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Batalha-Filho H, Barreto SB, Silveira MHB, Miyaki CY, Afonso S, Ferrand N, Carneiro M, Sequeira F. Disentangling the contemporary and historical effects of landscape on the population genomic variation of two bird species restricted to the highland forest enclaves of northeastern Brazil. Heredity (Edinb) 2024; 132:77-88. [PMID: 37985738 PMCID: PMC10844224 DOI: 10.1038/s41437-023-00662-1] [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: 01/18/2023] [Revised: 11/02/2023] [Accepted: 11/02/2023] [Indexed: 11/22/2023] Open
Abstract
Investigating the impact of landscape features on patterns of genetic variation is crucial to understand spatially dependent evolutionary processes. Here, we assess the population genomic variation of two bird species (Conopophaga cearae and Sclerurus cearensis) through the Caatinga moist forest enclaves in northeastern Brazil. To infer the evolutionary dynamics of bird populations through the Late Quaternary, we used genome-wide polymorphism data obtained from double-digestion restriction-site-associated DNA sequencing (ddRADseq), and integrated population structure analyses, historical demography models, paleodistribution modeling, and landscape genetics analyses. We found the population differentiation among enclaves to be significantly related to the geographic distance and historical resistance across the rugged landscape. The climate changes at the end of the Pleistocene to the Holocene likely triggered synchronic population decline in all enclaves for both species. Our findings revealed that both geographic distance and historical connectivity through highlands are important factors that can explain the current patterns of genetic variation. Our results further suggest that levels of population differentiation and connectivity cannot be explained purely on the basis of contemporary environmental conditions. By combining historical demographic analyses and niche modeling predictions in a historical framework, we provide strong evidence that climate fluctuations of the Quaternary promoted population differentiation and a high degree of temporal synchrony among population size changes in both species.
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Affiliation(s)
- Henrique Batalha-Filho
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil.
| | - Silvia Britto Barreto
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil
| | - Mario Henrique Barros Silveira
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil
| | - Cristina Yumi Miyaki
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - Nuno Ferrand
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - Fernando Sequeira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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2
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Maldonado-Coelho M, Dos Santos SS, Isler ML, Svensson-Coelho M, Sotelo-Muñoz M, Miyaki CY, Ricklefs RE, Blake JG. Evolutionary and Ecological Processes Underlying Geographic Variation in Innate Bird Songs. Am Nat 2023; 202:E31-E52. [PMID: 37531273 DOI: 10.1086/725016] [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: 08/04/2023]
Abstract
AbstractEcological and evolutionary processes underlying spatial variation in signals involved in mate recognition and reproductive isolation are crucial to understanding the causes of population divergence and speciation. Here, to test hypotheses concerning the causes of song divergence, we examine how songs of two sister species of Atlantic Forest suboscine birds with innate songs, the Pyriglena fire-eye antbirds, vary across their ranges. Specifically, we evaluated the influence of isolation by distance and introgressive hybridization, as well as morphological and environmental variation, on geographic variation in male songs. Analyses based on 496 male vocalizations from 63 locations across a 2,200-km latitudinal transect revealed clinal changes in the structure of songs and showed that introgressive hybridization increases both the variability and the homogenization of songs in the contact zone between the two species. We also found that isolation by distance, morphological constraints, the environment, and genetic introgression independently predicted song variation across geographic space. Our study shows the importance of an integrative approach that investigates the roles of distinct ecological and evolutionary processes that influence acoustic signal evolution.
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Cruz CEF, Funkler GR, Zani ALS, Wagner PGC, Andretta I, Segura LN, Fagundes NJR. A Preliminary Assessment of the Potential Health and Genetic Impacts of Releasing Confiscated Passerines Into the Wild: A Reduced-Risk Approach. Front Vet Sci 2021; 8:679049. [PMID: 34708099 PMCID: PMC8542797 DOI: 10.3389/fvets.2021.679049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
The illegal capture and trade of wild birds have long been threats to biodiversity. The rehabilitation and release of confiscated animals may be a useful conservation tool in species management. However, differences between populations regarding health (e.g., different pathogens) and adaptation (e.g., local adaptation) must be taken into account, since both can negatively impact the recipient population. In this pilot study, we used two of the most illegally trafficked Brazilian wild passerine species, namely the red-crested cardinal (Paroaria coronata) and green-winged saltator (Saltator similis) as case studies and assessed some of the health threats that the release of confiscated passerines may pose to free-living birds. We also investigated the level of difference in mitochondrial genetic structure among populations living in different ecoregions. Blood, feces, and oropharyngeal swabs from confiscated (n = 115) and free-living (n = 120) passerines from the release sites were tested for the Newcastle disease virus, Salmonella spp., and Mycoplasma gallisepticum. These are considered major avian diseases by the Brazilian National Avian Health Program. We analyzed mtDNA to study the difference in genetic structure between populations using samples from 127 free-living passerines. We found no evidence of the Newcastle disease virus or Salmonella spp. in confiscated or free-living passerines from either species. However, the levels of infection with M. galissepticum detected in our study for red-crested cardinals and green-winged saltators calls for a high degree of caution in captive release programs. The difference in genetic structure between populations occurring in different regions was low, and was not significant between those from the Pampa/Subtropical Grasslands region. These results suggest that it may be possible to establish a cost-effective and sensitive protocol for releasing confiscated songbirds, provided that further genome-wide studies indicate that the functional genetic diversity among (at least some of the) populations is also low.
