University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln USGS Staff -- Published Research US Geological Survey 2011 Genetic Applications in Avian Conservation Susan M. Haig U.S. Geological Survey, [email protected] Whitcomb M. Bronaugh Oregon State University Rachel S. Crowhurst Oregon State University Jesse D'Elia U.S. Fish and Wildlife Service Collin A. Eagles-Smith U.S. Geological Survey See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/usgsstaffpub Haig, Susan M.; Bronaugh, Whitcomb M.; Crowhurst, Rachel S.; D'Elia, Jesse; Eagles-Smith, Collin A.; Epps, Clinton W.; Knaus, Brian; Miller, Mark P.; Moses, Michael L.; Oyler-McCance, Sara; Robinson, W. Douglas; and Sidlauskas, Brian, "Genetic Applications in Avian Conservation" (2011). USGS Staff -- Published Research. 668. https://digitalcommons.unl.edu/usgsstaffpub/668 This Article is brought to you for free and open access by the US Geological Survey at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in USGS Staff -- Published Research by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Susan M. Haig, Whitcomb M. Bronaugh, Rachel S. Crowhurst, Jesse D'Elia, Collin A. Eagles-Smith, Clinton W. Epps, Brian Knaus, Mark P. Miller, Michael L. Moses, Sara Oyler-McCance, W. Douglas Robinson, and Brian Sidlauskas This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/ usgsstaffpub/668 The Auk 128(2):205–229, 2011 The American Ornithologists’ Union, 2011. Printed in USA. SPECIAL REVIEWS IN ORNITHOLOGY GENETIC APPLICATIONS IN AVIAN CONSERVATION SUSAN M. HAIG,1,6 WHITCOMB M. BRONAUGH,2 RACHEL S. CROWHURST,2 JESSE D’ELIA,2,3 COLLIN A. EAGLES-SMITH,1 CLINTON W. EPPS,2 BRIAN KNAUS,4 MARK P. M ILLER,1 MICHAEL L. MOSES,2 SARA OYLER-MCCANCE,5 W. DOUGLAS ROBINSON,2 AND BRIAN SIDLAUSKAS2 1U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, 3200 SW Jefferson Way, Corvallis, Oregon 97331, USA; 2Department of Fisheries and Wildlife, Oregon State University, 104 Nash Hall, Corvallis, Oregon 97331, USA; 3U.S. Fish and Wildlife Service, Pacific Regional Office, 911 NE 11th Avenue, Portland, Oregon 97232, USA; 4U.S. Forest Service, Pacific Northwest Research Station, 3200 SW Jefferson Way, Corvallis, Oregon 97331, USA; and 5U.S. Geological Survey, Fort Collins Science Center, 2150 Centre Avenue, Building C, Fort Collins, Colorado 80526, USA A fundamental need in conserving species and their hab- , Garnett and Christidis , Haig and D’Elia ). Despite itats is defining distinct entities that range from individuals to the importance of defining these units, boundaries of species, sub- species to ecosystems and beyond (Table ; Ryder , Moritz species, and populations are not always clear, and hybridization , Mayden and Wood , Haig and Avise , Hazevoet can further conflate taxonomic analyses and conservation options , Palumbi and Cipriano , Hebert et al. , Mace , (Haig and Allendorf ). Advances in conservation genetics Wheeler et al. , Armstrong and Ball , Baker , Ellis have proved helpful in resolving some long-standing taxonomic et al. , Winker and Haig ). Rapid progression in this inter- questions in birds, but philosophical disagreements over funda- disciplinary field continues at an exponential rate; thus, periodic mental taxonomic concepts remain. updates on theory, techniques, and applications are important for Species.—Although birds are arguably the best-studied informing practitioners and consumers of genetic information. vertebrate group, vigorous debate continues over which spe- Here, we outline conservation topics for which genetic informa- cies definition best applies to them. The three top contenders tion can be helpful, provide examples of where genetic techniques include the biological species concept (BSC; see Tobias et al. , have been used best in avian conservation, and point to current Winker a)—the most commonly used in avian taxonomy— technical bottlenecks that prevent better use of genomics to re- and two that have emerged from cladistics (the phylogenetic and solve conservation issues related to birds. We hope this review will monophyletic species concepts; Cracraft , ; Mishler and provide geneticists and avian ecologists with a mutually beneficial Brandon ; McKitrick and Zink ; Zink and McKitrick dialogue on how this integrated field can solve current and future ). In part because of the multiplicity of applied species con- problems. cepts, avian taxonomy is far from stable at any level, and this has real-world conservation implications. For example, patterns TAXONOMY of endemism in the birds of Mexico (Peterson and Navarro- Sigüenza ) and the Philippines (Peterson ) depend on If conservation strives to preserve as much variation as possible