Publications

We strive to make our publications public whenever possible. Explore our publications directly below!

2024 |2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2000

2024

Sexually selected differences in warbler plumage are related to a putative inversion on the Z chromosome

Dunn PO, Sly ND, Freeman-Gallant CR, Henschen AE, Bossu CM, Ruegg KC, Minias P, and Whittingham LA.

Molecular Ecology

Broad-scale seasonal climate tracking is a consequence, not a driver, of avian migratory connectivity

Somveille M, Bossu CM, DeSaix MG, Alvarado AH, Villaverde SG, Rodriguez Otero G, Hernandez-Banos BE, Smith TB, and Ruegg KC.

Ecology Letters

2023

Genetic and ecological drivers of molt in a migratory bird

Contina A, Bossu CM, Allen D, Wunder MB, and KC Ruegg.

Scientific Report 13: 814

 

Genetic and environmental drivers of migratory behavior in western burrowing owls and implications for conservation and management

Barr K, Bossu C, Bay R, Anderson E, Belthoff J, Trulio L, Chromczak D, Wisinski C, Smith T, and K Ruegg.

Evolutionary Applications

 

Historical DNA reveals climate adaptation in an endangered bird

Turbek SP, Bossu C, Rayne C, Gruppi C, Kus BE, Whitfield M, Smith TB, Paxton EH, Bay RA, and KC Ruegg

Nature Climate Change 13: 735-741

 

Winter connectivity and leapfrog migration in a migratory passerine

Rueda-Hernandez R, Bossu CM, Smith TB, Contina A, Canales del Castillo R, Ruegg K & BE Hernandez-Banos.

Ecology and Evolution 13: e9769.

 

Widespread gene flow following range expansion in Anna’s Hummingbird

Adams NA, Bandivadekar RR, Battey CJ, Clark MW, Epperly K, Klicka J & K Ruegg.

Molecular Ecology: 22541/au.166505052.20953845/v1

 

Where to draw the line? Expanding the delineation of conservation units to highly mobile taxa

Turbek SP, Funk WC & KC Ruegg.

Journal of Heredity 114: 300-311.

Evolutionary potential mitigates extinction risk under climate change in the endagered southwestern willow flycatcher

Forester BR, Day CC, Ruegg K & EL Landguth.

Journal of Heredity: 1093/jhered/esac067

 

Genetic evidence for widespread population size expansion in north american boreal birds prior to the last glacial maximum

Kimmitt AA, Pegan TM, Jones AW, Brenna CL, Hudon J, Kirchman J, Ruegg KC, Benz BW, Herman R & BM Winger.

Proceedings of the Royal Society Series B: 1098/rspb.2022.1334

 

Estimating global genetic diversity loss – a mathematical framework may help inform conservation efforts

Ruegg KC & S Turbek.

Perspective: Science 22: 1384-1385.

Genomics-informed conservation units reveal spatial variation in climate vulnerability in a migratory bird

Miller CV et al.

Molecular Ecology: 10.1111/mec.17199

2022

Genotype-environment associations across spatial scales reveal the importance of putative adaptive genetic variation in divergence

Alvarado AH, Bossu CM, Harrigan RJ, Bay RA, Nelson ARP, Smith TB, and KC Ruegg.

Evolutionary Applications 00: 1-18.

 

Clock-linked genes underlie seasonal migratory timing in a diurnal raptor

Bossu CM, Heath JA, Kaltnecker GS, Helm B, and KC Ruegg.

Proceedings of the Royal Society B 289: 20212507

 

Genetic assignment of fisheries bycatch reveals disproportionate mortality among Alaska Northern Fulmar breeding colonies

Baetscher DS, Beck J, Anderson EC, Ruegg K, Ramey AM, Hatch S, Nevins H, Fitzgerald SM, and JC Garza.

Evolutionary Applications 15: 447-458

2021

Linking climate niches across seasons to assess population vulnerability in a migratory bird

Ruegg KC, Anderson EC, Bay RA, Whitfield M, Paxton EH, and TB Smith.

Global Change Biology 27: 3519-3531

 

Leveraging genomics to understand threats in a migratory waterfowl

Larison B, Lindsay AR, Bossu C, Sorenson MD, Kaplan JD, Evers DC, Paruk J, DaCosta JM, and TB Smith.

Evolutionary Applications 14: 1646-1658

 

Genetic variation reveals individual-level climate tracking across the full annual cycle of a migratory bird.

