Alfred L Roca

Summary

Affiliation: University of Illinois
Country: USA

Publications

  1. doi request reprint The mastodon mitochondrial genome: a mammoth accomplishment
    Alfred L Roca
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Trends Genet 24:49-52. 2008
  2. doi request reprint Forest elephant mitochondrial genomes reveal that elephantid diversification in Africa tracked climate transitions
    Adam L Brandt
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Mol Ecol 21:1175-89. 2012
  3. doi request reprint The elephants of Gash-Barka, Eritrea: nuclear and mitochondrial genetic patterns
    Adam L Brandt
    The Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801
    J Hered 105:82-90. 2014
  4. doi request reprint Successful genotyping of microsatellites in the woolly mammoth
    Yasuko Ishida
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA
    J Hered 103:459-64. 2012
  5. doi request reprint Distinguishing forest and savanna African elephants using short nuclear DNA sequences
    Yasuko Ishida
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    J Hered 102:610-6. 2011
  6. ncbi request reprint Polymorphisms of the Toll-Like Receptor 2 of Goats (Capra hircus) may be Associated with Somatic Cell Count in Milk
    Christina T Ruiz-Rodriguez
    a Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
    Anim Biotechnol . 2016
  7. pmc Evidence for selection at HIV host susceptibility genes in a West Central African human population
    Kai Zhao
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    BMC Evol Biol 12:237. 2012
  8. pmc Proliferation of endogenous retroviruses in the early stages of a host germ line invasion
    Yasuko Ishida
    Department of Animal Sciences, University of Illinois at Urbana Champaign
    Mol Biol Evol 32:109-20. 2015
  9. pmc Sequence variation of koala retrovirus transmembrane protein p15E among koalas from different geographic regions
    Yasuko Ishida
    Department of Animal Sciences, University of Illinois at Urbana Champaign, 1207 W Gregory Drive, Urbana, IL 61801, USA Electronic address
    Virology 475:28-36. 2015
  10. pmc Reconciling apparent conflicts between mitochondrial and nuclear phylogenies in African elephants
    Yasuko Ishida
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
    PLoS ONE 6:e20642. 2011

Collaborators

  • Warren E Johnson
  • Sergios Orestis Kolokotronis
  • Alex D Greenwood
  • Taras K Oleksyk
  • Kai Zhao
  • Hendrik Jan Megens
  • Yohannes Hagos
  • Jeheskel Shoshani
  • Cheryl A Winkler
  • Mark S Springer
  • W J Murphy
  • STEPHEN J O'BRIEN
  • S K Wasser
  • Ross D E MacPhee
  • Yasuko Ishida
  • Adam L Brandt
  • Nicholas J Georgiadis
  • Christina T Ruiz-Rodriguez
  • Jessica R Brandt
  • Kwame A Darfour-Oduro
  • Natalie A Gugala
  • Lawrence B Schook
  • Nikolas Nikolaidis
  • Radhika S Ganu
  • Victor A David
  • Carlos A Driscoll
  • Cristian Capelli
  • Nicholas Georgiadis
  • Pavel Dobrynin
  • Gila Kahila Bar-Gal
  • Neil D Murray
  • Adrell Núñez
  • Martien A M Groenen
  • Luis E Rodriguez
  • J David Hernández-Martich
  • Jennifer A M Graves
  • Roberto Maria
  • Juan C Martinez-Cruzado
  • Yashira M Afanador-Hernández
  • Kirill Grigorev
  • Aleksey Komissarov
  • Ryan Oliverio
  • Liz A Paulino
  • Felipe C Cardoso
  • Edgar F Garrett
  • Noa Guedj
  • Chelsea McCallister
  • Markos Koutmos
  • Kyriakos Tsangaras
  • Timothy A Garrow
  • Kristofer M Helgen
  • Thomas L Serfass
  • Yohannes Yacob
  • Frank K Ammer
  • Kenine E Comstock
  • Tomoko Hondo
  • Stephen Fratpietro
  • Virginia E Fox
  • Robert M Stephens
  • Yirmed Demeke
  • Peter J van Coeverden de Groot
  • Keith E A Leggett
  • Karsten Hupe
  • Dominique Pontier
  • Miguel Delibes
  • Marilyn Menotti-Raymond
  • Eric H Harley
  • David W Macdonald
  • Nobuyuki Yamaguchi
  • Eli Geffen
  • Andrew C Kitchener
  • Francesca Brisighelli
  • Elaine A Ostrander
  • Jill Pecon-Slattery