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Affiliation(s)
- Cláudio E F Cruz
- Centro de Estudos em Manejo de Aves Silvestres, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Ciências Veterinárias, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Gustavo R Funkler
- Programa de Pós-Graduação em Ciências Veterinárias, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Laboratório Porto Belo, Porto Alegre, Brazil
| | - André L S Zani
- Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Paulo G C Wagner
- Centro de Triagem de Animais Silvestres, Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis, Porto Alegre, Brazil
| | - Inês Andretta
- Laboratório de Ensino Zootécnico, Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luciano N Segura
- Museo de La Plata, Sección Ornitología, Universidad Nacional de La Plata, La Plata, Argentina
| | - Nelson J R Fagundes
- Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biologia Animal, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Deep-time climate legacies affect origination rates of marine genera. Proc Natl Acad Sci U S A 2021; 118:2105769118. [PMID: 34475215 DOI: 10.1073/pnas.2105769118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/04/2021] [Indexed: 11/18/2022] Open
Abstract
Biodiversity dynamics are shaped by a complex interplay between current conditions and historic legacy. The interaction of short- and long-term climate change may mask the true relationship of evolutionary responses to climate change if not specifically accounted for. These paleoclimate interactions have been demonstrated for extinction risk and biodiversity change, but their importance for origination dynamics remains untested. Here, we show that origination probability in marine fossil genera is strongly affected by paleoclimate interactions. Overall, origination probability increases by 27.8% [95% CI (27.4%, 28.3%)] when a short-term cooling adds to a long-term cooling trend. This large effect is consistent through time and all studied groups. The mechanisms of the detected effect might be manifold but are likely connected to increased allopatric speciation with eustatic sea level drop caused by sustained global cooling. We tested this potential mechanism through which paleoclimate interactions can act on origination rates by additionally examining a proxy for habitat fragmentation. This proxy, continental fragmentation, has a similar effect on origination rates as paleoclimate interactions, supporting the importance of allopatric speciation through habitat fragmentation in the deep-time fossil record. The identified complex nature of paleoclimate interactions might explain contradictory conclusions on the relationship between temperature and origination in the previous literature. Our results highlight the need to account for complex interactions in evolutionary studies both between and among biotic and abiotic factors.
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Menezes L, Batalha‐Filho H, Garda AA, Napoli M. Tiny treefrogs in the Pleistocene: Phylogeography of
Dendropsophus oliveirai
in the Atlantic Forest and associated enclaves in northeastern Brazil. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Lucas Menezes
- Programa de Pós‐Graduação em Biodiversidade e Evolução Instituto de Biologia Universidade Federal da Bahia Salvador Brazil
| | - Henrique Batalha‐Filho
- Programa de Pós‐Graduação em Biodiversidade e Evolução Instituto de Biologia Universidade Federal da Bahia Salvador Brazil
- Museu de História Natural (“Museu de Zoologia”) Instituto de Biologia Universidade Federal da Bahia Salvador Bahia Brazil
| | - Adrian Antonio Garda
- Laboratório de Anfíbios e Répteis ‐ LAR Departamento de Botânica e Zoologia Universidade Federal do Rio Grande do Norte Natal Brazil
| | - Marcelo Napoli
- Programa de Pós‐Graduação em Biodiversidade e Evolução Instituto de Biologia Universidade Federal da Bahia Salvador Brazil
- Museu de História Natural (“Museu de Zoologia”) Instituto de Biologia Universidade Federal da Bahia Salvador Bahia Brazil
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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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da Silva Ribeiro T, Batalha-Filho H, Silveira LF, Miyaki CY, Maldonado-Coelho M. Life history and ecology might explain incongruent population structure in two co-distributed montane bird species of the Atlantic Forest. Mol Phylogenet Evol 2020; 153:106925. [PMID: 32771546 DOI: 10.1016/j.ympev.2020.106925] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 07/03/2020] [Accepted: 08/03/2020] [Indexed: 11/16/2022]
Abstract
Comparative phylogeography is a powerful approach to investigate the role of historical and environmental processes in the evolution of biodiversity within a region. In this regard, comparative studies of species with similar habitat preferences are valuable to reduce the confounding influence of habitat association when interpreting phylogeographic patterns. In the Atlantic Forest of South America, phylogeographic studies of highland and lowland species have shown distinct population structure patterns so far, suggesting that such species have responded differently to Pleistocene glacial cycles. Herein, we performed a comparative analysis using molecular data and paleodistribution models of two Montane Atlantic Forest (MAF) co-distributed passerine birds with similar habitat requirements but with distinct life-history traits and ecologies: the frugivore lek-breeding Blue Manakin (Chiroxiphia caudata) and the insectivore and socially monogamous Drab-Breasted Bamboo Tyrant (Hemitriccus diops). We aimed to shed light on the role of contrasting life histories and ecologies onto the demography and population structure of MAF species. We sampled both species throughout most of their distribution range, sequenced a mitochondrial and a nuclear molecular marker, and used standard phylogeographic methods to investigate population structure and ecological niche modeling (ENM) to infer the species' paleodistributions. Our analyses recovered a phylogeographic break in H. diops in the region of the Doce River, but no genetic structure in C. caudata. We also found higher differentiation among subpopulations within each lineage of H. diops than among subpopulations of C. caudata. We suggest that these discrepancies in population structure might be due to distinct life-history traits and their impact on gene flow and generation time. For example, while H. diops is an insectivore species, C. caudata is a frugivore and the latter ecological aspect likely selects for a higher dispersion distance. Additionally, because C. caudata is a lek-breeding species, it has a longer generation time than H. diops. These traits could hinder genetic differentiation when populations become geographically isolated. Nonetheless, both species showed some common biological features, such as signatures of synchronous population expansion and larger distribution ranges during the Last Glacial Maximum, possibly due to similar cold tolerance.
