Phenotypic and genetic structure support gene flow generating gene tree discordances in an Amazonian floodplain endemic species
Before populations become independent evolutionary lineages, the effects of micro evolutionary processes tend to generate complex scenarios of diversification that may affect phylogenetic reconstruction. Not accounting for gene flow in species tree estimates can directly impact topology, effective p...
| Autor principal: | Thom, Gregory |
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| Outros Autores: | Amaral, Fábio Raposo do, Hickerson, Michael J., Aleixo, Alexandre, Araújo-Silva, Lucas Eduardo, Ribas, Camila Cherem, Choueri, Érik Lacerda, Miyaki, Cristina Yumi |
| Grau: | Artigo |
| Idioma: | English |
| Publicado em: |
Systematic Biology
2020
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| Assuntos: | |
| Acesso em linha: |
https://repositorio.inpa.gov.br/handle/1/15623 |
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oai:repositorio:1-15623 |
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oai:repositorio:1-15623 Phenotypic and genetic structure support gene flow generating gene tree discordances in an Amazonian floodplain endemic species Thom, Gregory Amaral, Fábio Raposo do Hickerson, Michael J. Aleixo, Alexandre Araújo-Silva, Lucas Eduardo Ribas, Camila Cherem Choueri, Érik Lacerda Miyaki, Cristina Yumi Dna, Mitochondrial Animals Biological Model Brasil Classification Gene Flow Genetics Genotype Evolution, Molecular Passeriformes Phenotype Phylogeny Species Differentiation Animal Brasil Dna, Mitochondrial Evolution, Molecular Gene Flow Genetic Speciation Genotype Models, Genetic Passeriformes Phenotype Phylogeny Before populations become independent evolutionary lineages, the effects of micro evolutionary processes tend to generate complex scenarios of diversification that may affect phylogenetic reconstruction. Not accounting for gene flow in species tree estimates can directly impact topology, effective population sizes and branch lengths, and the resulting estimation errors are still poorly understood in wild populations. In this study, we used an integrative approach, including sequence capture of ultra-conserved elements (UCEs), mtDNA Sanger sequencing and morphological data to investigate species limits and phylogenetic relationships in face of gene flow in an Amazonian endemic species (Myrmoborus lugubris: Aves).We used commonly implemented species tree and model-based approaches to understand the potential effects of gene flow in phylogenetic reconstructions. The genetic structure observed was congruent with the four recognized subspecies of M. lugubris. Morphological and UCEs data supported the presence of a wide hybrid zone between M. l. femininus from the Madeira river and M. l. lugubris from the Middle and lower Amazon river, which were recovered as sister taxa by species tree methods. When fitting gene flowinto simulated demographic models with different topologies, the best-fit model indicated these two taxa as non-sister lineages, a finding that is in agreement with the results of mitochondrial and morphological analyses. Our results demonstrated that failing to account for gene flow when estimating phylogenies at shallow divergence levels can generate topological uncertainty, which can nevertheless be statistically well supported, and that model testing approaches using simulated data can be useful tools to test alternative phylogenetic hypotheses. © The Author(s) 2018. 2020-05-15T14:59:47Z 2020-05-15T14:59:47Z 2018 Artigo https://repositorio.inpa.gov.br/handle/1/15623 10.1093/sysbio/syy004 en Volume 67, Número 4, Pags. 700-718 Attribution-NonCommercial-NoDerivs 3.0 Brazil http://creativecommons.org/licenses/by-nc-nd/3.0/br/ application/pdf Systematic Biology |
| institution |
Instituto Nacional de Pesquisas da Amazônia - Repositório Institucional |
| collection |
INPA-RI |
| language |
English |
| topic |
Dna, Mitochondrial Animals Biological Model Brasil Classification Gene Flow Genetics Genotype Evolution, Molecular Passeriformes Phenotype Phylogeny Species Differentiation Animal Brasil Dna, Mitochondrial Evolution, Molecular Gene Flow Genetic Speciation Genotype Models, Genetic Passeriformes Phenotype Phylogeny |
