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ND2 As an Additional Genetic Marker to Improve Identification of Diving Ducks Involved in Bird Strikes Sarah A

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ND2 As an Additional Genetic Marker to Improve Identification of Diving Ducks Involved in Bird Strikes Sarah A Human–Wildlife Interactions 14(3):365–375, Winter 2020 • digitalcommons.usu.edu/hwi ND2 as an additional genetic marker to improve identification of diving ducks involved in bird strikes Sarah A. M. Luttrell, Division of Birds, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Ave. NW, Washington, DC 20560, USA [email protected] Sergei Drovetski,1 Division of Birds, National Museum of Natural History, Smithsonian Institu- tion, 10th and Constitution Ave. NW, Washington, DC 20560, USA Nor Faridah Dahlan, Division of Birds, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Ave. NW, Washington, DC 20560, USA Damani Eubanks,2 Division of Birds, National Museum of Natural History, Smithsonian Institu- tion, 10th and Constitution Ave. NW, Washington, DC 20560, USA Carla J. Dove, Division of Birds, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Ave. NW, Washington, DC 20560, USA Abstract: Knowing the exact species of birds involved in damaging collisions with aircraft (bird strikes) is paramount to managing and preventing these types of human–wildlife conflicts. While a standard genetic marker, or DNA barcode (mitochondrial DNA gene cytochrome-c oxidase 1, or CO1), can reliably identify most avian species, this marker cannot distinguish among some closely related species. Diving ducks within the genus Aythya are an example of congeneric waterfowl involved in bird strikes where several species pairs cannot be reliably identified with the standard DNA barcode. Here, we describe methods for using an additional genetic marker (mitochondrial DNA gene NADH dehydrogenase subunit 2, or ND2) for identification of 9Aythya spp. Gene-specific phylogenetic trees and genetic distances among taxa reveal that ND2 is more effective than CO1 at genetic identification of diving ducks studied here. Compared with CO1, the ND2 gene tree is more statistically robust, has a minimum of 1.5 times greater genetic distance between sister clades, and resolves paraphyly in 2 clades. While CO1 is effective for identification of most bird strike cases, this study underscores the value of targeted incorporation of additional genetic markers for species identification of taxa that are known to be problematic using standard DNA barcoding. Key words: Aythya spp., birds, bird strikes, CO1, diving ducks, DNA barcoding, human– wildlife conflicts, mtDNA, ND2 Bird collisions with aircraft (hereafter, bird patterns in bird occurrence, management strat- strikes) are a daily occurrence among civil and egies for airfield habitats, and aids in the pre- military aircraft and pose indirect economic vention of this type of human–wildlife conflict losses due to delays, direct damages to air- (Dolbeer et al. 2000, Dove et al. 2008, Marra et craft, and rarely, but tragically, loss of human al. 2009, DeVault et al. 2011). life (Zakrajsek and Bissonette 2005, Pfeiffer et When diagnostic morphological evidence is al. 2018, Dolbeer et al. 2019). Most bird strikes available (e.g., feathers or feather fragments), it occur within 152 m of the ground and 3,048 can be compared with museum specimens for m of the runway, highlighting the importance rapid, accurate species identification (Dove et of airfield wildlife management to reduce the al. 2009). However, when only non-diagnostic presence of birds (Dolbeer 2006). Correct iden- or prohibitively small amounts of physical tification of species involved in bird strikes is evidence remain, or when physical identifica- crucial for understanding temporal and spatial tion expertise is unavailable, DNA sequencing 1Present address: USGS Patuxent Wildlife Research Center, 10300 Baltimore Ave, BARC-East Bldg. 308, Beltsville, MD 20705, USA 2Present address: Department of Biology, Biology-Psychology Building, 4094 Campus Dr., College Park, MD 20742, USA 366 Human–Wildlife Interactions 14(3) may be the only method for obtaining species- sequences are similar to inter-specific differ- level identifications. In these cases, a technique ences (greater scaup [A. marila]/lesser scaup [A. called “DNA barcoding” is widely used for affinis], common pochard [A. ferina]/canvasback taxonomic identification of unknown samples [A. valisineria], ferruginous duck [A. nyroca]/ (Dove et al. 2008, 2009; Waugh et al. 2011). hardhead [A. australis], and ring-necked duck DNA barcoding relies on the amplification [A. collaris]/redhead [A. americana]). We chose of a short, sufficiently variable portion of the the ND2 gene as an additional marker for genome that can provide species-level identi- molecular identification of these birds because fication when compared with a library of ref- it has the fastest substitution rate (0.029 substi- erence sequences (reviewed in DeSalle and tutions/site per Ma; 95% CI 0.024–0.033) among Goldstein 2019). In birds, as in most animals, the mtDNA genes at nearly twice the rate of the a ~650 base pair portion of