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Affiliation(s)
- Tiago da Silva Ribeiro
- Laboratório de Genética e Evolução Molecular de Aves, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, SP, Brazil.
| | - Henrique Batalha-Filho
- Laboratório de Genética e Evolução Molecular de Aves, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, SP, Brazil
| | - Luis Fábio Silveira
- Museu de Zoologia, Universidade de São Paulo, 04263-000 São Paulo, SP, Brazil
| | - Cristina Yumi Miyaki
- Laboratório de Genética e Evolução Molecular de Aves, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, SP, Brazil
| | - Marcos Maldonado-Coelho
- Laboratório de Genética e Evolução Molecular de Aves, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, SP, Brazil
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Buainain N, Canton R, Zuquim G, Tuomisto H, Hrbek T, Sato H, Ribas CC. Paleoclimatic evolution as the main driver of current genomic diversity in the widespread and polymorphic Neotropical songbird Arremon taciturnus. Mol Ecol 2020; 29:2922-2939. [PMID: 32623766 DOI: 10.1111/mec.15534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 06/04/2020] [Accepted: 06/18/2020] [Indexed: 01/27/2023]
Abstract
Several factors have been proposed as drivers of species diversification in the Neotropics, including environmental heterogeneity, the development of drainage systems and historical changes in forest distribution due to climatic oscillations. Here, we investigate which drivers contributed to the evolutionary history and current patterns of diversity of a polymorphic songbird (Arremon taciturnus) that is widely distributed in Amazonian and Atlantic forests as well as in Cerrado gallery and seasonally-dry forests. We use genomic, phenotypic and habitat heterogeneity data coupled with climatic niche modelling. Results suggest the evolutionary history of the species is mainly related to paleoclimatic changes, although changes in the strength of the Amazon river as a barrier to dispersal, current habitat heterogeneity and geographic distance were also relevant. We propose an ancestral distribution in the Guyana Shield, and recent colonization of areas south of the Amazon river at ~380 to 166 kya, and expansion of the distribution to southern Amazonia, Cerrado and the Atlantic Forest. Since then, populations south of the Amazon River have been subjected to cycles of isolation and possibly secondary contact due to climatic changes that affected habitat heterogeneity and population connectivity. Most Amazonian rivers are not associated with long lasting isolation of populations, but some might act as secondary barriers, susceptible to crossing under specific climatic conditions. Morphological variation, while stable in some parts of the distribution, is not a reliable indicator of genetic structure or phylogenetic relationships.
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Affiliation(s)
- Nelson Buainain
- Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, AM, Brazil
| | - Roberta Canton
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Gabriela Zuquim
- Department of Biology, University of Turku, Turun Yliopisto, Finland
| | - Hanna Tuomisto
- Department of Biology, University of Turku, Turun Yliopisto, Finland
| | - Tomas Hrbek
- Departmento de Genetica, Universidade Federal do Amazonas, Manaus, AM, Brazil
| | - Hiromitsu Sato
- Department of Earth Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Camila C Ribas
- Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, AM, Brazil
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Almeida JPFA, Thomé MTC, Sturaro MJ, Pereira RJ, Mott T. The relative role of glacial refugia and longstanding barriers in the diversification of a fossorial squamate. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1783716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- João P. F. A. Almeida
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, AL 57072-970, Brazil
| | - Maria Tereza C. Thomé
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, AL 57072-970, Brazil
| | - Marcelo J. Sturaro
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Av. Professor Artur Riedel, 275, Jardim Eldorado, Diadema, São Paulo, CEP 09972-270, Brazil
| | - Ricardo J. Pereira
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig- Maximilians-Universität München, Grosshaderner Strasse 2, München, 82152, Germany
| | - Tamí Mott
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, AL 57072-970, Brazil
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Bolívar-Leguizamón SD, Silveira LF, Derryberry EP, Brumfield RT, Bravo GA. Phylogeography of the Variable Antshrike (Thamnophilus caerulescens), a South American passerine distributed along multiple environmental gradients. Mol Phylogenet Evol 2020; 148:106810. [DOI: 10.1016/j.ympev.2020.106810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/23/2020] [Accepted: 03/25/2020] [Indexed: 12/21/2022]
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11
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Sotelo-Muñoz M, Maldonado-Coelho M, Svensson-Coelho M, Dos Santos SS, Miyaki CY. Vicariance, dispersal, extinction and hybridization underlie the evolutionary history of Atlantic forest fire-eye antbirds (Aves: Thamnophilidae). Mol Phylogenet Evol 2020; 148:106820. [PMID: 32283137 DOI: 10.1016/j.ympev.2020.106820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 03/20/2020] [Accepted: 04/01/2020] [Indexed: 11/25/2022]
Abstract
In order to gain insights into the biogeographic processes underlying biotic diversification in the Atlantic Forest (AF), we used a multi-locus approach to examine the evolutionary history of the White-shouldered Fire-eye (Pyriglena leucoptera) and the Fringe-backed Fire-eye (Pyriglena atra), two parapatric sister species endemic to the AF. We sequenced one mitochondrial, three Z chromosome-linked and three anonymous markers of 556 individuals from 66 localities. We recovered four lineages throughout the AF: P. atra and three populations within P. leucoptera. All populations diverged during the late Pleistocene and presented varying levels of admixture. One Z-linked locus showed the highest level of differentiation between the two species. On the other hand, a mitochondrial haplotype was shared extensively between them. Our data supported vicariance driving speciation along with extinction and dispersal as processes underlying intraspecific diversification. Furthermore, signatures of demographic expansion in most populations and areas of genetic admixture were recovered throughout the AF, suggesting that forest fragmentation was also important in differentiation. Genetic admixture areas are located between large rivers suggesting that AF rivers may diminish gene flow. Our results indicated a complex and dynamic biogeographic history of Pyriglena in the AF, with vicariance, extinction, dispersal and secondary contact followed by introgression likely influencing the current patterns of genetic distribution.
