.
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Affiliation(s)
- Michael Deininger
- Institute of Geosciences, Johannes Gutenberg University Mainz, J.-J.-Becher-Weg 21, 55128, Mainz, Germany.
| | - Frank McDermott
- UCD School of Earth Sciences, University College Dublin, Belfield, Dublin 4, Ireland
| | - Francisco W Cruz
- Instituto de Geociências, Universidade de São Paulo, Rua do Lago 562, São Paulo, Brazil
| | - Juan Pablo Bernal
- Centro de Geociencias, Universidad Nacional Autónoma de México, Campus UNAM -Juriquilla, 76230, Querétaro, Mexico
| | - Manfred Mudelsee
- Climate Risk Analysis, Kreuzstrasse 27, Heckenbeck, 37581, Bad Gandersheim, Germany.,Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bussestrasse 24, 27570, Bremerhaven, Germany
| | - Hubert Vonhof
- Max-Planck-Institute for Chemistry, Hahn-Meitner-Weg 1, 55128, Mainz, Germany
| | - Christian Millo
- Instituto Oceanográfico, Universidade de São Paulo, Praça do Oceanográfico 191, São Paulo, Brazil
| | - Christoph Spötl
- Institute of Geology, University of Innsbruck, Innrain 52, 6020, Innsbruck, Austria
| | - Pauline C Treble
- Connected Waters Initiative Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia.,ANSTO, Locked Bag 2001, Kirrawee DC, NSW, 2232, Australia
| | - Robyn Pickering
- Department of Geological Sciences, University of Cape Town, University Avenue, Rondebosch, 7701, South Africa.,Human Evolution Research Institute, University of Cape Town, Rondebosch, 7701, South Africa
| | - Denis Scholz
- Institute of Geosciences, Johannes Gutenberg University Mainz, J.-J.-Becher-Weg 21, 55128, Mainz, Germany
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47
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Damasceno RP, Carnaval AC, Sass C, Sousa Recoder R, Moritz C, Trefaut Rodrigues M. Geographic restriction, genetic divergence, and morphological disparity in the Brazilian Atlantic Forests: Insights from Leposoma lizards (Gymnophthalmidae, Squamata). Mol Phylogenet Evol 2020; 154:106993. [PMID: 33148523 DOI: 10.1016/j.ympev.2020.106993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 09/01/2020] [Accepted: 09/28/2020] [Indexed: 10/23/2022]
Abstract
Lineage differentiation, long-term persistence, and range limitation promote high levels of phylogenetic and phylogeographic endemisms and likely underlie the abundant morphologically cryptic diversity observed in the Brazilian Atlantic Forests (AF). We explore lineage differentiation and range restriction in the AF and ask if genetic divergence and morphological disparity are correlated by integrating coalescent-based species delimitation, molecular phylogenetic, and morphological analyses in the lizard genus Leposoma. We present the first species tree for Leposoma and of their tribe, the Ecpleopodini. The analyses are based on the largest dataset ever assembled for Leposoma in terms of number of species (all represented), genetic markers (12 loci), and geographic coverage (~2,500 km). The exercise allows us to robustly delimit species within the genus and phylogeographic lineages within all species. We find support for the monophyly of the genus and for the recognition of a yet undescribed species around the Baía de Todos-os-Santos, in the state of Bahia; this form is distinct from all other congeners, both genetically and morphologically. We find that L. baturitensis, from the northeastern state of Ceará, is basal to the genus - and sister to a clade of six species restricted to the AF across the eastern coast of Brazil. Relationships within this coastal clade are ((((L. annectans, Leposoma sp.), L. scincoides), L. puk) (L. nanodactylus, L. sinepollex)). Phylogenetic and phylogeographic analyses, together with precise distribution data, allowed us to update the ranges of species and phylogeographic lineages. We reveal pervasive geographic restriction of divergent lineages in Leposoma at and below species level and discuss how forest refuges and rivers might have contributed to it. We find that morphological disparity lags behind genetic divergence in the genus because although they are correlated, the first accumulates at a much slower rate than the latter. We hope to encourage new studies in the area of AF north of the Doce river; phylogeographic sampling in that region has been much less common relative to southern sites, yet it may hold the key to several important processes defining biodiversity patterns in eastern Brazil. This appears to specially apply to processes underlying geographic restriction of morphologically cryptic, yet genetic divergent lineages, as the case of Leposoma.
