Mapping migration in a songbird using high-resolution genetic markers

Molecular Ecology

Volumn 23, Issue 23, 2014, Pages 5726-5739

  Ruegg, Kristen C ^a,b   Anderson, Eric C ^b,c   Paxton, Kristina L ^d,e   Apkenas, Vanessa ^c   Lao, Sirena ^a   Siegel, Rodney B ^f   Desante, David F ^f   Moore, Frank ^e   Smith, Thomas B ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c SOUTHWEST FISHERIES SCIENCE CENTER   (United States)

^d UNIVERSITY OF SOUTHERN MISSISSIPPI   (United States)

^e UNIVERSITY OF HAWAII AT HILO   (United States)

^f Institute for Bird Populations   (United States)

Author keywords

conservation genetics; neotropical migrant; RAD sequencing; wildlife management

Indexed keywords

PASSERI;

GENETIC MARKER;

ANIMAL; DNA SEQUENCE; ENVIRONMENTAL PROTECTION; GENETIC MARKER; GENETICS; HIGH THROUGHPUT SEQUENCING; POPULATION GENETICS; POPULATION MIGRATION; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM; SONGBIRD;

ANIMAL MIGRATION; ANIMALS; CONSERVATION OF NATURAL RESOURCES; GENETIC MARKERS; GENETICS, POPULATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SONGBIRDS;

EID: 84912075078     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12977     Document Type: Article

References (72)