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Affiliation(s)
- Manuelita Sotelo-Muñoz
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, Rua do Matão 277, 05508-090 São Paulo, Brazil.
| | | | - Maria Svensson-Coelho
- Lund University, Department of Biology, Ekologihuset, Sölvegatan 37, 22362 Lund, Sweden
| | - Sidnei S Dos Santos
- Programa de Pós-graduação em Diversidade Animal, Instituto de Biologia, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Cristina Y Miyaki
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, Rua do Matão 277, 05508-090 São Paulo, Brazil
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12
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Trevisan CC, Batalha-Filho H, Garda AA, Menezes L, Dias IR, Solé M, Canedo C, Juncá FA, Napoli MF. Cryptic diversity and ancient diversification in the northern Atlantic Forest Pristimantis (Amphibia, Anura, Craugastoridae). Mol Phylogenet Evol 2020; 148:106811. [PMID: 32259656 DOI: 10.1016/j.ympev.2020.106811] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 03/12/2020] [Accepted: 03/18/2020] [Indexed: 10/24/2022]
Abstract
The Neotropical region is known both for its megadiverse fauna and for the significant deficiency of our knowledge on species limits. The Amazon and Atlantic Forest are the two most diverse and large rainforests in South America, and they harbor many groups of sister species and sister genera. The frog genus Pristimantis is the most speciose genus of terrestrial vertebrates with 546 species, but only three of them occur in the Atlantic forest. Herein, we investigate the diversification history and phylogenetic relationship among the Atlantic Forest Pristimantis lineages in a spatial-temporal framework, using mitochondrial and nuclear genes. Our results reveal a remarkable hidden diversity, with nine highly structure lineages that may correspond to undescribed species, with many cases of sympatry among these divergent lineages. Atlantic forest Pristimantis form a monophyletic group that started to diversify over 40 million years ago. This ancient group shows diversification events that remount the early bursts of the Atlantic Forest diversification history, as well as lineage diversification likely resulting from recent Pleistocene climatic fluctuations. Future work must concentrate in comparing these lineages under an integrative framework including morphology, advertisement calls and other ecology traits to confidently delimit species of Pristimantis in the Atlantic Forest.
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Affiliation(s)
- Camila Costa Trevisan
- Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, Campus Universitário de Ondina, 40170-115 Salvador, Bahia, Brazil.
| | - Henrique Batalha-Filho
- Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, Campus Universitário de Ondina, 40170-115 Salvador, Bahia, Brazil; Museu de História Natural ("Museu de Zoologia"), Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, Campus Universitário de Ondina, 40170-115 Salvador, Bahia, Brazil
| | - Adrian Antonio Garda
- Laboratório de Anfíbios e Répteis - LAR, Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Av. Salgado Filho S/N, Lagoa Nova, 59072-970 Natal, Rio Grande do Norte, Brazil
| | - Lucas Menezes
- Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, Campus Universitário de Ondina, 40170-115 Salvador, Bahia, Brazil
| | - Iuri Ribeiro Dias
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, 45662-900 Ilhéus, Bahia, Brazil
| | - Mirco Solé
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, 45662-900 Ilhéus, Bahia, Brazil
| | - Clarissa Canedo
- Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Departamento de Zoologia, Rua São Francisco Xavier, 524, Maracanã, 20550-013 Rio de Janeiro, Rio de Janeiro, Brazil; Museu Nacional, Departamento de Vertebrados, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, 20940-040 São Cristóvão, Rio de Janeiro, Brazil
| | - Flora Acuña Juncá
- Museu de Zoologia, Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina, 44036-900 Feira de Santana, Bahia, Brazil
| | - Marcelo Felgueiras Napoli
- Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, Campus Universitário de Ondina, 40170-115 Salvador, Bahia, Brazil; Museu de História Natural ("Museu de Zoologia"), Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, Campus Universitário de Ondina, 40170-115 Salvador, Bahia, Brazil
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13
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Thom G, Xue AT, Sawakuchi AO, Ribas CC, Hickerson MJ, Aleixo A, Miyaki C. Quaternary climate changes as speciation drivers in the Amazon floodplains. SCIENCE ADVANCES 2020; 6:eaax4718. [PMID: 32195336 PMCID: PMC7065905 DOI: 10.1126/sciadv.aax4718] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 12/13/2019] [Indexed: 05/04/2023]
Abstract
The role of climate as a speciation driver in the Amazon has long been discussed. Phylogeographic studies have failed to recover synchronous demographic responses across taxa, although recent evidence supports the interaction between rivers and climate in promoting speciation. Most studies, however, are biased toward upland forest organisms, while other habitats are poorly explored and could hold valuable information about major historical processes. We conducted a comparative phylogenomic analysis of floodplain forest birds to explore the effects of historical environmental changes and current connectivity on population differentiation. Our findings support a similar demographic history among species complexes, indicating that the central portion of the Amazon River basin is a suture zone for taxa isolated across the main Amazonian sub-basins. Our results also suggest that changes in the fluvial landscape induced by climate variation during the Mid- and Late Pleistocene drove population isolation, leading to diversification with subsequent secondary contact.
