Carla Cicero

DNA Barcoding: Promise and Pitfalls

In this issue of PLoS Biology, Hebert et al. (2004) have set out to test the resolution and performance of “DNA barcoding,” using a single mtDNA gene, cytochrome c oxidase I (COI), for a sample of North American birds. Before turning to details of this study, it is useful as context to consider the following questions: What is DNA barcoding, and what does it promise? What is new about it? Why is it controversial? What are the potential pitfalls?

NEW MITOCHONDRIAL DNA DATA AFFIRM THE IMPORTANCE OF PLEISTOCENE SPECIATION IN NORTH AMERICAN BIRDS

Abstract The timing of origin of modern North American bird species in relation to Pleistocene glaciations has long been the topic of significant discussion and disagreement. Recently, Klicka and Zink (1997) and Avise and Walker (1998) enlivened this debate by using calibrated molecular distance values to estimate timing of speciations. Here we use new molecular studies to test their conclusions. Molecular distance values for 39 pairs of proven sister species, 27 of which are based on new data, alter the currently perceived pattern that avian species splits occurred mainly in the Pliocene and early‐mid‐Pleistocene. Mitochondrial DNA divergence values for this set of taxa showed a skewed distribution pointing toward relatively young speciation times, in contrast to the pattern presented by Klicka and Zink (1997) for 35 sister plus non‐sister species pairs. Our pattern was not significantly different from that of Avise and Walker (1998) for “intraspecific phylogroups,” some of which are species. We conclude that the entire Pleistocene, including the last two glacial cycles (<250,000 years ago), was important in speciations of modern North American birds. A substantial number of speciations were both initiated and completed in the last 250,000 years. Simultaneously, many taxa began to diverge in the Pleistocene but their speciations are not yet complete (per Avise and Walker 1998). The suggestion that durations of speciations average two million years is probably a substantial overestimate.

Fifty-Second Supplement to the American Ornithologists' Union check-list of North American Birds

The Auk, Vol. 128, Number 3, pages 600−613. ISSN 0004-8038, electronic ISSN 1938-4254.  2011 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: 10.1525/auk.2011.128.3.600 R. TeRRy ChesseR,1,12,13 RiChaRd C. Banks,1 F. keiTh BaRkeR,2 CaRla CiCeRo,3 Jon l. dunn,4 andRew w. kRaTTeR,5 iRBy J. loveTTe,6 Pamela C. Rasmussen,7 J. v. Remsen, JR.,8 James d. Rising,9 douglas F. sToTz,10 and kevin winkeR11

Fifty-First Supplement to the American Ornithologists' Union Check-List of North American Birds

The Auk, Vol. 127, Number 3, pages 726−744. ISSN 0004-8038, electronic ISSN 1938-4254.  2010 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: 10.1525/auk.2010.127.3.726. R. TeRRy ChesseR,1,12,13 RiChaRd C. Banks,1 F. keiTh BaRkeR,2 CaRla CiCeRo,3 Jon l. dunn,4 andRew w. kRaTTeR,5 iRBy J. loveTTe,6 Pamela C. Rasmussen,7 J. v. Remsen, JR.,8 James d. Rising,9 douglas F. sToTz,10 and kevin winkeR11

FORTY-FIFTH SUPPLEMENT TO THE AMERICAN ORNITHOLOGISTS’ UNION CHECK-LIST OF NORTH AMERICAN BIRDS

1 U.S. Geological Survey, Patuxent Wildlife Research Center, National Museum of Natural History, Washington, DC, USA 2 Alexandria, Virginia, USA 3 Museum of Vertebrate Zoology, University of California, Berkeley, California, USA 4 Bishop, California, USA 5 Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA 6 Cornell Laboratory of Ornithology, Ithaca, New York, USA 7 Museo de Zoologia, Facultad de Ciencias, Universidad Nacional Autonoma de Mexico, Mexico 8 Michigan State University Museum and Department of Zoology, East Lansing, Michigan, USA 9 Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, USA 10 Department of Ecology and Evolutionary Biology, Ramsay Wright Labs, University of Toronto, Toronto, Ontario, Canada 11 Environment, Culture and Conservation, Field Museum of Natural History, Chicago, Illinois, USA 12 University of Alaska Museum, Fairbanks, Alaska, USA * Corresponding author: chessert@si.edu; Chairman of the Committee on Classification and Nomenclature—North and Middle America, of the American Ornithologists’ Union. All authors are members of the Committee and are listed alphabetically after the Chairman.

