LB 20-207 - Feather DNA solves sex determination mysteries and identifies cryptic species of San Francisco Bay Area birds.

Thursday, August 18, 2022

5:00 PM – 6:30 PM EDT

Located in: ESA Exhibit Hall

Presenting Author(s)

SA

Sebastian Acevedo

Santa Clara University, United States

Coauthor(s)

DC

D’Angelo Castillo

Santa Clara University, United States
DW

Dan Wenny

San Francisco Bay Bird Observatory, United States
KL

Katie LaBarbera

San Francisco Bay Bird Observatory
Milpitas, CA, United States
YW

Yiwei Wang

San Francisco Bay Bird Observatory, United States
AB

Anthony Barnosky

Stanford University, California, United States
Jorge Ramos

Associate Director for Environmental Education
Jasper Ridge Biological University, Stanford University
Woodside, California, United States
JT

Julian D. Tattoni

San Francisco Bay Bird Observatory, United States
JW

Justen Whittall

Santa Clara University, United States

Background/Question/Methods:

Birds are renowned for their morphological diversity, which is typically sufficient to distinguish species and the sexes therein. However, in some species, morphology cannot accurately separate closely related cryptic species and fails to decipher the sexes. In such cases, DNA markers can provide new perspectives. For instance, the sex of many Yellow-rumped Warblers (Setophaga coronata) is indiscernible based on plumage. Similarly, “Western Flycatcher” refers to two species that are nearly impossible to distinguish in the hand (Empidonax difficilis and Empidonax occidentalis). Therefore, we extracted DNA from feathers of these two species collected at bird-banding stations in the San Francisco Bay Area, amplified specific DNA regions using PCR, and analyzed these amplified regions with agarose gels and Sanger sequencing. For Yellow-rumped Warblers, we amplified a region that differentiates sex chromosomes and distinguished sex on agarose gels. For Western Flycatchers, we amplified and sequenced the CO1 gene, a region of the mitochondrial genome used to distinguish closely related species of birds.

Results/Conclusions:

We successfully distinguished the sex of Yellow-rumped Warblers in 13/14 feather samples. The molecularly determined sex ratio was approximately equal (6 males:7 females), suggesting no strong seasonal pattern. We confirmed morphology-based predictions for 8/8 birds and solved unknown sex determination in 5/5 birds with completely unknown sex. For Western Flycatchers, we successfully identified the species of 7/9 feather samples. All seven identified feather samples belonged to Pacific-slope Flycatchers (Empidonax difficilis), consistent with the species’ published breeding distribution. One flycatcher feather sample exhibited a unique, 3x-confirmed polymorphism suggesting an additional layer of cryptic variation. Overall, we demonstrate that sufficient DNA can be extracted from bird feathers collected at bird-banding stations to launch future studies involving sex-specific migration trends and hidden biodiversity among cryptic species. For example, molecular sex determination data for Yellow-rumped Warblers may be compared to morphological data to uncover reliable physical characteristics for identifying sex. The challenges of identifying morphologically-similar sexes and cryptic species in the field can be overcome using DNA markers, with resulting studies able to inform conservation and management decisions.