Overcoming challenges to morphological and molecular identification of Empidonax flycatchers: a case study with a Dusky Flycatcher

Abstract

ABSTRACT. Flycatchers in the genus Empidonax are among the most difficult avian taxonomic groups to identify to species. Observers often rely on calls or songs in the field or detailed morphometrics in the hand to identify species. In January and February 2013, we twice captured an Empidonax flycatcher at the Virginia Zoo in Norfolk, Virginia. After being unable to identify the flycatcher to species level using morphometrics and photographs, we extracted DNA from two tail feathers collected during the second encounter to identify the individual genetically.Comparison of cytochrome c oxidase I (COI) with reference sequences in the Barcode of Life Database (BOLD) suggested that the specimen had a >99.8% probability of placement as a Dusky Flycatcher (Empidonax oberholseri). Additional comparisons of NADH dehydrogenase subunit 2 (ND2) to reference sequences in GenBank, however, suggested that the specimen was a Pine Flycatcher (Empidonax affinis), a species not represented in BOLD and confined geographically to a small area in Mexico and Guatemala. After analyzing both COI and ND2 from additional vouchered specimens, the bird caught in Virginia was determined to be a Dusky Flycatcher. We also suspect that some of the sequences in GenBank might derive from incorrectly identified specimens or otherwise could represent overlooked pseudogenes. Because the putative identification, based on GenBank sequences, would have represented the first record of Pine Flycatcher from the United States, our results reinforce the need for carefully vetted and taxonomically comprehensive molecular databases to allow definitive conclusions about sample identity. Further molecular phylogeographic review of this genus is warranted to resolve haplotype ambiguities.RESUMEN. Retos sobre la identificación morfológica y molecular de papamoscas del genero Empidonax: un caso de estudio con Empidonax oberholseri Los papamoscas Empidonax se encuentran entre el grupo de aves más difíciles de identificar taxonómicamente a nivel de especies. Para identificar estos pájaros, los observadores dependen, particularmente, del canto o de las llamadas o de detalles que se pueden observar cuando tienen el ave en la mano En enero y febrero del 2013, en dos ocasiones capturamos un Empidonax en el Zoológico de Virginia, Virginia. No pudimos identificar la especie utilizando fotografías o rasgos morfométricos y a tales efectos extrajimos ADN de dos de las plumas del rabo, para tratar de identificar el segundo individuo genéticamente. La comparación de la oxidasa c citocromica I (COI), con la referencia secuencial en la base de datos del "Código de Barras de la Vida" (BOLD) sugirió que el espécimen tenía >99.8% de probabilidad de ser un Empidonax oberholseri. No obstante, una comparación de NADH dehidrogenasa, subunidad 2 (ND2) del Banco Genético (GenBank) sugería que el ave era Empidonax affinis, una especie que no estaba representada en BOLD y geográficamente confinada a unárea pequeña de México y Guatemala. Luego de analizar el COI y el ND2 de especímenes adicio...

Evaluating Data Quality and Changes in Species Identification in a Citizen Science Bird Monitoring Project

“…Certain bird species and taxonomic groups can be more challenging than others to identify (Rigby et al 2019;Gorleri et al 2022). We found that the species that were detected less often by volunteers were species with more traditionally challenging identification characteristics, such as warblers or Empidonax flycatchers (Heller et al 2016). For example, in our dataset, professional biologists detected 5 times more Wilson's Warblers (Cardellina pusilla), 4.4 times more Yellow-breasted Chats (Icteria virens), and 1.4 times more Yellow-rumped Warblers (Setophaga coronata) than citizen scientists.…”

Digital Accessible Knowledge and well-inventoried sites for birds in Mexico: baseline sites for measuring faunistic change

“…We avoided the temptation to attempt to take the taxonomic treatment to a newer authority list (e.g., Gill & Donsker, 2014 ; Navarro-Sigüenza & Peterson, 2004 ; Peterson & Navarro-Sigüenza, 2006 ) because taxonomic splitting, which has dominated recent years of taxonomic work, would cause considerable confusion of names applied to older records. Hence, we reduced the initial, highly redundant set of names to 1,027 names that coincided with the taxonomy of the American Ornithologists’ Union ( AOU, 1998 ), except that we merged Empidonax traillii and E. alnorum , in light of very frequent confusion in identification ( Heller et al, 2016 ). This step was achieved based on long years of experience with Mexican bird taxonomy, plus occasional consultation of the literature ( Monroe & Sibley, 1993 ; Peters, 1931–1987 ) and online ( http://avibase.bsc-eoc.org/ ) resources.…”

Peer Review #1 of "Digital Accessible Knowledge and well-inventoried sites for birds in Mexico: baseline sites for measuring faunistic change (v0.1)"

“…We avoided the temptation to attempt to take the taxonomic treatment to a newer authority list (e.g., Gill & Donsker 2014;Navarro-Sigüenza & Peterson 2004;Peterson & Navarro-Sigüenza 2006) because taxonomic splitting, which has dominated recent years of taxonomic work, would cause considerable confusion of names applied to older records. Hence, we reduced the initial, highly redundant set of names to 1027 names that coincided with the taxonomy of the American Ornithologists' Union (AOU 1998), except that we merged Empidonax traillii and E. alnorum, in light of very frequent confusion in identification (Heller et al 2016). This step was achieved based on long years of experience with Mexican bird taxonomy, plus occasional consultation of the literature (Monroe & Sibley 1993;Peters 1931Peters -1987 and online (http://avibase.bsc-eoc.org/) resources.…”