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Browsing by Author "Campana, Michael G."

Browsing by Author "Campana, Michael G."

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  • Adaptive Radiation Genomics of Two Ecologically Divergent Hawai'ian Honeycreepers: The 'akiapola'au and the Hawai'i 'amakihi 
    Campana, Michael G.; Corvelo, André; Shelton, Jennifer; Callicrate, Taylor E.; Bunting, Karen L.; Riley-Gillis, Bridget; Wos, Frank; DeGrazia, Justin; Jarvis, Erich D.; Fleischer, Robert C. (2020)
    The Hawai'ian honeycreepers (drepanids) are a classic example of adaptive radiation: they adapted to a variety of novel dietary niches, evolving a wide range of bill morphologies. Here we investigated genomic diversity, ...
  • Ancient DNA 
    Tuross, Noreen; Campana, Michael G. (Princeton University Press, 2018)
  • Annotation for Asian Elephant Em538 10x+Hi-C Genome Assembly 
    Prado, Natalia; Armstrong, Ellie E.; Brown, Janine L.; Goldenberg, Shifra; Leimgruber, Peter; Pearson, Virginia R.; Maldonado, Jesús E.; Campana, Michael G. (Smithsonian National Zoo and Conservation Biology Institute, 2023)
    Genome sequence (Em538.fa.gz) and AUGUSTUS v. 3.3.2 gene predictions (Em538.gff) for the Em538 ("Kandula") 10x+Hi-C assembly (NCBI Accession: JAOTIA020000000). Also provided are the InterProScan v. 5.60-92.0 functional ...
  • Annotations for ‘akiapola‘au and Hawai‘i ‘amakihi genomes 
    Campana, Michael G.; Corvelo, André; Shelton, Jennifer; Callicrate, Taylor E.; Bunting, Karen L.; Riley-Gillis, Bridget; Wos, Frank; DeGrazia, Justin; Jarvis, Erich D.; Fleischer, Robert C. (Smithsonian National Zoo and Conservation Biology Institute, 2023)
    This repository provides the annotations and genome assemblies generated in Campana et al. (2020). The de novo ‘akiapola‘au assembly is provided in file Aki.fa.gz, with its gene predictions in Aki_augustus_all.gff.gz. The ...
  • As wild as they come: Study confirms that Przewalski's horses are the best of the rest 
    Leimgruber, Peter; Campana, Michael G.; Maldonado, Jesús E.; Harris, Tara R.; Dejid, Nandintsetseg; Cao, Qing; Songer, Melissa A. (2018)
  • Assessing Biodiversity in the Phylogenomic Era 
    Campana, Michael G.; Hawkins, Melissa T. R.; Caballero, Susana (2021)
  • Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf 
    Ferrari, Giada; Lischer, Heidi E. L.; Neukamm, Judith; Rayo, Enrique; Borel, Nicole; Pospischil, Andreas; Rühli, Frank; Bouwman, Abigail S.; Campana, Michael G. (2018)
    The reconstruction of ancient metagenomes from archaeological material, and their implication in human health and evolution, is one of the most recent advances in paleomicrobiological studies. However, as for all ancient ...
  • BaitsTools: software for hybridization capture bait design 
    Campana, Michael G. (2018)
    Nucleic acid hybridization capture is a principal technology in molecular ecology and genomics. Bait design, however, is a non-trivial task and few resources currently exist to automate the process. Here, I present BaitsTools, ...
  • The Challenges of Reconstructing Tropical Biodiversity With Sedimentary Ancient DNA: A 2200-Year-Long Metagenomic Record From Bwindi Impenetrable Forest, Uganda 
    Dommain, René; Andama, Morgan; McDonough, Molly M.; Prado, Natalia A.; Goldhammer, Tobias; Potts, Richard; Maldonado, Jesús E.; Nkurunungi, John Bosco; Campana, Michael G. (2020)
  • A comparative study of RNA yields from museum specimens, including an optimized protocol for extracting RNA from formalin-fixed specimens 
    Speer, Kelly A.; Hawkins, Melissa T. R.; Flores, Mary Faith C.; McGowen, Michael R.; Fleischer, Robert C.; Maldonado, Jesús E.; Campana, Michael G.; Muletz-Wolz, Carly (2022)
    Animal specimens in natural history collections are invaluable resources in examining the historical context of pathogen dynamics in wildlife and spillovers to humans. For example, natural history specimens may reveal new ...
