4.7 Article

Molecular systematics and biogeography of lowland antpittas (Aves, Grallariidae): The role of vicariance and dispersal in the diversification of a widespread Neotropical lineage

期刊

MOLECULAR PHYLOGENETICS AND EVOLUTION
卷 120, 期 -, 页码 375-389

出版社

ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ympev.2017.11.019

关键词

Amazonia; Ancestral range estimation; Dispersal; Diversification rates; Plio-Pleistocene; Phylogeny

资金

  1. CNPq [310593/2009-3, 574008/2008-0, 563236/2010-8, 471342/2011-4, 306843/2016-1]
  2. FAPESPA [ICAAF 023/2011, 010/2012]
  3. US National Science Foundation [NSF DEB 1241056]
  4. National Aeronautics and Space Administration (NASA)
  5. Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP grant) [2012/50260-6]
  6. NSF [DEB-1011435]
  7. CAPES fellowship [021/2016]
  8. FAPESPA fellowship [021/2016]

向作者/读者索取更多资源

We infer phylogenetic relationships, divergence times, and the diversification history of the avian Neotropical antpitta genera Hylopezus and Myrmothera (Grallariidae), based on sequence data (3,139 base pairs) from two mitochondrial (ND2 and ND3) and three nuclear nuclear introns (TGFB2, MUSK and FGB-I5) from 142 individuals of the 12 currently recognized species in Hylopezus and Myrmothera and 5 outgroup species. Phylogenetic analyses recovered 19 lineages clustered into two major clades, both distributed in Central and South America. Hylopezus nattereri, previously considered a subspecies of H. ochroleucus, was consistently recovered as the most divergent lineage within the Grallaricula/Hylopezus/Myrmothera clade. Ancestral range estimation suggested that modern lowland antpittas probably originated in the Amazonian Sedimentary basin during the middle Miocene, and that most lineages within the Hylopezus/Myrmothera clade appeared in the Plio-Pleistocene. However, the rate of diversification in the Hylopezus/Myrmothera clade appeared to have remained constant through time, with no major shifts over the 20 million years. Although the timing when most modern lineages of the Hylopezus/Myrmothera clade coincides with a period of intense landscape changes in the Neotropics (Plio-Pleistocene), the absence of any significant shifts in diversification rates over the last 20 million years challenges the view that there is a strict causal relationship between intensification of landscape changes and cladogenesis. The relative old age of the Hylopezus/Myrmothera clade coupled with an important role ascribed to dispersal for its diversification, favor an alternative scenario whereby long-term persistence and dispersal across an ever-changing landscape might explain constant rates of cladogenesis through time.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.7
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

Article Ecology

Genomic differentiation with gene flow in a widespread Amazonian floodplain-specialist bird species

Leilton Willians Luna, Camila Cherem Ribas, Alexandre Aleixo

Summary: Ecological, climatic, and palaeogeographical processes drive biological diversification. Our study found three genetic clusters in the Striped Woodcreeper, distributed in the western, central, and eastern parts of the Amazon Basin. Migration rates indicate historical barriers along the Amazonas-Solimoes River.

JOURNAL OF BIOGEOGRAPHY (2022)

Article Ornithology

Diversification across the Isthmus of Tehuantepec explains the phylogeographic arrangement of the widespread bright-rumped Attila (Attila spadiceus; Tyrannidae) and reveals the existence of two major lineages

Patricia Mendonca, Cleyssian Dias, Alexandre Aleixo, Lincoln Silva Carneiro, Juliana Araripe, Pericles Sena do Rego

Summary: The phylogeographic structure of Attila spadiceus was described using partial Cytb amplicon region analysis, revealing two principal molecular lineages and lack of reflection of morphological variation in the mitochondrial gene tree. The diversification of A. spadiceus is inferred to have started in the Pleistocene, around 1.5 million years ago, driven by the Isthmus of Tehuantepec region forming two molecular lineages.

JOURNAL OF ORNITHOLOGY (2022)

Article Ecology

Habitat association constrains population history in two sympatric ovenbirds along Amazonian floodplains

Waleska Elizangela dos Santos Barbosa, Mateus Ferreira, Eduardo de Deus Schultz, Leilton Willians Luna, Thiago Orsi Laranjeiras, Alexandre Aleixo, Camila Cherem Ribas

Summary: Distinct types of seasonally flooded habitats along Amazonian floodplains have different impacts on the population histories of two closely related ovenbird species. Differences in habitat preferences lead to varied demographic changes, gene flow, and population sizes, influenced by late Pleistocene and Holocene climatic variations.