the mitochondrial CO1 gene (0.016 substitutions/site per Ma; 95% (mtDNA) gene cytochrome-c oxidase 1 (CO1) CI 0.014–0.019; Lerner et al. 2011). Like CO1, has been widely tested and applied to species ND2 can be amplified across a wide variety of identification (Hebert et al. 2003a, b; Hebert et avian taxa using a small set of primers (Hackett al. 2004; Lijtmaer et al. 2012), and extensive, 1996, Sorenson et al. 1999, Drovetski et al. 2004). publicly available reference libraries exist for We chose to sequence the entire ND2 gene comparison (Ratnasingham and Hebert 2007). (1,041 base pairs) to obtain the highest possible The CO1 fragment can be amplified from many inter-specific divergence. To make our work taxa using a small number of primers (e.g., applicable to the industry standard, we com- Folmer et al. 1994, Meyer 2003) and can reli- pare ND2 to the typical CO1 vertebrate barcod- ably identify >90% of avian species that have ing region (~650 base pairs), which relies on been barcoded to date (e.g., Nearctic: Kerr the 5’ region of the CO1 gene. Previous studies et al. 2007, 2009; Palearctic: Aliabadian et al. have successfully used ND2 in subspecies level 2009; Neotropics: Chavez et al. 2015; Japanese identifications in passerine birds and in the Archipelago: Saitoh et al. 2015; New Zealand: phylogenetic reconstruction of dabbling duck Tizard et al. 2019). CO1 barcoding has been (Anatidae, Anatini) genera (e.g., Johnson and successfully applied to identification of bird Sorenson 1998, Drovetski et al. 2005, Drovetski strikes for over a decade (Dove et al. 2008, 2009; and Fadeev 2010, Dove et al. 2013). Waugh et al. 2011). However, the compara- tively low mtDNA mutation rate that makes Methods CO1 powerful for most species-level discrimi- We analyzed 96 sequences from both genes nation appears insufficient for distinguish- (CO1 n = 58; ND2 n = 38). We obtained 45 ing closely related species or subspecific taxa sequences of CO1 (n = 35) and ND2 (n = 10) (Hebert et al. 2003b, Dove et al. 2013, Drovetski from online searches of GenBank (https:// et al. 2014). When a single barcoding marker www.ncbi.nlm.nih.gov/genbank/) and Barcode contains insufficient resolution for high-con- of Life Database (http://www.boldsystems. fidence taxonomic identification, the targeted org/) and generated 51 new sequences of CO1 use of an additional marker can maintain the (n = 23) and ND2 (n = 28) using frozen tissue high-throughput workflow of a single marker from vouchered museum specimens (Table (CO1) while increasing the confidence of iden- 1). These sequences represent 9 of 12 Aythya tifications among closely related taxa. spp. The 3 species that we did not include are Diving ducks in the genus Aythya that are unlikely to be involved in bird strikes due to involved in bird strikes are a good example their conservation status and range restrictions. of taxa in which CO1 barcoding has limited They include 2 endangered species (Baer’s effectiveness (Kerr et al. 2009). In this study, pochard [A. baeri], native to southeast Asia, and we explore the usefulness of an additional Madagascan pochard [A. innotata], Madagascar molecular marker, NADH dehydrogenase sub- endemic) and 1 New Zealand endemic spe- unit 2 (ND2), for distinguishing Aythya spp. cies (New Zealand scaup [A. novaeseelandiae]). frequently involved in bird strikes. We focus We used red-crested pochard (Netta rufina; 1 specifically on 4 closely related sister species sequence for each CO1 and ND2, obtained from pairs where intra-specific differences in CO1 GenBank) as an outgroup. ND2 and diving ducks in bird strikes • Luttrell et al. 367 Table 1. Sequences used to build phylogenetic gene trees of 9 diving duck species (Aythya spp.), including unique identifiers for sequences available on public online databases. Genus Species Common NCBI NCBI BOLD ID/Catalog Date Lat Lon name (ND2) (CO1) (CO1) number* Aythya affinis Lesser DQ434306 BRDC155-5 CWS149010151 Oct. 27, 50.08 -95.59 scaup 2003 Aythya affinis Lesser DQ434307 BRDC156-5 CWS149020192 May 11, 44.16 -79.30 scaup 2004 Aythya affinis Lesser DQ434308 BRDC157-5 CWS149020200 Aug. 11, 42.36 -80.29 scaup 2004 Aythya affinis Lesser MW151590 MW151618 USNM601772 Aug. 24, 64.70 -147.13 scaup 2000 Aythya affinis Lesser BROMB434-6 ROM93289 Mar. 23, 43.38 -79.22 scaup 2003 Aythya affinis Lesser MW151591 MW151619 USNM638910 Nov. 10, 58.36 -134.58 scaup 2007 Aythya affinis Lesser MW151592 USNM643706 Jan. 5, 38.93 -76.30 scaup 2011 Aythya affinis Lesser EU585684 IPMB22515 scaup Aythya americana Redhead AF090337 AF090337 CYTC4103-12 26.66 -97.40 Aythya americana Redhead DQ434315 BRDC144-5 CWS146010097 Sep. 25, 53.19 -112.42 2003 Aythya americana Redhead DQ434316 BRDC145-5 CWS146010098 Nov. 9, 51.19 -113.28 2003 Aythya americana Redhead DQ434313 BRDC147-5 CWS146010100 Sep. 22, 54.25 -113.36 2003 Aythya americana Redhead DQ434314 BRDC148-5 CWS146010169 Oct. 21, 50.51 -112.34 2003 Aythya americana Redhead MW151593 MW151620 USNM639463 Jan. 26, 39.15 -77.52 2008 Aythya americana Redhead MW151594 MW151621 USNM644365 Jun. 17, 40.79 -111.98 2010 Aythya australis Hardhead MW151595 MW151622 ANWC B28997 Apr.
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