MtDNA ND2 sequence identifies Streaked Horned Lark (Eremophila alpestris strigata) from birdstrike to US Air Force F-15 at Portland International Airport, Oregon

Dove, Carla J.; Dahlan, Nor Faridah; Drovetski, Sergei V.

doi:10.1007/s12686-013-9952-2

Cited by 3 publications

(4 citation statements)

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“…() for COI and Dove et al. () for ND2. We constructed maximum likelihood trees with additional Empidonax sequences from GenBank using PhyML 3.0 (Guindon et al.…”

Section: Methodsmentioning

confidence: 97%

“…Calami were excised from the rectrices using sterile scissors and DNA extraction methods followed Dove et al. (). No other Empidonax specimens were handled in the lab at this time.…”

Section: Methodsmentioning

confidence: 99%

“…Two of four rectrices collected were used for genetic analysis at the Feather Identification Lab (Smithsonian Institution, Washington, D.C.). Calami were excised from the rectrices using sterile scissors and DNA extraction methods followed Dove et al (2013). No other Empidonax specimens were handled in the lab at this time.…”

Section: Methodsmentioning

confidence: 99%

“…Because the Dusky Flycatcher was only represented in GenBank by a single specimen, we sequenced both COI and ND2 genes from five additional museum specimens of Dusky Flycatchers and also from five museum specimens of the closely related Pine Flycatcher (Empidonax affinis; Table 1). PCR and sequencing methods followed Dove et al (2008) for COI and Dove et al (2013) for ND2. We constructed J.…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2016

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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...

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“…() for COI and Dove et al. () for ND2. We constructed maximum likelihood trees with additional Empidonax sequences from GenBank using PhyML 3.0 (Guindon et al.…”

Section: Methodsmentioning

confidence: 97%

“…Calami were excised from the rectrices using sterile scissors and DNA extraction methods followed Dove et al. (). No other Empidonax specimens were handled in the lab at this time.…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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

et al. 2016

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Mass mortality of birds on railway track genetically identified as critically endangered Red-headed Vulture (Sarcogyps calvus) in Ranipur Wildlife Sanctuary, Uttar Pradesh, India

Khatri

Ghosh

Jabin

et al. 2019

Conservation Genet Resour

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Limited Phylogeographic Signal in Sex-Linked and Autosomal Loci Despite Geographically, Ecologically, and Phenotypically Concordant Structure of mtDNA Variation in the Holarctic Avian Genus Eremophila

Drovetski

Raković²,

Semenov

et al. 2014

PLoS ONE

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Phylogeographic studies of Holarctic birds are challenging because they involve vast geographic scale, complex glacial history, extensive phenotypic variation, and heterogeneous taxonomic treatment across countries, all of which require large sample sizes. Knowledge about the quality of phylogeographic information provided by different loci is crucial for study design. We use sequences of one mtDNA gene, one sex-linked intron, and one autosomal intron to elucidate large scale phylogeographic patterns in the Holarctic lark genus Eremophila. The mtDNA ND2 gene identified six geographically, ecologically, and phenotypically concordant clades in the Palearctic that diverged in the Early - Middle Pleistocene and suggested paraphyly of the horned lark (E. alpestris) with respect to the Temminck's lark (E. bilopha). In the Nearctic, ND2 identified five subclades which diverged in the Late Pleistocene. They overlapped geographically and were not concordant phenotypically or ecologically. Nuclear alleles provided little information on geographic structuring of genetic variation in horned larks beyond supporting the monophyly of Eremophila and paraphyly of the horned lark. Multilocus species trees based on two nuclear or all three loci provided poor support for haplogroups identified by mtDNA. The node ages calculated using mtDNA were consistent with the available paleontological data, whereas individual nuclear loci and multilocus species trees appeared to underestimate node ages. We argue that mtDNA is capable of discovering independent evolutionary units within avian taxa and can provide a reasonable phylogeographic hypothesis when geographic scale, geologic history, and phenotypic variation in the study system are too complex for proposing reasonable a priori hypotheses required for multilocus methods. Finally, we suggest splitting the currently recognized horned lark into five Palearctic and one Nearctic species.

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MtDNA ND2 sequence identifies Streaked Horned Lark (Eremophila alpestris strigata) from birdstrike to US Air Force F-15 at Portland International Airport, Oregon

Cited by 3 publications

References 9 publications

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

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

Mass mortality of birds on railway track genetically identified as critically endangered Red-headed Vulture (Sarcogyps calvus) in Ranipur Wildlife Sanctuary, Uttar Pradesh, India

Limited Phylogeographic Signal in Sex-Linked and Autosomal Loci Despite Geographically, Ecologically, and Phenotypically Concordant Structure of mtDNA Variation in the Holarctic Avian Genus Eremophila

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