JOURNAL OF BIOGEOGRAPHY (2022)

Article Evolutionary Biology

Integrative taxonomy of Flatbill Flycatchers (Tyrannidae) reveals a new species from the Amazonian lowlands

Carlynne C. Simoes, Pablo Vieira Cerqueira, Pedro Peloso, Alexandre Aleixo

Summary: Integrative taxonomic studies revealed taxonomic inconsistencies within Rhynchocyclus olivaceus, with evidence supporting its paraphyletic nature. The study identified at least four morphologically cryptic lineages within R. olivaceus, prompting the proposal to split these groups into separate species, including an undescribed species named Rhynchocyclus cryptus, sp. nov.

ZOOLOGICA SCRIPTA (2022)

Article Ecology

AVONET: morphological, ecological and geographical data for all birds

Joseph A. Tobias, Catherine Sheard, Alex L. Pigot, Adam J. M. Devenish, Jingyi Yang, Ferran Sayol, Montague H. C. Neate-Clegg, Nico Alioravainen, Thomas L. Weeks, Robert A. Barber, Patrick A. Walkden, Hannah E. A. MacGregor, Samuel E. I. Jones, Claire Vincent, Anna G. Phillips, Nicola M. Marples, Flavia A. Montano-Centellas, Victor Leandro-Silva, Santiago Claramunt, Bianca Darski, Benjamin G. Freeman, Tom P. Bregman, Christopher R. Cooney, Emma C. Hughes, Elliot J. R. Capp, Zoe K. Varley, Nicholas R. Friedman, Heiko Korntheuer, Andrea Corrales-Vargas, Christopher H. Trisos, Brian C. Weeks, Dagmar M. Hanz, Till Topfer, Gustavo A. Bravo, Vladimir Remes, Larissa Nowak, Lincoln S. Carneiro, Amilkar J. Moncada R., Beata Matysiokova, Daniel T. Baldassarre, Alejandra Martinez-Salinas, Jared D. Wolfe, Philip M. Chapman, Benjamin G. Daly, Marjorie C. Sorensen, Alexander Neu, Michael A. Ford, Rebekah J. Mayhew, Luis Fabio Silveira, David J. Kelly, Nathaniel N. D. Annorbah, Henry S. Pollock, Ada M. Grabowska-Zhang, Jay P. McEntee, Juan Carlos T. Gonzalez, Camila G. Meneses, Marcia C. Munoz, Luke L. Powell, Gabriel A. Jamie, Thomas J. Matthews, Oscar Johnson, Guilherme R. R. Brito, Kristof Zyskowski, Ross Crates, Michael G. Harvey, Maura Jurado Zevallos, Peter A. Hosner, Tom Bradfer-Lawrence, James M. Maley, F. Gary Stiles, Hevana S. Lima, Kaiya L. Provost, Moses Chibesa, Mmatjie Mashao, Jeffrey T. Howard, Edson Mlamba, Marcus A. H. Chua, Bicheng Li, M. Isabel Gomez, Natalia C. Garcia, Martin Packert, Jerome Fuchs, Jarome R. Ali, Elizabeth P. Derryberry, Monica L. Carlson, Rolly C. Urriza, Kristin E. Brzeski, Dewi M. Prawiradilaga, Matt J. Rayner, Eliot T. Miller, Rauri C. K. Bowie, Rene-Marie Lafontaine, R. Paul Scofield, Yingqiang Lou, Lankani Somarathna, Denis Lepage, Marshall Illif, Eike Lena Neuschulz, Mathias Templin, D. Matthias Dehling, Jacob C. Cooper, Olivier S. G. Pauwels, Kangkuso Analuddin, Jon Fjeldsa, Nathalie Seddon, Paul R. Sweet, Fabrice A. J. DeClerck, Luciano N. Naka, Jeffrey D. Brawn, Alexandre Aleixo, Katrin Bohning-Gaese, Carsten Rahbek, Susanne A. Fritz, Gavin H. Thomas, Matthias Schleuning

Summary: Functional traits provide a quantitative framework for theories in evolutionary biology, ecology, and ecosystem science. The AVONET dataset contains comprehensive functional trait data for all bird species, allowing integration with other datasets and providing a global template for testing hypotheses and exploring the origins, structure, and functioning of biodiversity.