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Affiliation(s)
- Gregory Thom
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP 05508-090, Brazil
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA
| | - Alexander T Xue
- Department of Biology, Marshak Science Building, City College of New York, New York, NY 10031, USA
- Human Genetics Institute of New Jersey and Department of Genetics, Rutgers University, 604 Allison Road, Piscataway, NJ 08854, USA
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - André O Sawakuchi
- Instituto de Geociências, Universidade de São Paulo, Rua do Lago 562, São Paulo, SP 05508-080, Brazil
| | - Camila C Ribas
- Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo 2936, Manaus, AM 69060-001, Brazil
| | - Michael J Hickerson
- Department of Biology, Marshak Science Building, City College of New York, New York, NY 10031, USA
- The Graduate Center, City University of New York, New York, NY 10016, USA
- New York Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Alexandre Aleixo
- Museu Paraense Emílio Goeldi (MPEG), Caixa Postal 399, Belém, PA 66040-170, Brazil
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Cristina Miyaki
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP 05508-090, Brazil
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14
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Batalha-Filho H, Maldonado-Coelho M, Miyaki CY. Historical climate changes and hybridization shaped the evolution of Atlantic Forest spinetails (Aves: Furnariidae). Heredity (Edinb) 2019; 123:675-693. [PMID: 31123344 DOI: 10.1038/s41437-019-0234-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/04/2019] [Accepted: 05/09/2019] [Indexed: 01/23/2023] Open
Abstract
Combining phylogeographic approaches and hybrid zone inference in a single framework is a robust way to depict respectively the biogeographic history of lineages and the evolutionary processes responsible for speciation. Here, we studied the spatiotemporal patterns of diversification and characterize the hybrid zone between two Atlantic Forest spinetails (Synallaxis ruficapilla and Synallaxis cinerea) using mitochondrial DNA and nuclear (autosomal and Z-linked) genes. We consistently recovered divergence between and within the two species during the late Pliocene and Pleistocene using an isolation with migration model. Also, our results indicate distinct levels of introgression among lineages. Ecological niche models and demographic inferences, used to infer range distributions throughout the late Quaternary, were not consistent with the hypothesis of a large river as a primary barrier responsible for the divergence of the two species. Instead, a scenario of isolation and divergence followed by geographic expansion and admixture as a consequence of Quaternary climatic oscillations was supported. Paleomodels also were not consistent with the idea that the hybrid zone originated in primary differentiation and favor a secondary contact scenario. Model fitting indicated that clines of different loci spanning the hybrid zone are coincident and concordant. The narrow cline for one Z-linked locus could be indicative of some form of post-zygotic selection hindering genetic homogenization between the two species.
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Affiliation(s)
| | | | - Cristina Yumi Miyaki
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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15
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Raposo do Amaral F, Maldonado‐Coelho M, Aleixo A, Luna LW, Rêgo PSD, Araripe J, Souza TO, Silva WAG, Thom G. Recent chapters of Neotropical history overlooked in phylogeography: Shallow divergence explains phenotype and genotype uncoupling in
Antilophia
manakins. Mol Ecol 2018; 27:4108-4120. [DOI: 10.1111/mec.14843] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/06/2018] [Accepted: 06/11/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Fabio Raposo do Amaral
- Departamento de Ecologia e Biologia Evolutiva Universidade Federal de São Paulo Diadema SP Brazil
| | - Marcos Maldonado‐Coelho
- Departamento de Ecologia e Biologia Evolutiva Universidade Federal de São Paulo Diadema SP Brazil
| | - Alexandre Aleixo
- Coordenação de Zoologia Museu Paraense Emílio Goeldi Belém PA Brazil
| | - Leilton W. Luna
- Laboratório de Genética e Conservação Instituto de Estudos Costeiros Universidade Federal do Pará Bragança PA Brazil
| | - Péricles Sena do Rêgo
- Laboratório de Genética e Conservação Instituto de Estudos Costeiros Universidade Federal do Pará Bragança PA Brazil
| | - Juliana Araripe
- Laboratório de Genética e Conservação Instituto de Estudos Costeiros Universidade Federal do Pará Bragança PA Brazil
| | - Thainara O. Souza
- Laboratório de Genética e Conservação Instituto de Estudos Costeiros Universidade Federal do Pará Bragança PA Brazil
| | - Weber A. G. Silva
- Associação de Pesquisa e Preservação de Ecossistemas Aquáticos Fortaleza Brazil
| | - Gregory Thom
- Departamento de Genética e Biologia Evolutiva Universidade de São Paulo São Paulo SP Brazil
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16
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Thom G, Amaral FRD, Hickerson MJ, Aleixo A, Araujo-Silva LE, Ribas CC, Choueri E, Miyaki CY. Phenotypic and Genetic Structure Support Gene Flow Generating Gene Tree Discordances in an Amazonian Floodplain Endemic Species. Syst Biol 2018; 67:700-718. [DOI: 10.1093/sysbio/syy004] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 01/23/2018] [Indexed: 01/25/2023] Open
Affiliation(s)
- Gregory Thom
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP 05508-090, Brazil
| | - Fabio Raposo Do Amaral
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Laboratório de Genética Evolutiva, Universidade Federal de São Paulo, Rua Professor Artur Riedel, 275, Diadema, SP 09972–270, Brazil
| | - Michael J Hickerson
- Department of Biology, Marshak Science Building, City College of New York, 160, Convent Avenue, 10031 New York, NY, USA
| | - Alexandre Aleixo
- Departamento de Ornitologia, Museu Paraense Emílio Goeldi (MPEG), Caixa Postal 399, Belém, PA 66040-170, Brazil
| | - Lucas E Araujo-Silva
- Departamento de Ornitologia, Museu Paraense Emílio Goeldi (MPEG), Caixa Postal 399, Belém, PA 66040-170, Brazil
| | - Camila C Ribas
- Coordenação de biodiversidade, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo 2936, Manaus, AM 69060-001, Brazil
| | - Erik Choueri
- Coordenação de biodiversidade, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo 2936, Manaus, AM 69060-001, Brazil
| | - Cristina Y Miyaki
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP 05508-090, Brazil
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17
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The roles of barriers, refugia, and chromosomal clines underlying diversification in Atlantic Forest social wasps. Sci Rep 2017; 7:7689. [PMID: 28794485 PMCID: PMC5550474 DOI: 10.1038/s41598-017-07776-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 07/03/2017] [Indexed: 12/11/2022] Open
Abstract
Phylogeographic studies have sought to explain the genetic imprints of historical climatic changes and geographic barriers within the Brazilian Atlantic Forest (AF) biota, and consequently two processes of diversification (refugia and barriers) have been proposed. Additionally, there is evidence that eustatic changes influenced the biogeographic history of the AF. Here we evaluate these contrasting diversification processes using two AF social wasp species – the mid-montane Synoeca cyanea and the lowland Synoeca aff. septentrionalis. We analyzed several sources of data including multilocus DNA sequence, climatic niche models and chromosomal features. We find support for idiosyncratic phylogeographic patterns between these wasps, involving different levels of population structure and genetic diversity, contrary suitable climatic conditions during the last glaciation, and contrasting historical movements along the AF. Our data indicate that neotectonics and refugia played distinct roles in shaping the genetic structure of these wasps. However, we argue that eustatic changes influenced the demographic expansion but not population structure in AF biota. Notably, these wasps exhibited chromosomal clines, involving chromosome number and decreasing of GC content, latitudinally oriented along the AF. Together, these results reinforce the need to consider individual organismal histories and indicate that barriers and refugia are significant factors in understanding AF evolution.