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Affiliation(s)
- Roberta P Damasceno
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, trav. 14, n. 321, Cidade Universitária, São Paulo, SP 05508-090, Brazil; Museum of Vertebrate Zoology, University of California, Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA.
| | - Ana Carolina Carnaval
- Department of Biology, City College of New York and the Biology Program at the Graduate Center of CUNY, 160 Convent Avenue, Marshak Life Science Building J-526, New York, NY 10031, USA.
| | - Chodon Sass
- Museum of Vertebrate Zoology, University of California, Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA; University and Jepson Herbaria, University of California, Berkeley, 1001 Valley Life Sciences Building, Berkeley, CA 94720, USA.
| | - Renato Sousa Recoder
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, trav. 14, n. 321, Cidade Universitária, São Paulo, SP 05508-090, Brazil
| | - Craig Moritz
- Museum of Vertebrate Zoology, University of California, Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA; Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT 2601, Australia.
| | - Miguel Trefaut Rodrigues
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, trav. 14, n. 321, Cidade Universitária, São Paulo, SP 05508-090, Brazil.
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48
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Bocalini F, Bolívar-Leguizamón SD, Silveira LF, Bravo GA. Comparative phylogeographic and demographic analyses reveal a congruent pattern of sister relationships between bird populations of the northern and south-central Atlantic Forest. Mol Phylogenet Evol 2020; 154:106973. [PMID: 33059067 DOI: 10.1016/j.ympev.2020.106973] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 09/08/2020] [Accepted: 09/28/2020] [Indexed: 11/30/2022]
Abstract
The Pernambuco Center of Endemism (PCE) is the northernmost strip of the Atlantic Forest (AF). Biogeographic affinities among avifaunas in the PCE, the southern-central Atlantic Forest (SCAF), and Amazonia (AM) have not been studied comprehensively, and current patterns of genetic diversity in the PCE remain unclear. The interplay between species' ecological attributes and historical processes, such as Pleistocene climate fluctuations or the appearance of rivers, may have affected population genetic structures in the PCE. Moreover, the role of past connections between the PCE and AM and the elevational distribution of species in assembling the PCE avifauna remain untested. Here, we investigated the biogeographic history of seven taxa endemic to the PCE within a comparative phylogeographic framework based on a mean of 3,618 independent single nucleotide polymorphisms (SNPs) extracted from flanking regions of ultraconserved elements (UCEs) and one mitochondrial gene. We found that PCE populations were more closely related to SCAF populations than they were to those in AM, regardless of their elevational range, with divergence times placed during the Mid-Pleistocene. These splits were consistent with a pattern of allopatric divergence with gene flow until the upper Pleistocene and no signal of rapid changes in population sizes. Our results support the existence of a Pleistocene refugium driving current genetic diversity in the PCE, thereby rejecting the role of the São Francisco River as a primary barrier for population divergence. Additionally, we found that connections with Amazonia also played a significant role in assembling the PCE avifauna through subsequent migration events.
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Affiliation(s)
- Fernanda Bocalini
- Museu de Zoologia da Universidade de São Paulo, 04263-000 Ipiranga, São Paulo, SP, Brazil; Departamento de Zoologia do Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, SP, Brazil.