Detail Information

Publications25

  1. doi request reprint The mastodon mitochondrial genome: a mammoth accomplishment
    Alfred L Roca
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Trends Genet 24:49-52. 2008
    ..However, it also suggests that a complex evolutionary picture could ultimately emerge and points to similarities between the early evolution of the Elephantidae and that of the gorilla-human-chimpanzee clade...
  2. doi request reprint Forest elephant mitochondrial genomes reveal that elephantid diversification in Africa tracked climate transitions
    Adam L Brandt
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Mol Ecol 21:1175-89. 2012
    ....
  3. doi request reprint The elephants of Gash-Barka, Eritrea: nuclear and mitochondrial genetic patterns
    Adam L Brandt
    The Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801
    J Hered 105:82-90. 2014
    ..Conservation efforts should aim to protect Eritrean elephants and their habitat in the short run, with restoration of habitat connectivity and genetic diversity as long-term goals. ..
  4. doi request reprint Successful genotyping of microsatellites in the woolly mammoth
    Yasuko Ishida
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA
    J Hered 103:459-64. 2012
    ....
  5. doi request reprint Distinguishing forest and savanna African elephants using short nuclear DNA sequences
    Yasuko Ishida
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    J Hered 102:610-6. 2011
    ..Nuclear genotyping of museum, dung, or ivory samples will provide better-informed conservation management of Africa's elephants...
  6. ncbi request reprint Polymorphisms of the Toll-Like Receptor 2 of Goats (Capra hircus) may be Associated with Somatic Cell Count in Milk
    Christina T Ruiz-Rodriguez
    a Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
    Anim Biotechnol . 2016
    ..941). Because factors other than mastitis can affect SCC and our sample sizes were limited, additional studies are needed to corroborate an association between TLR2 genotype and SCC or mastitis in goats...
  7. pmc Evidence for selection at HIV host susceptibility genes in a West Central African human population
    Kai Zhao
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    BMC Evol Biol 12:237. 2012
    ....
  8. pmc Proliferation of endogenous retroviruses in the early stages of a host germ line invasion
    Yasuko Ishida
    Department of Animal Sciences, University of Illinois at Urbana Champaign
    Mol Biol Evol 32:109-20. 2015
    ..Across the ten proviruses, seven LTR haplotypes were detected, indicating that at least seven different retroviral sequences had entered the koala germ line. ..
  9. pmc Sequence variation of koala retrovirus transmembrane protein p15E among koalas from different geographic regions
    Yasuko Ishida
    Department of Animal Sciences, University of Illinois at Urbana Champaign, 1207 W Gregory Drive, Urbana, IL 61801, USA Electronic address
    Virology 475:28-36. 2015
    ..Important epitopes and domains were highly conserved across the p15E sequences and in previously reported exogenous KoRVs. Overall, these results support the potential use of p15E for KoRV vaccine development. ..
  10. pmc Reconciling apparent conflicts between mitochondrial and nuclear phylogenies in African elephants
    Yasuko Ishida
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
    PLoS ONE 6:e20642. 2011
    ....
  11. pmc Koalas (Phascolarctos cinereus) From Queensland Are Genetically Distinct From 2 Populations in Victoria
    Christina T Ruiz-Rodriguez
    From the Department of Animal Sciences, University of Illinois at Urbana Champaign, 1207 West Gregory Drive, Urbana, IL Ruiz Rodriguez, Ishida, Roca Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria, Australia Murray Theodosius Dobzhansky Center for Genome Bioinformatics, St Petersburg State University, St Petersburg, Russia O Brien Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL O Brien School of Life Sciences, La Trobe University, Melbourne Victoria, Australia Graves Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany Greenwood Department of Veterinary Medicine, Freie Universitat Berlin, Berlin, Germany Greenwood and Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL Roca
    J Hered 107:573-580. 2016
    ..753) and nucleotide diversity (π = 0.0072), indicating along with the microsatellite data that North American zoos have maintained high levels of genetic diversity among their Queensland koalas...
  12. pmc Development and characterization of microsatellite markers in the African forest elephant (Loxodonta cyclotis)
    Natalie A Gugala
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL, 61801, USA
    BMC Res Notes 9:364. 2016
    ..The application of microsatellite markers across deeply divergent lineages may produce irregular patterns such as large indels or null alleles. Thus we developed novel microsatellite markers using DNA from two African forest elephants...