  • Conservation genomics and systematics of a near-extinct island radiation 
    Kearns, Anna M.; Campana, Michael G.; Slikas, Beth; Berry, Lainie; Saitoh, Takema; Cibois, Alice; Fleischer, Robert C. (2022)
  • Dataset for "High-resolution canid identification from scats using SNP capture: the FAECES* method" 
    Parker, Lillian; Campana, Michael G. (Smithsonian National Zoo and Conservation Biology Institute, 2022)
    Two capture bait sets: one to enrich for ~20,000 SNP loci polymorphic in African wild dogs (<i>Lycaon pictus</i>) and one to enrich for ~800 SNPs polymorphic in desert kit fox (<i>Vulpes arsipus</i>) and coyotes (<i>Canis ...
  • Dataset for Gene flow across elevations in Tupaia montana 
    Parker, Lillian D.; Campana, Michael G. (The Smithsonian Institution, 2020)
    This dataset contains three files:1. MIGRATEN_InputFile_Phase1.dat. Description: Input file for MIGRATE-N. Contains phased pseudo-haplotype UCE alignments for 20 mountain treeshrews divided into four populations as follows: ...
  • Dense sampling of bird diversity increases power of comparative genomics 
    Feng, Shaohong; Stiller, Josefin; Deng, Yuan; Armstrong, Joel; Fang, Qi; Reeve, Andrew Hart; Xie, Duo; Chen, Guangji; Guo, Chunxue; Faircloth, Brant C.; Petersen, Bent; Wang, Zongji; Zhou, Qi; Diekhans, Mark; Chen, Wanjun; Andreu-Sánchez, Sergio; Margaryan, Ashot; Howard, Jason Travis; Parent, Carole; Pacheco, George; Sinding, Mikkel-Holger S.; Puetz, Lara; Cavill, Emily; Ribeiro, Ângela M.; Eckhart, Leopold; Fjeldså, Jon; Hosner, Peter A.; Brumfield, Robb T.; Christidis, Les; Bertelsen, Mads F.; Sicheritz-Ponten, Thomas; Tietze, Dieter Thomas; Robertson, Bruce C.; Song, Gang; Borgia, Gerald; Claramunt, Santiago; Lovette, Irby J.; Cowen, Saul J.; Njoroge, Peter; Dumbacher, John Philip; Ryder, Oliver A.; Fuchs, Jérôme; Bunce, Michael; Burt, David W.; Cracraft, Joel; Meng, Guanliang; Hackett, Shannon J.; Ryan, Peter G.; Jønsson, Knud Andreas; Jamieson, Ian G.; da Fonseca, Rute R.; Braun, Edward L.; Houde, Peter; Mirarab, Siavash; Suh, Alexander; Hansson, Bengt; Ponnikas, Suvi; Sigeman, Hanna; Stervander, Martin; Frandsen, Paul B.; van der Zwan, Henriette; van der Sluis, Rencia; Visser, Carina; Balakrishnan, Christopher N.; Clark, Andrew G.; Fitzpatrick, John W.; Bowman, Reed; Chen, Nancy; Cloutier, Alison; Sackton, Timothy B.; Edwards, Scott V.; Foote, Dustin J.; Shakya, Subir B.; Sheldon, Frederick H.; Vignal, Alain; Soares, André E. R.; Shapiro, Beth; González-Solís, Jacob; Ferrer-Obiol, Joan; Rozas, Julio; Riutort, Marta; Tigano, Anna; Friesen, Vicki; Dalén, Love; Urrutia, Araxi O.; Székely, Tamás; Liu, Yang; Campana, Michael G.; Corvelo, André; Fleischer, Robert C.; Rutherford, Kim M.; Gemmell, Neil J.; Dussex, Nicolas; Mouritsen, Henrik; Thiele, Nadine; Delmore, Kira; Liedvogel, Miriam; Franke, Andre; Hoeppner, Marc P.; Krone, Oliver; Fudickar, Adam M.; Milá, Borja; Ketterson, Ellen D.; Fidler, Andrew Eric; Friis, Guillermo; Parody-Merino, Ángela M.; Battley, Phil F.; Cox, Murray P.; Lima, Nicholas Costa Barroso; Prosdocimi, Francisco; Parchman, Thomas Lee; Schlinger, Barney A.; Loiselle, Bette A.; Blake, John G.; Lim, Haw Chuan; Day, Lainy B.; Fuxjager, Matthew J.; Baldwin, Maude W.; Braun, Michael J.; Wirthlin, Morgan; Dikow, Rebecca B.; Ryder, T. B.; Camenisch, Glauco; Keller, Lukas F.; DaCosta, Jeffrey M.; Hauber, Mark E.; Louder, Matthew I. M.; Witt, Christopher C.; McGuire, Jimmy A.; Mudge, Joann; Megna, Libby C.; Carling, Matthew D.; Wang, Biao; Taylor, Scott A.; Del-Rio, Glaucia; Aleixo, Alexandre; Vasconcelos, Ana Tereza Ribeiro; Mello, Claudio V.; Weir, Jason T.; Haussler, David; Li, Qiye; Yang, Huanming; Wang, Jian; Lei, Fumin; Rahbek, Carsten; Gilbert, M. T.; Graves, Gary R.; Jarvis, Erich D.; Paten, Benedict; Zhang, Guojie (2020)
    Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a ...
