Phylogenetic inferences in Passiflora based on the analysis of chloroplast genomes
| Full text | |
| Author(s): |
Thom, Gregory
[1]
;
Do Amaral, Fabio Raposo
[2]
;
Hickerson, Michael J.
[3]
;
Aleixo, Alexandre
[4]
;
Araujo-Silva, Lucas E.
[4]
;
Ribas, Camila C.
[5]
;
Choueri, Erik
[5]
;
Miyaki, Cristina Y.
[1]
Total Authors: 8
|
| Affiliation: | [1] Univ Sao Paulo, Dept Genet & Biol Evolut, Rua Matao 277, Sala 230, Cidade Univ, BR-05508090 Sao Paulo, SP - Brazil
[2] Univ Fed Sao Paulo, Lab Genet Evolut, Inst Ciencias Ambientais Quim & Farmaceut, Rua Prof Artur Riedel, BR-09972270 Diadema, SP - Brazil
[3] CUNY City Coll, Dept Biol, Marshak Sci Bldg, 160 Convent Ave, New York, NY 10031 - USA
[4] Museu Paraense Emilio Goeldi, Dept Ornitol, Caixa Postal 399, BR-66040170 Belem, PA - Brazil
[5] INPA, Coordenacao Biodiversidade, Ave Andre Araujo 2936, BR-69060001 Manaus, AM - Brazil
Total Affiliations: 5
|
| Document type: | Journal article |
| Source: | Systematic Biology; v. 67, n. 4, p. 700-718, JUL 2018. |
| Web of Science Citations: | 10 |
| Abstract | |
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 theMiddle and lowerAmazon river, whichwere 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 flowwhen estimating phylogenies at shallowdivergence 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. (AU) | |
| FAPESP's process: | 11/50143-7 - Comparative multilocus phylogeography of three species of Poospiza (Aves, Passeriformes): exploring the history of the montane Atlantic Forest |
| Grantee: | Fábio Sarubbi Raposo do Amaral |
| Support type: | BIOTA-FAPESP Program - Young Investigators Grants |
| FAPESP's process: | 13/50297-0 - Dimensions US-BIOTA São Paulo: a multidisciplinary framework for biodiversity prediction in the Brazilian Atlantic forest hotspot |
| Grantee: | Cristina Yumi Miyaki |
| Support type: | BIOTA-FAPESP Program - Thematic Grants |
| FAPESP's process: | 11/23155-4 - Comparative multilocus phylogeography of three species of Poospiza (Aves, Passeriformes): exploring the history of the montane Atlantic Forest |
| Grantee: | Fábio Sarubbi Raposo do Amaral |
| Support type: | Scholarships in Brazil - BIOTA - Young Researchers |
| FAPESP's process: | 14/00113-2 - Comparative phylogeography of four Amazonian lineages of birds: accessing biogeographic patterns based on ultra-conserved elements |
| Grantee: | Gregory Thom e Silva |
| Support type: | Scholarships in Brazil - Doctorate |
| FAPESP's process: | 12/50260-6 - Structure and evolution of the Amazonian biota and its environment: an integrative approach |
| Grantee: | Lúcia Garcez Lohmann |
| Support type: | BIOTA-FAPESP Program - Thematic Grants |
| FAPESP's process: | 15/12551-7 - Comparative phylogeography of three "varzea" forest bird lineages: surveying new biogeographic patterns for Amazonia |
| Grantee: | Gregory Thom e Silva |
| Support type: | Scholarships abroad - Research Internship - Doctorate |