Publications

• Bodawatta KH, Hird SM, Grond K, Poulsen M, Jønsson KA. Avian gut microbiomes taking flight Trends in Microbiology 2021;
  DOI: 10.1016/j.tim.2021.07.003 · [Download PDF]
• Chen J, Li H, Hird SM, Chen M, Wanli X, Maas K, Cong X. Sex Differences in Gut Microbial Development of Preterm Infant Twins in Early Life: A Longitudinal Analysis Frontiers in Cellular and Infection Microbiology 2021;
  DOI: 10.3389/fcimb.2021.671074 · [Download PDF]
• Hamchand R, Lafountain AM, Büchel R, Maas KR, Hird SM, Warren M, Frank HA, Brückner C. Red Fluorescence of European Hedgehog (Erinaceus europaeus) Spines Results from Free-Base Porphyrins of Potential Microbial Origin Journal of Chemical Ecology 2021;
  DOI: 10.1007/s10886-021-01279-6 · [Download PDF]
• Herder EA, Spence AR, Tingley MW, Hird SM. Elevation Correlates With Significant Changes in Relative Abundance in Hummingbird Fecal Microbiota, but Composition Changes Little Frontiers in Ecology and Evolution 2021;
  DOI: 10.3389/fevo.2020.597756 · [Download PDF]
• Gil JC, Helal ZH, Risatti G, Hird SM. Ixodes scapularis microbiome correlates with life stage, not the presence of human pathogens, in ticks submitted for diagnostic testing PeerJ 2020;
  DOI: 10.7717/peerj.10424 · [Download PDF]
• Hird SM. Context is Key: Comparative biology illuminates the vertebrate microbiome mBio 2020;
  DOI: 10.1128/mBio.00153-20 · [Download PDF]
• Capunitan DC, Johnson O, Terrill RS, Hird SM . Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea Molecular Ecology 2020;
  DOI: 10.1111/mec.15354 · [Download PDF]
• Capunitan DC, Johnson O, Terrill RS, Hird SM. Señal evolutiva en los microbiomas intestinales de 74 especies de aves de Guinea Ecuatorial Molecular Ecology 2020;
  DOI: 10.1111/mec.15354 · [Download PDF]
• Grond K, Guilani H, Hird SM. Spatial heterogeneity of the shorebird gastrointestinal microbiome Royal Society Open Science 2020;
  DOI: https://doi.org/10.1098/rsos.191609 · [Download PDF]
• Grond K, Bell KC, Demboski JR, Santos M, Sullivan JM, Hird SM. . No evidence for phylosymbiosis in western chipmunk species FEMS Microbiology Ecology 2020; 96(1)
  DOI: 10.1093/femsec/fiz182 · [Download PDF]
• Grond H, Perreau JM, Loo WT, Spring JA, Cavanaugh CM, Hird SM. Longitudinal microbiome profiling reveals impermanence of probiotic bacteria in domestic pigeons PLoS One 2019; 14(6):e0217804
  DOI: 10.1371/journal.pone.0217804 · [Download PDF]
• Bik HM, Alexiev A, Aulakh SK, Bharadwaj L, Flanagan J, Haggerty JM, Hird SM, Jospin G, Lang JM, Sauder LA, Neufeld JD, Shaver A, Sethi A, Eisen JA, Coil DA. Microbial Community Succession and Nutrient Cycling Responses following Perturbations of Experimental Saltwater Aquaria mSphere 2019; 4(1):e00043-19
  DOI: 10.1128/mSphere.00043-19 · [Download PDF]
• Hird SM. Microbiomes, community ecology and the comparative method mSystems 2019; 4(3):e00112-19
  DOI: 10.1128/mSystems.00112-19 · [Download PDF]
• Hird SM, Ganz H, Eisen JA, Boyce WM. The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status mSphere 2018;
  DOI: 10.1128/mSphere.00382-18 · [Download PDF]
• Hird SM. Evolutionary biology needs wild microbiomes. Frontiers in Microbiology 2017;
  DOI: 10.3389/fmicb.2017.00725 · [Download PDF]
• Ganz HH, Doroud L, Firl AJ, Hird SM, Eisen JA, Boyce WM. Community-Level Differences in the Microbiome of Healthy Wild Mallards and Those Infected by Influenza A Viruses. mSystems 2017; 2(1)
  PMID: 28293681 · [Download PDF]
• Hird SM, Sánchez C, Carstens BC, Brumfield RT. Comparative Gut Microbiota of 59 Neotropical Bird Species. Frontiers in Microbiology 2016; 6:1403
  PMID: 26733954 · [Download PDF]