BARRIERS TO SYMPATRY BETWEEN AVIAN SIBLING SPECIES (PARIDAE: BAEOLOPHUS) IN LOCAL SECONDARY CONTACT1

Abstract Range limits and secondary contact zones often occur at ecotones between major associations of habitat and climate. Therefore, understanding processes that limit sympatry between species in such areas provides an important framework for testing biogeographic and evolutionary hypotheses. Theoretical and empirical work has shown that the evolution of species borders is influenced by a complexity of factors, including gene flow from central to peripheral populations and the ability of species to adapt locally to environmental conditions. However, few studies have used bioclimatic models, combined with molecular and morphological data, to predict geographic range limits in the context of gene flow across a secondary contact zone. In this study, I applied these methods to test specific hypotheses about barriers to sympatry between closely related species where they approach and contact each other. Specifically, I examined the importance of historical isolation, local adaptation, and symmetry of gene flow in limiting sympatry and range expansion of ecologically distinct species across environmental gradients. Molecular (mitochondrial DNA, allozymes), morphological, and bioclimatic data were obtained for two avian sibling species (Baeolophus inornatus and B. ridgwayi) that exist in recent, narrow secondary contact in northern California. These species are broadly allopatric and occupy rangewide associations of oak and pinyon-juniper woodlands, respectively, although B. inornatus also inhabits mixed or juniper woodlands locally. Patterns of molecular variation generally were congruent with morphological and bioclimatic data, and support prior evidence for a history of isolation, adaptation, and divergence in distinctive, species-specific vegetation-climate associations. However, molecular and morphological clines fall east of the limit of oaks, and individuals of B. inornatus in this juniper-associated contact zone experience bioclimates that are more similar to B. ridgwayi than to B. inornatus in oak habitat. Thus, B. inornatus is able to adapt and expand locally into the range of its close relative, but not vice versa. These data support the hypothesis that gene flow is asymmetrical where peripheral populations meet at range boundaries. Physiological differences between species may play an important role in influencing these patterns. Empirical studies that highlight the importance of local adaptation and patterns of gene flow in which closely related species contact across ecotones are central to understanding limits on geographic ranges, sympatry, and introgression—a cornerstone of biogeographic and speciation theory.

Forty-ninth Supplement to the AmericAn ornithologiStS' union CheCk-list of North AmeriCAN Birds

1U.S. Geological Survey, Patuxent Wildlife Research Center, National Museum of Natural History, MRC-111, P.O. Box 37012, Washington, D.C. 20013, USA; 2Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building, Berkeley, California 94720, USA; 3Rural Route 2, Box 52R, Bishop, California 93514, USA; 4Florida Museum of Natural History, P.O. Box 117800, University of Florida, Gainesville, Florida 32611, USA; 5Cornell Laboratory of Ornithology, 159 Sapsucker Woods Road, Ithaca, New York 14850, USA; 6Museum and Department of Zoology, Michigan State, University, West Circle Drive, East Lansing, Michigan 48824, USA; 7Museum of Natural Science, Louisiana State University, Foster Hall 119, Baton Rouge, Louisiana 70803, USA; 8Department of Zoology and Evolutionary Biology, University of Toronto, 25 Harbord Street, Toronto, Ontario M5S 3G5, Canada; 9Environmental and Conservation Programs, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, Illinois 60605, USA; and 10University of Alaska Museum, 907 Yukon Drive, Fairbanks, Alaska 99775, USA

SONG TYPES AND VARIATION IN INSULAR POPULATIONS OF LINCOLN'S SPARROW (MELOSPIZA LINCOLNII), AND COMPARISONS WITH OTHER MELOSPIZA