1. Altizer S, Bartel R, Han BA, (2011) Animal migration and infectious disease risk. Science, 331, 296-302.
2. Ammon EM, Gilbert WM, (1999) Wilson's Warbler (Cardellina pusilla). In: The Birds of North America Online (ed., Poole A,). Cornell Lab of Ornithology, Ithaca, Greece Available from http://bna.birds.cornell.edu.oca.ucsc.edu/bna/species/478.
3. Anderson EC, (2010) Assessing the power of informative subsets of loci for population assignment: standard methods are upwardly biased. Molecular Ecology Resources, 10, 701-710.
4. Anderson EC, Waples RS, Kalinowski ST, (2008) An improved method for predicting the accuracy of genetic stock identification. Canadian Journal of Fisheries and Aquatic Sciences, 65, 1475-1486.
5. Arlt D, Low M, Part T, (2013) Effect of geolocators on migration and subsequent breeding performance of a long-distance passerine migrant. PLoS One, 8, e82316.
6. Baird NA, Etter PD, Atwood TS, et al,. (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One, 3, e3376.
7. Bearhop S, Fiedler W, Furness RW, et al,. (2005) Assortative mating as a mechanism for rapid evolution of a migratory divide. Science, 310, 502-504.
8. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F, (1996 -2004) genetix 4.05, Logiciel sous WindowsTM pour le Genetique does Populations. Laboratoire Genome, Populations, Interactions, Universite de Montpellier II, Montepellier, France.
9. Bivand R, Keitt T, Rowlingson B, (2014) rgdal: Bindings for the Geospatial Data Abstraction Library. r Package Version 0.8-16. Available from http://www.pwrc.usgs.gov/bbl/homepage/introduction.cfm.
10. Bonfil R, Meyer M, Scholl MC, et al,. (2005) Transoceanic migration, spatial dynamics, and population linkages of white sharks. Science, 310, 100-103.
11. Bonin A, Nicole F, Pompanon F, Miaud C, Taberlet P, (2007) Population adaptive index: a new method to help measure intraspecific genetic diversity and prioritize populations for conservation. Conservation Biology, 21, 697-708.
12. Bridge ES, Kelly JF, Contina A, et al,. (2013) Advances in tracking small migratory birds: a technical review of light-level geolocation. Journal of Field Ornithology, 84, 121-137.
13. Camacho C, (2009) blast +: Architecture and applications. BMC Bioinformatics, 10, 421.
14. Clegg SM, Kelly JF, Kimura M, Smith Thomas B, (2003) Combining genetic markers and stable isotopes to reveal population connectivity and migration patterns in a Neotropical migrant, Wilson's warbler (Wilsonia pusilla). Molecular Ecology, 12, 819-830.
15. Croxall JP, Silk JR, Phillips RA, Afanasyev V, Briggs DR, (2005) Global circumnavigations: tracking year-round ranges of nonbreeding albatrosses. Science, 307, 249-250.
16. Davey JW, Hohenlohe PA, Etter PD, et al,. (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12, 499-510.
17. Etter PD, Preston JL, Bassham S, Cresko WA, Johnson EA, (2011) Local de novo assembly of RAD paired-end contigs using short sequencing reads. PLoS One, 6, e18561.
18. Faaborg J, Holmes RT, Anders AD, et al,. (2010a) Recent advances in understanding migration systems of New World land birds. Ecological Monographs, 80, 3-48.
19. Faaborg J, Holmes RT, Anders AD, et al,. (2010b) Conserving migratory land birds in the new world: do we know enough? Ecological Applications, 20, 398-418.
20. Funk WC, McKay JK, Hohenlohe PA, Allendorf FW, (2012) Harnessing genomics for delineating conservation units. Trends in Ecology & Evolution, 27, 489-496.
21. Guillot G, Estoup A, Mortier F, Cosson JF, (2005) A spatial statistical model for landscape genetics. Genetics, 170, 1261-1280.
22. Guillot G, Santos F, Estoup A, (2008) Analysing georeferenced population genetics data with geneland: a new algorithm to deal with null alleles and a friendly graphical user interface. Bioinformatics, 24, 1406-1407.
23. Gustafson ME, Hildenbrand J, (1999) Bird Banding Laboratory Homepage, version 07-10-2005. Available from http://www.pwrc.usgs.gov/bbl/homepage/introduction.cfm.
24. Hess JE, Matala AP, Narum SR, (2011) Comparison of SNPs and microsatellites for fine-scale application of genetic stock identification of Chinook salmon in the Columbia River Basin. Molecular Ecology Resources, 11 (Suppl 1), 137-149.
25. Hijmans RJ, (2014) Raster: Geographic Data Analysis and Modeling. r Package Version 2.2-31. Available from http://R-Forge.R-project.org/projects/raster/.
26. Hobson KA, Van Wilgenburg SL, Wassenaar LI, Larson K, (2012) Linking hydrogen (delta2H) isotopes in feathers and precipitation: sources of variance and consequences for assignment to isoscapes. PLoS One, 7, e35137.
27. Hohenlohe PA, Amish SJ, Catchen JM, Allendorf FW, Luikart G, (2011) Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Molecular Ecology Resources, 11, 117-122.
28. Irwin DE, Irwin JH, Smith TB, (2011) Genetic variation and seasonal migratory connectivity in Wilson's warblers (Wilsonia pusilla): species-level differences in nuclear DNA between western and eastern populations. Molecular Ecology, 20, 3102-3115.
29. Jakobsson M, Rosenberg NA, (2007) clumpp: A cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics, 23, 1801-1806.
30. Jonzen N, Linden A, Ergon T, et al,. (2006) Rapid advance of spring arrival dates in long-distance migratory birds. Science, 312, 1959-1961.
31. Kelly JF, Ruegg KC, Smith TB, (2005) Combining isotopic and genetic markers to identify breeding origins of migrant birds. Ecological Applications, 15, 1487-1497.
32. Kimura M, Clegg SM, Lovette IJ, et al,. (2002) Phylogeographical approaches to assessing demographic connectivity between breeding and overwintering regions in a Nearctic-Neotropical warbler (Wilsonia pusilla). Molecular Ecology, 11, 1605-1616.
33. Kraus RH, van Hooft P, Megens HJ, et al,. (2013) Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms. Molecular Ecology, 22, 41-55.