• Martin LJ, Adams RI, Bateman A, Bik HM, Hawks J, Hird SM, Hughes D, Kembel SW, Kinney K, Kolokotronis SO, Levy G, McClain C, Meadow JF, Medina RF, Mhuireach G, Moreau CS, Munshi-South J, Nichols LM, Palmer C, Popova L, Schal C, Täubel M, Trautwein M, Ugalde JA, Dunn RR. Evolution of the indoor biome. Trends in Ecology & Evolution 2015; 30(4):223-32
  PMID: 25770744 · [Download PDF]
• Reid NM, Hird SM, Brown JM, Pelletier TA, McVay JD, Satler JD, Carstens BC. Poor fit to the multispecies coalescent is widely detectable in empirical data. Systematic Biology 2014; 63(3):322-33
  PMID: 23985785 · [Download PDF]
• Sullivan J, Demboski JR, Bell KC, Hird SM, Sarver B, Reid NM, Good JM. Divergence with gene flow within the recent chipmunk radiation (Tamias). Heredity 2014; 113:185-194
  DOI: 10.1038/hdy.2014.27 · [Download PDF]
• Hird SM, Carstens BC, Cardiff SW, Dittmann DL, Brumfield RT. Sampling locality is more detectable than taxonomy or ecology in the gut microbiota of the brood-parasitic Brown-headed Cowbird (Molothrus ater). PeerJ 2014; 2:e321
  PMID: 24711971 · [Download PDF]
• Hird SM. Novel computational tools and utilization of gut microbiota for phylogeographic inference. PHD DISSERTATION 2013;
• McCormack JE, Hird SM, Zellmer AJ, Carstens BC, Brumfield RT. Applications of next-generation sequencing to phylogeography and phylogenetics. Molecular Phylogenetics & Evolution 2013; 66(2):526-38
  PMID: 22197804 · [Download PDF]
• McCormack JE, Maley JM, Hird SM, Derryberry EP, Graves GR, Brumfield RT. Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences. Molecular Phylogenetics & Evolution 2012; 62(1):397-406
  PMID: 22063264 · [Download PDF]
• Hird SM. lociNGS: a lightweight alternative for assessing suitability of next-generation loci for evolutionary analysis. PLoS ONE 2012; 7(10):e46847
  PMID: 23071651 · [Download PDF]
• Zellmer AJ, Hanes MM, Hird SM, Carstens BC. Deep phylogeographic structure and environmental differentiation in the carnivorous plant Sarracenia alata. Systematic Biology 2012; 61(5):763-77
  PMID: 22556200 · [Download PDF]
• Hird SM, Brumfield RT, Carstens BC. PRGmatic: an efficient pipeline for collating genome-enriched second-generation sequencing data using a 'provisional-reference genome'. Molecular Ecology Resources 2011; 11(4):743-8
  PMID: 21676202 · [Download PDF]
• Reid N, Hird S, Schulte-Hostedde A and J Sullivan. Examination of nuclear markers at a zone of mitochondrial introgression in two chipmunk species (Tamias amoenus and Tamias ruficaudus). Journal of Mammalogy 2010; 91(6):1389-1400
  DOI: 10.1644/09-MAMM-A-082.1 · [Download PDF]
• Hird S, Kubatko L, Carstens B. Rapid and accurate species tree estimation for phylogeographic investigations using replicated subsampling. Molecular Phylogenetics & Evolution 2010; 57(2):888-98
  PMID: 20727977 · [Download PDF]
• Hird S, Reid N, Demboski J, Sullivan J. Introgression at differentially aged hybrid zones in red-tailed chipmunks. Genetica 2010; 138(8):869-83
  PMID: 20623163 · [Download PDF]
• Koopman MM, Fuselier DM, Hird S, Carstens BC. The carnivorous pale pitcher plant harbors diverse, distinct, and time-dependent bacterial communities. Applied & Environmental Microbiology 2010; 76(6):1851-60
  PMID: 20097807 · [Download PDF]
• Hird S, Sullivan J. Assessment of gene flow across a hybrid zone in red-tailed chipmunks (Tamias ruficaudus). Molecular Ecology 2009; 18(14):3097-109
  PMID: 19538343 · [Download PDF]
• Good JM, Hird S, Reid N, Demboski JR, Steppan SJ, Martin-Nims TR, Sullivan J. Ancient hybridization and mitochondrial capture between two species of chipmunks. Molecular Ecology 2008; 17(5):1313-27
  PMID: 18302691 · [Download PDF]