Bay RA, Karp DS, Saracco JF, Anderegg WRL, Frishkoff L, Wiedenfeld D, Smith TB, and KC Ruegg.

Ecology Letters 24: 819-828

 

A general theory of avian migratory connectivity

Somveille M, Bay RA, Smith TB, Marra PP, and KC Ruegg.

Ecology Letters 24: 1848-1858

2020

A genoscape-network model for conservation prioritization in a migratory bird.

Ruegg KC, Harrigan RJ, Saracco JF, Smith TB, and CM Taylor.

Conservation Biology 34: 1482-1491

 

The American Kestrel Genoscape (Falco sparverius): Implications for Monitoring, Management, and Subspecies Boundaries.

Ruegg KC, Brinkmeyer M, Bossu CM, et al.

Ornithology 138: 1-14

 

Persistent Panmixia Despite Extreme Habitat Loss and Population Decline in the Threatened Tricolored Blackbird (Agelaius tricolor).

Barr K, Beichman A, Kalhori P, Rajbhandary J, Bay R, Ruegg K, and T Smith.

Evolutionary Applications 14: 674-684

 

Phylogenomic data reveal widespread introgression across the range of an alpine and arctic specialist

Funk ER, Spellman GM, Winker K, Withrow JJ, Ruegg KC, Zavaleta E, and SA Taylor.

Systematic Biology 70: 527-541

 

A Genoscape Framework for Assessing the Population-Level Impacts of Renewable Energy Development on Migratory Bird Species in California

Ruegg KC, Bossu CM, Rajbhandary J, Fuller T, Harrigan R, and T Smith

California Energy Commission

2019

Characterization of SNP markers for the Painted Bunting (Passerina ciris) and their relevance in population differentiation and genome evolution studies.

Contina A, Bay RA, Underwood VL, Smith TB, Kelly J, Bridge E, and KC Ruegg.

Conservation Genetics Resources 11: 5-10

 

Genetic structure of the Painted Bunting and its implications for conservation of migratory

populations.

Contina A, Alcantara JL, Bridge E, Ross JD, Oakley WF, Kelly J, and KC Ruegg.

Ibis 161: 372-386.

2018

Genomic signals of selection predict climate-driven population declines in a migratory bird

Bay RA, Harrigan RJ, Underwood VL, Gibbs HL, Smith TB, and K Ruegg.

Science 359: 83-86

 

Response to comment on “Genomic signals of selection predict climate-driven population declines.”

Bay RA, Harrigan RJ, Beurmann W, Underwood VL, Gibbs HL, Smith TB, and KC Ruegg.

Science 361: 1-2.

 

Ecological genomics predicts climate vulnerability in an endangered southwestern songbird

Ruegg K, Bay RA, Anderson EC, Saracco JF, Harrigan RJ, Whitfield M, Paxton EH, and TB Smith.

Ecology Letters 21: 1085-1096

 

Genetic structure of the Painted Bunting and its implications for conservation of migratory populations

Contina A, Alcantara JL, Bridge ES, Ross JD, Oakley WF, Kelly JF, and KC Ruegg.

Ibis 161: 372-386

2017

Identifying migrant origins using genetics, isotopes, and habitat suitability: a migratory bird case study.

Ruegg K, Anderson EC, Harrigan RJ, Paxton K, Moore F, and TB Smith.

Methods in Ecology and Evolution, doi: 10.1111/2041-210X.12800

 

Genomic islands of divergence or opportunities for adaptive introgression.

Bay RA and K Ruegg.

Proceedings of the Royal Society of London: Series B 284: 20162414.

 

Genetic assignment with isotopes and habitat suitability (GAIAH), a migratory bird case study

Ruegg KC, Anderson EC, Harrigan RJ, Paxton KL, Kelly JF, Moore F, and TB Smith.

Methods in Ecology and Evolution 8: 1241-1252

2016

Analytic tools to assess and monitor impacts of existing and future energy facilities on aerial faunas in California

Winifred F, Kelly J, Shipley JR, and K Ruegg.

California Energy Commission: CEC-500-2016-071

2015

Persistent impacts of West Nile virus on North American bird populations

George TL, Harrigan RJ, LaManna JA, DeSante DF, Saracco JF, and TB Smith.

Proceedings of the National Academy of Sciences 112: 14290-14294

2014

Mapping migration in a songbird using high-resolution genetic markers

Ruegg KC, Anderson EC, Paxton KL, Apkenas V, Lao S, Siegel RB, DeSante DF, Moore F, and TB Smith.

