Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness

Author(s):Show less -

Leite, Rafael N. ^[1] ; Kimball, Rebecca T. ^[2] ; Braun, Edward L. ^[2] ; Derryberry, Elizabeth P. ^[3] ; Hosner, Peter A. ^{[4, 5]} ; Derryberry, Graham E. ^{[6, 7]} ; Anciaes, Marina ^[8] ; McKay, Jessica S. ^[9] ; Aleixo, Alexandre ^{[10, 11]} ; Ribas, Camila C. ^[8] ; Brumfield, Robb T. ^{[6, 7]} ; Cracraft, Joel ^[9]

Affiliation:Show less -

^[1] Univ Sao Paulo, Dept Genet & Evolutionary Biol, Sao Paulo, SP - Brazil

^[2] Univ Florida, Dept Biol, Gainesville, FL - USA

^[3] Univ Tennessee, Dept Ecol & Evolutionary Biol, Knoxville, TN - USA

^[4] Univ Copenhagen, Nat Hist Museum Denmark, Copenhagen - Denmark

^[5] Univ Copenhagen, Ctr Macroecol Evolut & Climate, Copenhagen - Denmark

^[6] Louisiana State Univ, Museum Nat Sci, Baton Rouge, LA 70803 - USA

^[7] Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 - USA

^[8] Inst Nacl de Pesquisas da Amazonia, Coordenacao Biodiversidade, Manaus, Amazonas - Brazil

^[9] Amer Museum Nat Hist, Dept Ornithol, New York, NY 10024 - USA

^[10] Univ Helsinki, Finnish Museum Nat Hist, Helsinki - Finland

^[11] Museu Paraense Emilio Goeldi, Dept Zool, Belem, PA - Brazil

• Document type: Journal article
• Source: Molecular Phylogenetics and Evolution; v. 155, FEB 2021.
• Web of Science Citations: 0

Abstract

Target capture sequencing effectively generates molecular marker arrays useful for molecular systematics. These extensive data sets are advantageous where previous studies using a few loci have failed to resolve relationships confidently. Moreover, target capture is well-suited to fragmented source DNA, allowing data collection from species that lack fresh tissues. Herein we use target capture to generate data for a phylogeny of the avian family Pipridae (manakins), a group that has been the subject of many behavioral and ecological studies. Most manakin species feature lek mating systems, where males exhibit complex behavioral displays including mechanical and vocal sounds, coordinated movements of multiple males, and high speed movements. We analyzed thousands of ultraconserved element (UCE) loci along with a smaller number of coding exons and their flanking regions from all but one species of Pipridae. We examined three different methods of phylogenetic estimation (concatenation and two multispecies coalescent methods). Phylogenetic inferences using UCE data yielded strongly supported estimates of phylogeny regardless of analytical method. Exon probes had limited capability to capture sequence data and resulted in phylogeny estimates with reduced support and modest topological differences relative to the UCE trees, although these conflicts had limited support. Two genera were paraphyletic among all analyses and data sets, with Antilophia nested within Chiroxiphia and Tyranneutes nested within Neopelma. The Chiroxiphia-Antilophia Glade was an exception to the generally high support we observed; the topology of this Glade differed among analyses, even those based on UCE data. To further explore relationships within this group, we employed two filtering strategies to remove low-information loci. Those analyses resulted in distinct topologies, suggesting that the relationships we identified within Chiroxiphia-Antilophia should be interpreted with caution. Despite the existence of a few continuing uncertainties, our analyses resulted in a robust phylogenetic hypothesis of the family Pipridae that provides a comparative framework for future ecomorphological and behavioral studies. (AU)

• FAPESP's process: 16/08356-7 - Structure and evolution of the Amazonian biota: bird biogeography
• Grantee: Rafael Do Nascimento Leite
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 12/50260-6 - Structure and evolution of the Amazonian biota and its environment: an integrative approach
• Grantee: Lúcia Garcez Lohmann
• Support Opportunities: BIOTA-FAPESP Program - Thematic Grants