| spellingShingle |
Dna, Mitochondrial Animals Biological Model Brasil Classification Gene Flow Genetics Genotype Evolution, Molecular Passeriformes Phenotype Phylogeny Species Differentiation Animal Brasil Dna, Mitochondrial Evolution, Molecular Gene Flow Genetic Speciation Genotype Models, Genetic Passeriformes Phenotype Phylogeny Thom, Gregory Phenotypic and genetic structure support gene flow generating gene tree discordances in an Amazonian floodplain endemic species |
| topic_facet |
Dna, Mitochondrial Animals Biological Model Brasil Classification Gene Flow Genetics Genotype Evolution, Molecular Passeriformes Phenotype Phylogeny Species Differentiation Animal Brasil Dna, Mitochondrial Evolution, Molecular Gene Flow Genetic Speciation Genotype Models, Genetic Passeriformes Phenotype Phylogeny |
| description |
Before populations become independent evolutionary lineages, the effects of micro evolutionary processes tend to generate complex scenarios of diversification that may affect phylogenetic reconstruction. Not accounting for gene flow in species tree estimates can directly impact topology, effective population sizes and branch lengths, and the resulting estimation errors are still poorly understood in wild populations. In this study, we used an integrative approach, including sequence capture of ultra-conserved elements (UCEs), mtDNA Sanger sequencing and morphological data to investigate species limits and phylogenetic relationships in face of gene flow in an Amazonian endemic species (Myrmoborus lugubris: Aves).We used commonly implemented species tree and model-based approaches to understand the potential effects of gene flow in phylogenetic reconstructions. The genetic structure observed was congruent with the four recognized subspecies of M. lugubris. Morphological and UCEs data supported the presence of a wide hybrid zone between M. l. femininus from the Madeira river and M. l. lugubris from the Middle and lower Amazon river, which were recovered as sister taxa by species tree methods. When fitting gene flowinto simulated demographic models with different topologies, the best-fit model indicated these two taxa as non-sister lineages, a finding that is in agreement with the results of mitochondrial and morphological analyses. Our results demonstrated that failing to account for gene flow when estimating phylogenies at shallow divergence levels can generate topological uncertainty, which can nevertheless be statistically well supported, and that model testing approaches using simulated data can be useful tools to test alternative phylogenetic hypotheses. © The Author(s) 2018. |
| format |
Artigo |
| author |
Thom, Gregory |
| author2 |
Amaral, Fábio Raposo do Hickerson, Michael J. Aleixo, Alexandre Araújo-Silva, Lucas Eduardo Ribas, Camila Cherem Choueri, Érik Lacerda Miyaki, Cristina Yumi |
| author2Str |
Amaral, Fábio Raposo do Hickerson, Michael J. Aleixo, Alexandre Araújo-Silva, Lucas Eduardo Ribas, Camila Cherem Choueri, Érik Lacerda Miyaki, Cristina Yumi |
| title |
Phenotypic and genetic structure support gene flow generating gene tree discordances in an Amazonian floodplain endemic species |
| title_short |
Phenotypic and genetic structure support gene flow generating gene tree discordances in an Amazonian floodplain endemic species |
| title_full |
Phenotypic and genetic structure support gene flow generating gene tree discordances in an Amazonian floodplain endemic species |
| title_fullStr |
Phenotypic and genetic structure support gene flow generating gene tree discordances in an Amazonian floodplain endemic species |
| title_full_unstemmed |
Phenotypic and genetic structure support gene flow generating gene tree discordances in an Amazonian floodplain endemic species |
| title_sort |
phenotypic and genetic structure support gene flow generating gene tree discordances in an amazonian floodplain endemic species |
| publisher |
Systematic Biology |
| publishDate |
2020 |
| url |
https://repositorio.inpa.gov.br/handle/1/15623 |
| _version_ |
1787144109084901376 |
| score |
11.755432 |