whether a biological or phylogenetic species concept is used. The at all levels of biodiversity, then conservation depends upon tax- use of different species concepts has also been shown to affect onomy. Whether conservation priorities are based on species, the composition of lists of endangered birds in Mexico (Rojas- subspecies, or evolutionarily significant units (ESUs), DNA is Soto et al. ), and vigorous discussion regarding the appro- increasingly being used to determine the evolutionary and geo- priateness of splitting polytypic species continues (Christidis graphic boundaries of these entities. Far from merely academic and Boles , Chesser et al. ). At the same time, new dia- considerations, these groupings are critically important in con- logues are emerging about the importance of studying specia- servation prioritization and can have important legal ramifica- tion patterns in migratory birds, given that differentiation and tions for threatened and endangered species, subspecies, distinct speciation appear to be common even in the absence of extended population segments (DPSs), or ESUs (reviewed in Haig et al. isolation (Winker b). 6Secondary authorship is alphabetical. E-mail: [email protected] The Auk, Vol. , Number , pages . ISSN -, electronic ISSN -. by The American Ornithologists’ Union. All rights reserved. Please direct all requests for permission to photocopy or reproduce article content through the University of California Press’s Rights and Permissions website, http://www.ucpressjournals. com/reprintInfo.asp. DOI: ./auk.... — 205 — 206 — SPECIAL REVIEWS IN ORNITHOLOGY — AUK,VOL. 128 TABLE 1. Issues addressed by avian conservation genetics. Taxonomy (Meta) populations Landscapes s 7HATARETHEEVOLUTIONARYAND s 7HATARELEVELSOFGENETICDIVERSITY s 7HATARETHEEFFECTSOFLANDSCAPEFEATURESAND GEOGRAPHICBOUNDARIESOFSPECIES POPULATIONSTRUCTURE EFFECTIVE LANDSCAPEHETEROGENEITYONGENETICDIVERSITY SUBSPECIES ANDMANAGEMENTUNITS POPULATIONSIZE ORGENEmOWAND ANDPOPULATIONSTRUCTURE s 7HATISTHEEXTENTOFINTROGRESSIONOR HOWHAVETHEYCHANGEDOVERTIME s (OWAREPHYLOGEOGRAPHICPATTERNSOFBIRDS HYBRIDIZATION s 7HATISTHEBESTSTRATEGYFORMANAGING CHANGINGINRESPONSETOCLIMATECHANGE s 7HICHSPECIESAREREPRESENTEDIN SMALLPOPULATIONSTOMAXIMIZE s 7HICHPOPULATIONSORLIFESTAGESAREMOST ILLEGALWILDLIFETRADE CONSERVATIONOFGENETICDIVERSITY AFFECTEDBYCONTAMINANTEXPOSUREARECERTAIN s 7HATCRYPTICSPECIESHAVEBEEN PEDIGREEANALYSES GENOTYPESMOREVULNERABLE MISCLASSIlED s 7HATISTHEEXTENTOFPOPULATION s )NMIXED STOCKPOPULATIONS WHATPROPORTION s (OWISBIODIVERSITYCHANGINGIN CONNECTIVITYORISOLATION OFEACHSTOCKISBEINGHARVESTEDORAFFECTEDBY RESPONSETOCLIMATECHANGE s 7HICHPOPULATIONSWOULDBETHE ENVIRONMENTALPERTURBATIONS s 7HATISTHEIDENTITYOFAHYBRID BESTSOURCEFORATRANSLOCATIONOR CRYPTICSPECIMEN ORTHEREMAINS REINTRODUCTION OFANANCIENTORRECENTSPECIMEN s (OWDOINDIVIDUALSANDPOPULATIONS s 7HATISTHEBESTAVIANTREEOFLIFEFOR MOVETHROUGHOUTTHEANNUALCYCLE PRIORITIZINGBIODIVERSITYCONSERVATION s (OWAREDISEASETRANSMISSION BYPHYLOGENETICDIVERSITY PATHWAYSLINKEDTOBIRDMOVEMENTS While debate over species concepts endures, the increasing four potential cryptic species, one within the White-breasted ease and affordability of DNA sequence analysis provides new Tapaculo (E. indigoticus) and three within the Mouse-colored power for discriminating among morphologically similar taxa, Tapaculo (S. speluncae). and continues to change our understanding of avian taxonomy Once putative cryptic species are identified with genet- (insets and ; Bickford et al. ). Nearly all easily recognized ics, analyses of song and closer inspection of morphology often bird species were thought to be described decades or centuries provide additional support for the species status. However, spe- ago, leading ornithologists to conclude by the s that there cies will not always diverge equally in all character systems, as were few undiscovered bird species or geographic races (Zimmer demonstrated by recent studies of warbler finches (Certhidea) and Mayr , Stresemann ). However, continued discovery in the Galápagos. These morphologically conservative birds are of new avian taxa into the st century indicates that conclusion the most basal and widespread of Darwin’s finches and do not to have been premature. Just within the antbirds (Thamnophili- exhibit any premating isolation due to song, so they have tradi- dae), the American Ornithologists’ Union (AOU) has recognized tionally been treated as one species (Grant and Grant ). Re- an additional species since and elevated subspecies to cent discovery of large intraspecific genetic differences resulted full species status while lumping just two species together (Remsen in recognition of