ECOLOGY LETTERS (2022)

Article Ecology

Biogeography and diversification of bare-eyes, an endemic Amazonian clade

Lincoln Carneiro, Tiberio C. T. Burlamaqui, Alexandre Aleixo, David C. Oren, Jose Maria Cardoso Da Silva

Summary: This study investigates the biogeographical history of bare-eyes, a bird genus, in the Amazon and explores the roles of speciation and biotic interchange in the assembly of Amazonian biota. The results show that vicariance was the most critical process in shaping the distribution and differentiation of most lineages, while one event of post-speciation dispersal led to sympatric occurrence in Western Amazonia. The study highlights the importance of alternating dispersal and vicariance events in assembling continental biotas.

JOURNAL OF BIOGEOGRAPHY (2022)

Article Zoology

Diversification and species limits in scale-backed antbirds (Willisornis: Thamnophilidae), an Amazonian endemic lineage

Tania Fontes Quaresma, Aurea A. Cronemberger, Romina Batista, Alexandre Aleixo

Summary: This article presents a phylogenetic and population genetic analysis of the Willisornis genus, endemic to the Amazon Basin. The study reveals 13 independent genetic lineages and confirms the monophyly of all recognized species. The diversification of Willisornis is linked to hydrographic and climate change cycles in the Amazon Basin.

ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY (2022)

Article Ecology

The evolution of sex similarities in social signals: Climatic seasonality is associated with lower sexual dimorphism and greater elaboration of female and male signals in antbirds (Thamnophilidae)

Gabriel Macedo, Rafael S. Marcondes, Cibele Biondo, Gustavo A. Bravo, Elizabeth P. Derryberry

Summary: Selection on signals is affected by resource availability, which is regulated by climate. Harsher environments may lead to convergent development of signals in both sexes, increasing sexual dimorphism.

EVOLUTION (2022)

Article Biochemistry & Molecular Biology

Late Pleistocene landscape changes and habitat specialization as promoters of population genomic divergence in Amazonian floodplain birds

Leilton Willians Luna, Luciano Nicolas Naka, Gregory Thom, Laura Lacey Knowles, Andre Oliveira Sawakuchi, Alexandre Aleixo, Camila Cherem Ribas

Summary: This study examines the genetic divergence of three bird species specialized in seasonally flooded habitats in the Amazon basin and Rio Branco, and finds that genetic divergence is influenced by habitat specialization and river color. The complete disruption of gene flow between populations occurred during the Late Pleistocene transition, about 250,000 years ago, leading to the current genetic differentiation.

MOLECULAR ECOLOGY (2023)

Article Ornithology

West-east diversification model explains pattern phylogeography of the Band-tailed Manakin Pipra fasciicauda

Dnilson Oliveira Ferraz, Larissa Sampaio, Keila de Araujo Lima, Juliana Araripe, Fernando Sequeira, Alexandre Aleixo, Pablo Vieira Cerqueira, Lincoln S. Carneiro, Pericles Sena do Rego

Summary: This study used a multilocus molecular approach to investigate the taxonomy and biogeographic configuration of Band-tailed Manakin. Three monophyletic lineages were identified, partially overlapping with the current subspecific classification. The diversification of this species was influenced by hydrographic dynamics and climatic shifts in the Amazon basin.

JOURNAL OF ORNITHOLOGY (2023)

Article Biochemistry & Molecular Biology

Amazonian birds in more dynamic habitats have less population genetic structure and higher gene flow

Oscar Johnson, Camila C. C. Ribas, Alexandre Aleixo, Luciano N. N. Naka, Michael G. G. Harvey, Robb T. T. Brumfield

Summary: Understanding the factors that influence genetic structure across species is essential for studying speciation and population genetics. This study examined population genetic data from bird species specialized in different Amazonian habitat types. The results showed that habitat type significantly affects population genetic structure, with species in more dynamic habitats having higher levels of gene flow. These differences in genetic variation across taxa specialized in distinct habitats could lead to divergent responses to environmental change and habitat-specific diversification dynamics over time.