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18
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Cabanne GS, Calderón L, Trujillo Arias N, Flores P, Pessoa R, d'Horta FM, Miyaki CY. Effects of Pleistocene climate changes on species ranges and evolutionary processes in the Neotropical Atlantic Forest. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12844] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gustavo S. Cabanne
- División de Ornitología; Museo Argentino de Ciencias Naturales ‘B. Rivadavia’; Ángel Gallardo 470 Ciudad de Buenos Aires (C1405DJR) Argentina
| | - Luciano Calderón
- División de Ornitología; Museo Argentino de Ciencias Naturales ‘B. Rivadavia’; Ángel Gallardo 470 Ciudad de Buenos Aires (C1405DJR) Argentina
| | - Natalia Trujillo Arias
- División de Ornitología; Museo Argentino de Ciencias Naturales ‘B. Rivadavia’; Ángel Gallardo 470 Ciudad de Buenos Aires (C1405DJR) Argentina
| | - Pamela Flores
- Instituto de Ciencias; Universidad Nacional de General Sarmiento; Malvinas Argentinas, Buenos Aires Argentina
| | - Rodrigo Pessoa
- Centro de Ciências Biológicas e da Saúde; Universidade Estadual de Montes Claros; Montes Claros Minas Gerais Brazil
| | - Fernando M. d'Horta
- Instituto Nacional de Pesquisas da Amazônia; Av. André Araújo 2936, Aleixo 69060-001 Manaus Brazil
| | - Cristina Y. Miyaki
- Departamento de Genética e Biologia Evolutiva; Instituto de Biociências; Universidade de São; Paulo, Rua do Matão 277 05508-090 São Paulo Brazil
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19
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Menezes L, Canedo C, Batalha-Filho H, Garda AA, Gehara M, Napoli MF. Multilocus Phylogeography of the Treefrog Scinax eurydice (Anura, Hylidae) Reveals a Plio-Pleistocene Diversification in the Atlantic Forest. PLoS One 2016; 11:e0154626. [PMID: 27248688 PMCID: PMC4889069 DOI: 10.1371/journal.pone.0154626] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/16/2016] [Indexed: 11/21/2022] Open
Abstract
We aim to evaluate the genetic structure of an Atlantic Forest amphibian species, Scinax eurydice, testing the congruence among patterns identified and proposed by the literature for Pleistocene refugia, microrefugia, and geographic barriers to gene flow such as major rivers. Furthermore, we aim to evaluate predictions of such barriers and refugia on the genetic structure of the species, such as presence/absence of dispersal, timing since separation, and population expansions/contractions. We sequenced mitochondrial and nuclear genetic markers on 94 tissue samples from 41 localities. We inferred a gene tree and estimated genetic distances using mtDNA sequences. We then ran population clustering and assignment methods, AMOVA, and estimated migration rates among populations identified through mtDNA and nDNA analyses. We used a dated species tree, skyline plots, and summary statistics to evaluate concordance between population's distributions and geographic barriers and Pleistocene refugia. Scinax eurydice showed high mtDNA divergences and four clearly distinct mtDNA lineages. Species tree and population assignment tests supported the existence of two major clades corresponding to northeastern and southeastern Atlantic Forest in Brazil, each one composed of two other clades. Lineage splitting events occurred from late Pliocene to Pleistocene. We identified demographic expansions in two clades, and inexistent to low levels of migrations among different populations. Genetic patterns and demographic data support the existence of two northern Refuge and corroborate microrefugia south of the Doce/Jequitinhonha Rivers biogeographic divide. The results agree with a scenario of recent demographic expansion of lowland taxa. Scinax eurydice comprises a species complex, harboring undescribed taxa consistent with Pleistocene refugia. Two rivers lie at the boundaries among populations and endorse their role as secondary barriers to gene flow.