34. Kraus RH, vonHoldt B, Cocchiararo B, et al,. (2014) A single-nucleotide polymorphism-based approach for rapid and cost-effective genetic wolf monitoring in Europe based on noninvasively collected samples. Molecular Ecology Resources. doi: 10.1111/1755-0998.12307.
35. Langmead B, Salzberg SL, (2012) Fast gapped-read alignment with Bowtie 2. Nature Methods, 9, 357-359.
36. Li H, Handsaker B, Wysoker A, et al,. (2009) The sequence alignment/map format and samtools. Bioinformatics, 25, 2078-2079.
37. Loss SR, Will T, Marra PP, (2013) The impact of free-ranging domestic cats on wildlife of the United States. Nature Communications, 4, 1396.
38. Louis EJ, Dempster ER, (1987) An exact test for Hardy-Weinberg and multiple alleles. Biometrics, 43, 805-811.
39. Lovette IJ, Clegg SM, Smith TB, (2004) Limited utility of mtDNA markers for determining connectivity among breeding and overwintering locations in three Neotropical migrant birds. Conservation Biology, 18, 156-166.
40. Marra PP, Hobson KA, Holmes RT, (1998) Linking winter and summer events in a migratory bird by using stable-carbon isotopes. Science, 282, 1884-1886.
41. Metzker ML, (2010) Sequencing technologies-the next generation. Nature Reviews Genetics, 11, 31-46.
42. NatureServe BIa (2012) Bird Species Distribution Maps of the World. NatureServe, Arlington, Virginia.
43. Nielsen EE, Hemmer-Hansen J, Larsen PF, Bekkevold D, (2009) Population genomics of marine fishes: identifying adaptive variation in space and time. Molecular Ecology, 18, 3128-3150.
44. Nielsen EE, Cariani A, Mac Aoidh E, et al,. (2012) Gene-Associated markers provide tools for tackling illegal fishing and false eco-certification. Nature Communications, 3, 851.
45. Norris DR, Taylor CM, (2006) Predicting the consequences of carry-over effects for migratory populations. Biology Letters, 2, 148-151.
46. Paxton KL, Van Ripper C III, Theimer TC, Paxton EH, (2007) Spatial and temporal migration patterns of Wilson's warbler (Wilsonia pusilla) in the southeast as revealed by stable isotopes. The Auk, 124, 162-175.
47. Paxton KL, Yau M, Moore FR, Irwin D, (2013) Differential migratory timing of western populations of wilson's warblers (Cardellina pusilla) revealed by mitochondrial DNA and stable isotopes. The Auk, 130, 689.
48. Pebesma EJ, Bivand RS, (2005) Classes and methods for spatial data in r. R News, 5. Avialble from http://cran.r-project.org/doc/Rnews/.
49. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
50. Rappole JH, (1995) The Ecology of Migrant Birds-A Neotropical Perspective. Smithsonian Institution Press, Washington, District of Columbia.
51. Robbins CS, Sauer JR, Greenberg R, Droege S, (1989) Population declines in North American birds that migrate to the Neotropics. Proceedings of the National Academy of Sciences of the United States of America, 86, 7658-7662.
52. Rosenberg NA, (2004) distruct: A program for the graphical display of population structure. Molecular Ecology Notes, 4, 137-138
53. Rousset F, (2008) genepop '007: A complete re-implementation of the genepop software for Windows and Linux. Molecular Ecology Resources, 8, 103-106.
54. Rubenstein DR, Chamberlain CP, Holmes RT, et al,. (2002) Linking breeding and wintering ranges of a migratory songbird using stable isotopes. Science, 295, 1062-1065.
55. Ruegg K, Anderson EC, Slabbekoorn H, (2012) Differences in timing of migration and response to sexual signalling drive asymmetric hybridization across a migratory divide. Journal of Evolutionary Biology, 25, 1741-1750.
56. Ruegg K, Anderson EC, Boone J, Pouls J, Smith TB, (2014) A role for migration-linked genes and genomic islands in divergence of a songbird. Molecular Ecology, 23, 4757-4769.
57. Rundel CW, Wunder MB, Alvarado AH, et al,. (2013) Novel statistical methods for integrating genetic and stable isotope data to infer individual-level migratory connectivity. Molecular Ecology, 22, 4163-4176.
58. Sauer JR, Hines JE, Fallon JE, et al,. (2012) The North American Breeding Bird Survey, Results and Analysis 1966-2011. USGS Patuxent Wildlife Research Center, Laurel, Maryland.
59. Segelbacher G, (2002) Noninvasive genetic analysis in birds: testing reliability of feather samples. Molecular Ecology Notes, 2, 367-369.
60. Seutin G, White BN, Boag PT, (1991) Preservation of avian blood and tissue samples for DNA analyses. Canadian Journal of Zoology, 69, 82-90.
61. Sillett TS, Holmes RT, Sherry TW, (2000) Impacts of a global climate cycle on population dynamics of a migratory songbird. Science, 288, 2040-2042.
62. Smith TB, Wayne RK, Marra PP, et al,. (2003) A call for feather sampling. The Auk, 120, 218-221.
63. Stanley CQ, McKinnon EA, Fraser KC, et al,. (2014) Connectivity of wood thrush breeding, wintering, and migration sites based on range-wide tracking. Conservation Biology. [online].
64. Stutchbury BJ, Tarof SA, Done T, et al,. (2009) Tracking long-distance songbird migration by using geolocators. Science, 323, 896.
65. Team RC (2014) r: A Language and Environment for Statistical Computing. Vienna, Austria. http://www.R-project.org/
66. Warren WC, Clayton DF, Ellegren H, et al,. (2010) The genome of a songbird. Nature, 464, 757-762.
67. Webster MS, Marra PP, (2004) Birds of Two Worlds-The Ecology and Evolution of Migration. The Johns Hopkins University Press, Baltimore, Maryland.
68. Webster MS, Marra PP, Haig SM, Bensch S, Holmes RT, (2002) Links between worlds: unraveling migratory connectivity. Trends in Ecology & Evolution, 17, 76-83.
69. Weir BS, Cockerham CC, (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358-1370.
70. Wunder MB, Kester CL, Knopf FL, Rye RO, (2005) A test of geographic assignment using isotope tracers in feathers of known origin. Oecologia, 144, 607-617.
71. Yong W, Finch DM, Moore FR, Kelly JF, (1998) Stopover ecology and habitat use of migratory Wilson's Warblers. The Auk, 115, 829-842.
72. Zerbino DR, Birney E, (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18, 821-829.