MOLECULAR ECOLOGY (2023)

Article Evolutionary Biology

Geographic Drivers of Genetic and Plumage Color Diversity in the Blue-Crowned Manakin

Pedro Paulo, Fernando Henrique Teofilo, Carolina Bertuol, Erico Polo, Andre E. E. Moncrieff, Lucas N. N. Bandeira, Claudia Nunez-Penichet, Igor Yuri Fernandes, Mariane Bosholn, Arielli F. F. Machado, Leilton Willians Luna, Willian Thomaz Pecanha, Aline Pessutti Rampini, Shizuka Hashimoto, Cleyssian Dias, Juliana Araripe, Alexandre Aleixo, Pericles Sena do Rego, Tomas Hrbek, Izeni P. P. Farias, A. Townsend Peterson, Igor L. L. Kaefer, Marina Anciaes

Summary: Investigating the parallel roles of geography and environmental heterogeneity in diversification provides insights into the driving forces behind the evolution of biological systems. In this study on Blue-crowned Manakins, it was found that both genetic and color diversity were influenced by geographic and climatic distances, with color variation being marginally associated with latitude and genetic distances being explained by linear and least-cost geographic distances.

EVOLUTIONARY BIOLOGY (2023)

Review Ornithology

On species concepts, species delimitation criteria, taxonomy committees, and biases: a response to Lima (2022a)

Alexandre Aleixo

Summary: In a recent commentary, Lima claims that the Brazilian Ornithological Records Committee (CBRO) is misinterpreting the general lineage species concept (GLSC) in making species ranking decisions, leading to misinformation within the Brazilian ornithological community and misleading users of the CBRO checklist. However, the arguments presented by Lima are unfounded and result from an inaccurate interpretation of the GLSC and a lack of understanding of the practical implementation of species concepts by taxonomists and taxonomy committees. Evidence from recent taxonomic treatments implemented by the CBRO confirms the use of the GLSC in guiding species ranking decisions. Unsubstantiated commentaries like Lima's may unintentionally amplify representation bias against Latin American ornithologists in global initiatives such as the publication of a single worldwide avian checklist.

ORNITHOLOGY RESEARCH (2023)

Article Biochemistry & Molecular Biology

Paraphyly and cryptic diversity unveils unexpected challenges in the naked lichens (Calvitimela, Lecanoromycetes, Ascomycota)

Markus Osaland Fjelde, Einar Timdal, Reidar Haugan, Mika Bendiksby

Summary: This study investigated the taxonomy of the crustose lichen genus Calvitimela using molecular phylogenetics and morphological observations. The results revealed evolutionarily old and deeply divergent lineages within Calvitimela, with overlapping morphological characters between different subgenera. Chemical characters were informative at the level of subgenera but often homoplastic at the species level. A practical taxonomy of Calvitimela was proposed based on these findings.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Diversification of freshwater crabs on the sky islands in the Hengduan Mountains Region, China

Bo-Yang Shi, Da Pan, Kang-Qin Zhang, Tian-Yu Gu, Darren C. J. Yeo, Peter K. L. Ng, Neil Cumberlidge, Hong-Ying Sun

Summary: This study investigates the evolutionary history and speciation mechanisms of montane potamids in the Hengduan Mountains Region. The results suggest that the vicariance events of these crabs are correlated with the emergence of sky islands due to the uplift of the mountains. The mountain ridges provided corridors for their dispersal and past climatic conditions played a crucial role in their evolutionary history. The mechanisms isolating sky islands are reinforced by the climatic features of dry-hot valleys and continue to affect local diversification.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Evolutionary history and systematics of European blind mole rats (Rodentia: Spalacidae: Nannospalax): Multilocus phylogeny and species delimitation in a puzzling group

Attila Nemeth, Edvard Mizsei, Levente Laczko, David Czaban, Zsolt Hegyeli, Szabolcs Lengyel, Gabor Csorba, Gabor Sramko

Summary: Species delimitation of European blind mole rats is challenging due to their small morphological differences and complex chromosomal evolution. This study provides a comprehensive framework to improve understanding of their evolutionary history and revise their taxonomy. The results reveal the presence of multiple superspecies and species, with distinct geographic patterns and rapid chromosomal evolution.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Phylogenomic analyses reveal a single deep-water colonisation in Patellogastropoda