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Affiliation(s)
- Lucas Menezes
- Programa de Pós-Graduação em Diversidade Animal, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
| | - Clarissa Canedo
- Universidade Federal do Rio de Janeiro, Museu Nacional, Departamento de Vertebrados, Quinta da Boa Vista, s/n, 20940–040, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Henrique Batalha-Filho
- Programa de Pós-Graduação em Diversidade Animal, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
- Museu de Zoologia, Departamento de Zoologia, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
| | - Adrian Antonio Garda
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Botânica, Ecologia e Zoologia, Laboratório de Anfíbios e Répteis-LAR, Campus Universitário, Lagoa Nova, 59078–900, Natal, Rio Grande do Norte, Brasil
| | - Marcelo Gehara
- Programa de Pós-Graduação em Sistemática e Evolução, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário Lagoa Nova, 59078–900, Natal, Rio Grande do Norte, Brasil
| | - Marcelo Felgueiras Napoli
- Programa de Pós-Graduação em Diversidade Animal, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
- Universidade Federal do Rio de Janeiro, Museu Nacional, Departamento de Vertebrados, Quinta da Boa Vista, s/n, 20940–040, Rio de Janeiro, Rio de Janeiro, Brasil
- Museu de Zoologia, Departamento de Zoologia, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
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20
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Batalha‐Filho H, Miyaki CY. Late Pleistocene divergence and postglacial expansion in the Brazilian Atlantic Forest: multilocus phylogeography of
Rhopias gularis
(Aves: Passeriformes). J ZOOL SYST EVOL RES 2016. [DOI: 10.1111/jzs.12118] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Henrique Batalha‐Filho
- Departamento de Genética e Biologia Evolutiva Instituto de Biociências Universidade de São Paulo São Paulo Brazil
- Departamento de Zoologia Instituto de Biologia Universidade Federal da Bahia Salvador Brazil
| | - Cristina Y. Miyaki
- Departamento de Genética e Biologia Evolutiva Instituto de Biociências Universidade de São Paulo São Paulo Brazil
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21
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Svenning JC, Eiserhardt WL, Normand S, Ordonez A, Sandel B. The Influence of Paleoclimate on Present-Day Patterns in Biodiversity and Ecosystems. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054314] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jens-Christian Svenning
- Section for Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, DK-8000 Aarhus, Denmark;
| | | | - Signe Normand
- Section for Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, DK-8000 Aarhus, Denmark;
| | - Alejandro Ordonez
- Section for Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, DK-8000 Aarhus, Denmark;
| | - Brody Sandel
- Section for Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, DK-8000 Aarhus, Denmark;
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22
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Dantas LG, Esposito T, de Sousa ACB, Félix L, Amorim LLB, Benko-Iseppon AM, Batalha-Filho H, Pedrosa-Harand A. Low genetic diversity and high differentiation among relict populations of the neotropical gymnosperm Podocarpus sellowii (Klotz.) in the Atlantic Forest. Genetica 2014; 143:21-30. [PMID: 25532751 DOI: 10.1007/s10709-014-9809-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 12/15/2014] [Indexed: 11/28/2022]
Abstract
Podocarpus sellowii (Podocarpaceae) is one of only a few gymnosperms native to Brazil and the sole species of the genus found in the northeastern region of that country. It has a very restricted distribution in this region, with only three known populations in highland forests (called Brejos de Altitude), which apparently have been isolated from each other since the Pleistocene. Due to this long-term isolation and the fact that these populations have few adult individuals and suffer great anthropogenic pressure, low genetic variability is expected, compromising their long-term viability. The present work assessed the genetic variability and structure of northeastern populations of P. sellowii to investigate the role of Pleistocene glaciations on the genetic relationships between them and to propose strategies for their conservation by analyzing the SSR and ISSR markers of adult and juvenile individuals. Low genetic diversity was found with both markers, associated with a high differentiation of the Brejo de Baturité population in relation to the others-suggesting their isolation at different points in time, probably during the Pleistocene. Actions directed towards increasing the genetic diversity of these populations will be needed, such as planting seedlings with high genetic variability-but the high degrees of differentiation observed between the populations must be taken into account.
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Affiliation(s)
- Liliane G Dantas
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco (UFPE), Recife, PE, 50670-420, Brazil
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23
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Cabanne GS, Trujillo-Arias N, Calderón L, d'Horta FM, Miyaki CY. Phenotypic evolution of an Atlantic Forest passerine (Xiphorhynchus fuscus): biogeographic and systematic implications. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12362] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Abstract
We studied the phenotypic variation of the Atlantic Forest passerine Xiphorhynchus fuscus (Aves: Dendrocolaptidae) with the broad aim of addressing whether the history and type of forest affected the evolution of endemic taxa. We also tested whether the different subspecies and genetic lineages of X. fuscus could be considered full species. We collected plumage and body size measurements and, in combination with genetic data, used multivariate tests to evaluate the working hypotheses. Our results, combined with previous biogeographic analyses, indicate that vicariant events have been important determinants in the evolution of phenotypic characters of X. fuscus, once genetic isolation was complete. Our analysis also suggests that forest heterogeneity and ecotones are important factors in the early evolution of Atlantic Forest taxa, perhaps via divergent selection. Forest instability during the Pleistocene was critical in the evolution of phenotypic traits. We confirm that the subspecies atlanticus should be considered a full species. Other lineages or populations are also phenotypically differentiated but we do not suggest considering them as full species. They share high levels of gene flow and are part of a continuous latitudinal cline of phenotypic variation. Our study suggests that not all the historic events in the Atlantic Forest that affected the evolution of genetic lineages also influenced the evolution of phenotypic characters in the same direction and intensity. Undoubtedly, natural selection played a major role in the evolution of Atlantic Forest organisms.