  13. pmc Evolutionary Analyses and Natural Selection of Betaine-Homocysteine S-Methyltransferase (BHMT) and BHMT2 Genes
    Radhika S Ganu
    Division of Nutritional Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, United States of America
    PLoS ONE 10:e0134084. 2015
    ..The dN/dS ratios in both BHMT and BHMT2 was highest following the gene duplication, suggesting that purifying selection played a lesser role as the two paralogs diverged in function. ..
  14. doi request reprint Impact of population expansion on genetic diversity and structure of river otters (Lontra canadensis) in Central North America
    Jessica R Brandt
    The Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL
    J Hered 105:39-47. 2014
    ..The genetic distinctiveness of river otters from different geographic regions should be considered when deciding on source populations for future translocations. ..
  15. pmc Triangulating the provenance of African elephants using mitochondrial DNA
    Yasuko Ishida
    Department of Animal Sciences, University of Illinois at Urbana Champaign Urbana, IL, USA
    Evol Appl 6:253-65. 2013
    ..For taxa such as elephants in which nuclear and mtDNA markers differ in phylogeography, combining the two markers can triangulate the origins of confiscated wildlife products. ..
  16. ncbi request reprint Mitogenomic sequences support a north-south subspecies subdivision within Solenodon paradoxus
    Adam L Brandt
    a Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA
    Mitochondrial DNA A DNA Mapp Seq Anal . 2016
    ..036) between north and south. This regional genetic divergence supports previous morphological and genetic reports recognizing northern (S. p. paradoxus) and southern (S. p. woodi) subspecies in need of separate conservation plans...
  17. pmc Evolutionary patterns of Toll-like receptor signaling pathway genes in the Suidae
    Kwame A Darfour-Oduro
    Department of Animal Sciences, University of Illinois, at Urbana Champaign, Urbana, Illinois, 61801, USA
    BMC Evol Biol 16:33. 2016
    ....
  18. pmc Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth
    Alfred L Roca
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    BMC Evol Biol 9:232. 2009
    ....
  19. pmc Genomically intact endogenous feline leukemia viruses of recent origin
    Alfred L Roca
    Laboratory of Genomic Diversity, Basic Research Program, SAIC Frederick, Maryland 21702, USA
    J Virol 78:4370-5. 2004
    ....
  20. ncbi request reprint The Near Eastern origin of cat domestication
    Carlos A Driscoll
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA
    Science 317:519-23. 2007
    ..Domestic cats derive from at least five founders from across this region, whose descendants were transported across the world by human assistance...
  21. ncbi request reprint Mesozoic origin for West Indian insectivores
    Alfred L Roca
    Laboratory of Genomic Diversity, Basic Research Program, SAIC Frederick, National Cancer Institute, Frederick, Maryland 21702, USA
    Nature 429:649-51. 2004
    ..Efforts to prevent extinction of the two surviving solenodon species would conserve an entire lineage as old or older than many mammalian orders...
  22. ncbi request reprint Cytonuclear genomic dissociation in African elephant species
    Alfred L Roca
    Laboratory of Genomic Diversity, Basic Research Program, SAIC Frederick, Frederick, Maryland 21702, USA
    Nat Genet 37:96-100. 2005
    ..The persistence of residual forest elephant mitochondria in savanna elephant herds renders evolutionary interpretations based on mitochondrial DNA alone misleading and preserves a genomic record of ancient habitat changes...
  23. ncbi request reprint Genomic inferences from Afrotheria and the evolution of elephants
    Alfred L Roca
    Laboratory of Genomic Diversity, Basic Research Program, SAIC Frederick and National Cancer Institute, Frederick, MD 21702, USA
    Curr Opin Genet Dev 15:652-9. 2005
    ..The elephant genome sequence might prove useful for comparative genomic studies of these advanced traits, which have appeared independently in only three mammalian orders: primates, cetaceans and proboscideans...
  24. ncbi request reprint A nuclear DNA phylogeny of the woolly mammoth (Mammuthus primigenius)
    Cristian Capelli
    Istituto di Medicina Legale, Universita Cattolica del Sacro Cuore, Rome, Italy
    Mol Phylogenet Evol 40:620-7. 2006
  25. ncbi request reprint Patterns of molecular genetic variation among African elephant populations
    Kenine E Comstock
    Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, D4 100, Seattle, WA 98109 1024, USA
    Mol Ecol 11:2489-98. 2002
    ..The savannah elephants show significantly lower genetic diversity than forest elephants, probably reflecting a founder effect in the recent history of the savannah species...