Ying Qi, Zhaoyan Zhong, Xu Liu, Xing He, Yadong Zhou, Lili Zhang, Chong Chen, Katrin Linse, Jian-Wen Qiu, Jin Sun

Summary: This study investigates the phylogenetic relationships among patellogastropod families using mitochondrial and phylogenomic data. The results show that the mitochondrial phylogeny recovers monophyly of most families, but the relationships among families are still contentious. However, a more robust family-level topology consistent with morphology is achieved by phylogenomics. Additionally, the mainly deep-water families are found to be monophyletic, suggesting a single colonization of the deep water during the Jurassic.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

A model of hybrid speciation process drawn from three new poplar species originating from distant hybridization between sections

Yu-Jie Shi, Jin -Liang Huang, Jia-Xuan Mi, Jing Li, Fan-Yu Meng, Yu Zhong, Fang He, Fei -Fei Tian, Fan Zhang, Liang-Hua Chen, Han-Bo Yang, Hong-Lin Hu, Xue-Qin Wan

Summary: Despite numerous studies on hybrid speciation, our understanding of this process remains limited. In this study, we conducted an 18-year systematic investigation on Populus taxa on the Qinghai-Tibet Plateau and discovered three new taxa that originated from distant hybridization between two different sections. These hybrid taxa demonstrate greater ecological adaptability than their ancestral species due to heterosis. We propose a hybrid speciation process model that can explain important evolutionary concerns.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Phylogenomic position of genetically diverse phagotrophic stramenopile flagellates in the sediment-associated MAST-6 lineage and a potentially halotolerant placididean

Anna Cho, Denis Tikhonenkov, Gordon Lax, Kristina I. Prokina, Patrick J. Keeling

Summary: Unlike conspicuous ochrophytes, many small and overlooked flagellates belonging to basally branching stramenopiles remain poorly characterized at the cellular or genomic level. This study describes four new species, including two new genera, of sediment-dwelling MAST-6 and provides updated phylogenomic tree of stramenopiles. The characterization of these flagellates is important due to their phylogenetic diversity and abundance in various environments.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Phylogenomic conflict analyses of the plastid and mitochondrial genomes via deep genome skimming highlight their independent evolutionary histories: A case study in the cinquefoil genus Potentilla sensu lato (Potentilleae, Rosaceae)

Tian-Tian Xue, Steven B. Janssens, Bin-Bin Liu, Sheng-Xiang Yu

Summary: Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigated the phylogenetic conflicts within and between plastid and mitochondrial genomes using Potentilla as a case study. We found that both plastid and mitochondrial genomes divided Potentilla into eight highly supported clades, with two newly identified clades. Our results demonstrate that mitochondrial genes can fully resolve phylogenetic relationships among major clades of Potentilla and are not always linked with plastomes in evolutionary history.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Co-phylogeny of a hyper-symbiotic system: Endosymbiotic bacteria (Gammaproteobacteria), chewing lice (Insecta: Phthiraptera) and birds (Passeriformes)

Alexandra A. Grossi, Chunpo Tian, Mengjiao Ren, Fasheng Zou, Daniel R. Gustafsson

Summary: This study suggests that the coevolutionary relationships between chewing lice, endosymbiotic bacteria, and birds are not independent, but the patterns vary depending on the analysis method used. Additionally, louse host-switching does not seem to affect bacterial strains.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)

Article Biochemistry & Molecular Biology

Hyper-Cryptic radiation of a tropical montane plant lineage

Ingrid Olivares, Sergio Tusso, Maria Jose Sanin, Marylaure de La Harpe, Oriane Loiseau, Jonathan Rolland, Nicolas Salamin, Michael Kessler, Kentaro K. Shimizu, Margot Paris

Summary: Traditionally, differences between species have been associated with morphological variation. However, the discovery of cryptic diversity suggests that the evolution of distinct lineages can occur without morphological differences. Through genetic analysis, we found that a tropical montane plant lineage is composed of numerous unrecognized genetic groups that are not morphologically distinct. Geographic distance and topography play a crucial role in determining the genetic divergence of these groups.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2024)