Abstract In contrast to the Swamp Sparrow (Melospiza georgiana) and Song Sparrow (M. melodia), vocal studies of the congeneric Lincolns Sparrow (M. lincolnii) are essentially lacking. To provide comparative data on song variation in this species, we obtained and analyzed recordings from 58 males (4,537 songs) breeding in montane meadows of the Sierra Nevada and San Bernardino Mountains, California. Males sang from one to six song types, and repertoire size averaged 3.7 types. No two males shared an identical song type. Males varied their types by changing the number of repetitions of a syllable or by adding, deleting, or substituting one or more syllables (i.e. by changing syllable composition). The number of variants, identified on the basis of differences in syllable composition, averaged 2.6 per song type (range 1 to 12). Individual variability was highest in the terminal elements of the song. Production of variants appears to be a process of “open-ended improvisation” of song types. Similarity of songs on the basis of shared syllables, as calculated by simple matching coefficients, showed a strong pattern of concordance with geography. Pairwise similarity declined with increasing distance between meadows, and meadows from different geographic regions clustered separately in a UPGMA tree. Patterns of geographic variation in song of Lincolns Sparrows are similar to those observed in Song Sparrows and Swamp Sparrows. Song complexity and repertoire size show different evolutionary trends within Melospiza.

Avian community structure in a large urban park: Controls of local richness and diversity

Abstract This study compared avifaunal richness and diversity at five ponds in Golden Gate Park, San Francisco, California. The objectives of the study were to: (1) determine interpond differences in avian community structure and composition; (2) evaluate avian-habitat relationships; (3) use these data to develop recommendations for enhancing avian habitats within urban refuges. Of eight environmental variables measured, three correlated highly with the over-all use of pond areas by birds; the width of buffer between the pond and park boundary; general habitat structure within the buffer zone (i.e. peripheral habitat structure); local habitat structure around the pond. Aquatic birds, unlike transitional or upland species, were not affected by either the width of buffer or peripheral habitat structure; rather, pond size largely dictated the number and diversity of aquatic bird species. Overall richness and diversity of birds were higher at the more natural and centrally located ponds, whereas abundance and biomass were greatest at the most unnatural and least isolated site. Avifaunal differences among sites were attributed to two factors: (1) the level of urban-related disturbance, which in turn is a function of the width of buffer and the structure of peripheral habitats: (2) the availability of species-specific habitat requirements, which depends on local habitat conditions. Interpond variation in avifaunal richness and diversity in Golden Gate Park was striking, and underscores the influence of man dictating local avifaunal differences within urban parks. Recommendations for designing and maintaining pond habitats to enrich bird communities in urban parks are: (1) construct ponds (preferably >1 ha) as far as possible from adjacent urban development, and maintain a complex mosaic of vegetation within the buffer zone surrounding the pond; (2) establish shrubby vegetation interspersed with bare ground and trees along the shoreline; (3) provide irregular shoreline shapes (i.e. high edge); (4) maintain overhanging vegetation or low artificial perches (e.g. flooded posts) in or near the water; (5) provide islands; (6) maintain standing dead trees (especially flooded).

Forty-eighth supplement to the American ornithologists' Union Check-list of North American Birds

tion of the 7th edition of the Check-list of North American Birds (American Ornithologists’ Union [AOU] 1998). It summarizes decisions made by the AOU’s Committ ee on Classifi cation and Nomenclature—North America between 1 January and 31 December 2006. The Committ ee has continued to operate in the manner outlined in the 42nd Supplement (AOU 2000). Two new members were added to the committ ee in 2006— R. Terry Chesser and Irby J. Lovett e. Changes in this Supplement fall into the following categories: (1) two species are added because of splits in species already on the list (Anser serrirostris, Buteogallus gundlachii); (2) three species are added (two transferred from the Appendix) because of new distributional information (Oceanodroma hornbyi, Mesophoyx intermedia, Falco vespertinus); (3) the name of one species is changed because of a split from an extralimital species (Larus michahellis); (4) three generic names are changed, one because of a merger of genera (Spizastur into Spizaetus), two because of a splitt ing of genera (Megaceryle from Ceryle); (5) one English name is changed because of a split of the species (Anser fabalis) and (6) one species is added to the Appendix (Threskiornis aethiopicus). Further, one family (Cathartidae) is removed from the Order Ciconiiformes and returned provisionally to the Order Falconiformes, its traditional placement before 1998, although its true phylogenetic position remains uncertain.