  • An efficient method for simultaneous species, individual, and sex identification via in-solution single nucleotide polymorphism capture from low-quality scat samples 
    Parker, Lillian D.; Campana, Michael G.; Quinta, Jessica D.; Cypher, Brian; Rivera, Isabel; Fleischer, Robert C.; Ralls, Katherine; Wilbert, Tammy R.; Boarman, Ryan; Boarman, William, I.; Maldonado, Jesus E. (2021)
    Understanding predator population dynamics is important for conservation management because of the critical roles predators play within ecosystems. Noninvasive genetic sampling methods are useful for the study of predators ...
  • An efficient noninvasive method for simultaneous species, individual, and sex identification of sympatric Mojave Desert canids via in-solution SNP capture 
    Parker, Lillian D.; Campana, Michael G.; Quinta, Jessica D.; Cypher, Brian; Rivera, Isabel; Fleischer, Robert C.; Ralls, Katherine; Wilbert, Tammy R.; Boarman, Ryan; Boarman, William I.; Maldonado, Jesús E. (2021)
  • Epigenetic clock and methylation studies in elephants 
    Prado, Natalia A.; Brown, Janine L.; Zoller, Joseph A.; Haghani, Amin; Yao, Mingjia; Bagryanova, Lora R.; Campana, Michael G.; Maldonado, Jesús E.; Raj, Ken; Schmitt, Dennis; Robeck, Todd R.; Horvath, Steve (2021)
    Age-associated DNA-methylation profiles have been used successfully to develop highly accurate biomarkers of age (&quot;epigenetic clocks&quot;) in humans, mice, dogs, and other species. Here we present epigenetic clocks ...
  • Gene expression reveals immune response strategies of naïve Hawaiian honeycreepers experimentally infected with introduced avian malaria 
    Paxton, Kristina L.; Cassin-Sackett, Loren; Atkinson, Carter T.; Videvall, Elin; Campana, Michael G.; Fleischer, Robert C. (2023)
    The unprecedented rise in the number of new and emerging infectious diseases in the last quarter century poses direct threats to human and wildlife health. The introduction to the Hawaiian archipelago of Plasmodium relictum ...
  • A gene-based capture assay for surveying patterns of genetic diversity and insecticide resistance in a worldwide group of invasive mosquitoes 
    Aardema, Matthew L.; Campana, Michael G.; Wagner, Nicole E.; Ferreira, Francisco C.; Fonseca, Dina M. (2022)
    Understanding patterns of diversification, genetic exchange, and pesticide resistance in arthropod disease vectors is necessary for effective population management. With the availability of next-generation sequencing ...
  • Genetic analyses are more sensitive than morphological inspection at detecting the presence of threatened Mojave desert tortoise (Gopherus agassizii) remains in canid scat and raven pellets 
    Parker, Lillian D.; Quinta, Jessica D.; Rivera, Isabel; Cypher, Brian L.; Kelly, Erica C.; Campana, Michael G.; Fleischer, Robert C.; Boarman, Ryan; Boarman, William I.; Maldonado, Jesus E. (2022)
    Subsidization of predator populations increases predation pressure on prey species, which is exacerbated when natural resources are scarce. Estimating the frequency of predation by subsidized predators on vulnerable species, ...

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