Molecular Ecology 23: 5726-5739

 

Integrative tracking methods elucidate the evolutionary dynamics of a migratory divide

Alvarado AH, Fuller TL, and TB Smith.

Ecology and Evolution 4: 3456-3469

 

 A role for migration-linked genes in genomic islands in divergence of a songbird

Ruegg KC, Anderson EC, Boone J, Pouls J, and TB Smith.

Molecular Ecology 23: 4757-4769

2013

Novel statistical methods for integrating genetic and stable isotope data to infer individual-level migratory connectivity

Rundel CW, Wunder MB, Alvarado AH, Ruegg KC, Harrigan R, Schuh A, Kelly JF, Siegal RB, DeSante DF, Smith TB, and J Novembre.

Molecular Ecology 22: 4163-4176

 

Predicting bird song from space

Smith TB, Harrigan RJ, Kirschel AN, Buermann W, Saatchi S, Blumstein DT, de Kort SR, and H Slabbekoorn.

Evolutionary Applications 6: 865-874

2010

Projected changes in elevational distribution and flight performance of montane neotropical hummingbirds in response to climate change

Buermann W, Chaves JA, Dudley R, Mcguire JA, Smith TB, and DL Altshuler.

Global Change Biology 17: 1671-1680

2009

The prevalence of avian plasmodium is higher in undisturbed tropical forests in Cameroon

Bonneaud C, Sepil I, Milá B, Buermann W, Pollinger J, Sehgal RN, Valkiūnas G, Iezhova RA, Saatchi S, and TB Smith.

Journal of Tropical Ecology 25: 439-447

2007

Recent postglacial range expansion drives the rapid diversification of songbird lineage in the genus junco

Milá B, McCormack JE, Castenada G, Wayne RK, and TB Smith.

Proceedings of the Royal Society B 274: 2653-2660

 

Divergence between subspecies groups of Swainson’s thrush (Catharus ustulatus ustulatus and C. u. swainsoni)

K Ruegg.

Ornithological Monographs 63: 67-77

 

Widespread and structured distributions of blood parasite haplotypes across a migratory divide of the Swainson’s thrush (Catharus ustulatus)

Ruegg K, Svensson LME, Sekercioglu CH, and RNM Sehgal.

Journal of Parasitology 93: 1488-1495

2005

Molecular  genetic approaches to linking breeding and overwintering areas in five neotropical migrant passerines, edited by P. Marra and R. Greenburg

Kimura M, Ruegg K, Smith TB, Clegg SM, Lovette I, and B Milá.

Smithsonian Press

 

Combining isotopic and genetic markers to identify breeding origins of migrant birds

Kelly J, Ruegg K, and TB Smith.

Ecological Applications 15: 1487-1494

 

Molecular genetic approaches to linking breeding and overwintering areas in five neotropical migrant passerines

Smith TB, Clegg SM, Kimura M, Ruegg K, Milá B, and I Lovette.

Birds of Two Worlds: The Ecology and Evolution of Migration 223-231

2003

Stable isotopes as indicators of altitudinal distributions and movements in an Ecuadorean hummingbird community

Hobson KA, Wassenaar LI, Milá B, Lovette I, Dingle C, and TB Smith.

Oecologia 136: 302-308

 

Combining genetic markers and stable isotopes to reveal population connectivity and migration patterns in a neotropical migrant, Wilson’s warbler (Wilsonia pusilla)

Clegg SM, Kelley JF, Kimura M, and TB Smith.

Molecular Ecology 12: 819-830

 

A call for feather sampling

Smith TB, Marra PP, Webster MS, Lovette I, Gibbs L, Holmes RT, and Rohwer S.

The Auk 120: 218-221

2002

Phylogeographic approaches to assessing demographic connectivity between breeding and overwintering regions in a nearctcic-neotropical warbler (Wilsonia pusilla)

Kimura M, Clegg SM, Lovette IJ, Holder KR, Girman DJ, Milá B, Wade P, and TB Smith.

Molecular Ecology 11: 1605-1616

 

Not as the crow flies: a historical explanation for circuitous migration in Swainon’s thrush (Catharus ustulatus)

Ruegg K and TB Smith.

Proceedings of the Royal Society, London 269: 1375-1381

2000

Genetic evidence for the effect of a postglacial population expansion on the phylogeography of a north American songbird

Milá B, Girman D, Kimura M, and TB Smith.

Proceedings of the Royal Society 267: 1033-1040

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