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Affiliation(s)
- Gustavo S. Cabanne
- División de Ornitología, Museo Argentino de Ciencias Naturales ‘B. Rivadavia’, Ángel Gallardo 470, Ciudad de Buenos Aires, (C1405DJR) Argentina
| | - Natalia Trujillo-Arias
- División de Ornitología, Museo Argentino de Ciencias Naturales ‘B. Rivadavia’, Ángel Gallardo 470, Ciudad de Buenos Aires, (C1405DJR) Argentina
| | - Luciano Calderón
- División de Ornitología, Museo Argentino de Ciencias Naturales ‘B. Rivadavia’, Ángel Gallardo 470, Ciudad de Buenos Aires, (C1405DJR) Argentina
| | - Fernando M. d'Horta
- Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Aleixo, 69060-001 Manaus, Brazil
| | - Cristina Y. Miyaki
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São, Paulo, Rua do Matão 277, 05508-090 São Paulo, Brazil
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24
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Brunes TO, Alexandrino J, Baêta D, Zina J, Haddad CF, Sequeira F. Species limits, phylogeographic and hybridization patterns in Neotropical leaf frogs (Phyllomedusinae). ZOOL SCR 2014. [DOI: 10.1111/zsc.12079] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tuliana O. Brunes
- Departamento de Biologia; Faculdade de Ciências da Universidade do Porto; 4169-007 Porto Portugal
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Laboratório Associado; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
| | - João Alexandrino
- Departamento de Ciências Biológicas; Universidade Federal de São Paulo; 09972-270 Diadema Brasil
| | - Délio Baêta
- Departamento de Zoologia; Instituto de Biociências; Universidade Estadual Paulista; 13506-900 Rio Claro São Paulo Brasil
- Museu Nacional; Departamento de Vertebrados; Setor de Herpetologia; Universidade Federal do Rio de Janeiro; 20940-040 Rio de Janeiro Brasil
| | - Juliana Zina
- Departamento de Ciências Biológicas; Universidade Estadual do Sudoeste da Bahia; 45206-190 Jequié Bahia Brasil
| | - Célio F.B. Haddad
- Departamento de Zoologia; Instituto de Biociências; Universidade Estadual Paulista; 13506-900 Rio Claro São Paulo Brasil
| | - Fernando Sequeira
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Laboratório Associado; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
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25
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Raposo do Amaral F, Albers PK, Edwards SV, Miyaki CY. Multilocus tests of Pleistocene refugia and ancient divergence in a pair of Atlantic Forest antbirds (Myrmeciza). Mol Ecol 2013; 22:3996-4013. [DOI: 10.1111/mec.12361] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 03/24/2013] [Accepted: 03/28/2013] [Indexed: 01/23/2023]
Affiliation(s)
- Fábio Raposo do Amaral
- Departamento de Genética e Biologia Evolutiva; Universidade de São Paulo; Rua do Matão, 277, Cidade Universitária São Paulo SP CEP 05508-090 Brazil
| | - Patrick K. Albers
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology; Harvard University; 26 Oxford Street Cambridge MA 02138 USA
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology; Harvard University; 26 Oxford Street Cambridge MA 02138 USA
| | - Cristina Y. Miyaki
- Departamento de Genética e Biologia Evolutiva; Universidade de São Paulo; Rua do Matão, 277, Cidade Universitária São Paulo SP CEP 05508-090 Brazil
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26
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Molecular systematics and evolution of the Synallaxis ruficapilla complex (Aves: Furnariidae) in the Atlantic Forest. Mol Phylogenet Evol 2013; 67:86-94. [DOI: 10.1016/j.ympev.2013.01.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 01/07/2013] [Accepted: 01/09/2013] [Indexed: 10/27/2022]
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Maldonado-Coelho M, Blake JG, Silveira LF, Batalha-Filho H, Ricklefs RE. Rivers, refuges and population divergence of fire-eye antbirds (Pyriglena) in the Amazon Basin. J Evol Biol 2013; 26:1090-107. [PMID: 23442128 DOI: 10.1111/jeb.12123] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Accepted: 01/04/2013] [Indexed: 11/30/2022]
Abstract
The identification of ecological and evolutionary mechanisms that might account for the elevated biotic diversity in tropical forests is a central theme in evolutionary biology. This issue is especially relevant in the Neotropical region, where biological diversity is the highest in the world, but where few studies have been conducted to test factors causing population differentiation and speciation. We used mtDNA sequence data to examine the genetic structure within white-backed fire-eye (Pyriglena leuconota) populations along the Tocantins River valley in the south-eastern Amazon Basin, and we confront the predictions of the river and the Pleistocene refuge hypotheses with patterns of genetic variation observed in these populations. We also investigated whether these patterns reflect the recently detected shift in the course of the Tocantins River. We sampled a total of 32 individuals east of, and 52 individuals west of, the Tocantins River. Coalescent simulations and phylogeographical and population genetics analytical approaches revealed that mtDNA variation observed for fire-eye populations provides little support for the hypothesis that populations were isolated in glacial forest refuges. Instead, our data strongly support a key prediction of the river hypothesis. Our study shows that the Tocantins River has probably been the historical barrier promoting population divergence in fire-eye antbirds. Our results have important implications for a better understanding of the importance of large Amazonian rivers in vertebrate diversification in the Neotropics.
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Affiliation(s)
- M Maldonado-Coelho
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO, USA.
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28
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Batalha-Filho H, Cabanne GS, Miyaki CY. Phylogeography of an Atlantic forest passerine reveals demographic stability through the last glacial maximum. Mol Phylogenet Evol 2012; 65:892-902. [DOI: 10.1016/j.ympev.2012.08.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 07/17/2012] [Accepted: 08/14/2012] [Indexed: 10/28/2022]
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29
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Smith BT, Ribas CC, Whitney BM, HernÁndez-baÑos BE, Klicka J. Identifying biases at different spatial and temporal scales of diversification: a case study in the Neotropical parrotlet genusForpus. Mol Ecol 2012. [DOI: 10.1111/mec.12118] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brian Tilston Smith
- Museum of Natural Science; Louisiana State University; 119 Foster Hall Baton Rouge LA 70803 USA
- Marjorie Barrick Museum of Natural History; University of Nevada; Las Vegas, 4505 S. Maryland Parkway Box 454012 Las Vegas NV 89154-4012 USA
- School of Life Sciences; University of Nevada; Las Vegas, 4505 S. Maryland Parkway Las Vegas NV 89154 USA
| | - Camila C. Ribas
- Coordenação de Biodiversidade; Instituto Nacional de Pesquisas da Amazônia; Av. André Araújo Manaus AM 2936 Brasil
| | - Bret M. Whitney
- Museum of Natural Science; Louisiana State University; 119 Foster Hall Baton Rouge LA 70803 USA
| | - Blanca E. HernÁndez-baÑos
- Museo de Zoología, Facultad de Ciencias; Universidad Nacional Autónoma de México; Apartado Postal 70-399 México DF 04510 México
| | - John Klicka
- Marjorie Barrick Museum of Natural History; University of Nevada; Las Vegas, 4505 S. Maryland Parkway Box 454012 Las Vegas NV 89154-4012 USA
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