| | | | - Luís F Silveira
- Museu de Zoologia da Universidade de São Paulo, 04263-000 Ipiranga, São Paulo, SP, Brazil
| | - Gustavo A Bravo
- Museu de Zoologia da Universidade de São Paulo, 04263-000 Ipiranga, São Paulo, SP, Brazil; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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49
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Ledent A, Gauthier J, Pereira M, Overson R, Laenen B, Mardulyn P, Gradstein SR, de Haan M, Ballings P, Van der Beeten I, Zartman CE, Vanderpoorten A. What do tropical cryptogams reveal? Strong genetic structure in Amazonian bryophytes. THE NEW PHYTOLOGIST 2020; 228:640-650. [PMID: 32488881 DOI: 10.1111/nph.16720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
Lowland tropical bryophytes have been perceived as excellent dispersers. In such groups, the inverse isolation hypothesis proposes that spatial genetic structure is erased beyond the limits of short-distance dispersal. Here, we determine the influence of environmental variation and geographic barriers on the spatial genetic structure of a widely dispersed and phylogenetically independent sample of Amazonian bryophytes. Single nucleotide polymorphism data were produced from a restriction site-associated DNA sequencing protocol for 10 species and analyzed through F-statistics and Mantel tests. Neither isolation-by-environment nor the impact of geographic barriers were recovered from the analyses. However, significant isolation-by-distance patterns were observed for 8 out of the 10 investigated species beyond the scale of short-distance dispersal (> 1 km), offering evidence contrary to the inverse isolation hypothesis. Despite a cadre of life-history traits and distributional patterns suggesting that tropical bryophytes are highly vagile, our analyses reveal spatial genetic structures comparable to those documented for angiosperms, whose diaspores are orders of magnitude larger. Dispersal limitation for tropical bryophytes flies in the face of traditional assumptions regarding their dispersal potential, and suggests that the plight of this component of cryptic biodiversity is more dire than previously considered in light of accelerated forest fragmentation in the Amazon.
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Affiliation(s)
- Alice Ledent
- Institute of Botany, University of Liège, B22 Sart Tilman, Liège, 4000, Belgium
| | - Jérémy Gauthier
- Muséum d'Histoire Naturelle, route de Malagnou 1, Genève, 1208, Switzerland
| | - Martinha Pereira
- Department of Biodiversity, National Institute for Amazonian Research, Petrópolis, CEP 69060-001, Manaus, Amazonas, Brazil
| | - Rick Overson
- Global Institute of Sustainability, Arizona State University, Tempe, AZ, 85281, USA
| | - Benjamin Laenen
- Department of Ecology, Environment and Plant Sciences, Science for Life laboratory, Stockholm University, Stockholm, 106 91, Sweden
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Brussels, 1050, Belgium
| | - S Robbert Gradstein
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, EPHE, Sorbonne Université, CP 39, 57 rue Cuvier, Paris, F-75005, France
| | - Myriam de Haan
- Research Department, Meise Botanic Garden, Meise, 1860, Belgium
| | - Petra Ballings
- Research Department, Meise Botanic Garden, Meise, 1860, Belgium
| | | | - Charles E Zartman
- Muséum d'Histoire Naturelle, route de Malagnou 1, Genève, 1208, Switzerland
| | - Alain Vanderpoorten
- Institute of Botany, University of Liège, B22 Sart Tilman, Liège, 4000, Belgium
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50
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Systematics of a Neotropical clade of dead-leaf-foraging antwrens (Aves: Thamnophilidae; Epinecrophylla). Mol Phylogenet Evol 2020; 154:106962. [PMID: 32950682 DOI: 10.1016/j.ympev.2020.106962] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 08/19/2020] [Accepted: 09/10/2020] [Indexed: 11/22/2022]
Abstract
The stipple-throated antwrens of the genus Epinecrophylla (Aves: Thamnophilidae) are represented by eight species primarily found in the lowlands of the Amazon Basin and the Guiana Shield. The genus has a long and convoluted taxonomic history, with many attempts made to address the taxonomy and systematics of the group. Here we employ massively parallel sequencing of thousands of ultraconserved elements (UCEs) to provide both the most comprehensive subspecies-level phylogeny of Epinecrophylla antwrens and the first population-level genetic analyses for most species in the genus. Most of our results are robust to a diversity of phylogenetic and population genetic methods, but we show that even with thousands of loci we are unable to fully resolve the relationships between some western Amazonian species in the haematonota group. We uncovered phylogenetic relationships between taxa and patterns of population structure that are discordant with both morphology and current taxonomy. For example, we found deep genetic breaks between taxa in the ornata group that are currently regarded as species, and in the haematonota and leucophthalma groups we found paraphyly at the species and subspecies levels, respectively. As has been found in many Amazonian taxa, our phylogenetic results show that the major river systems of the Amazon Basin appear to have an effect on the genetic structure and range limits within Epinecrophylla. Our population genetics analyses showed extensive admixture between some taxa despite their deep genetic divergence. We present a revised taxonomy for the group and suggest areas for further study.
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