Rob DeSalle

Summary

Affiliation: American Museum of Natural History
Country: USA

Publications

  1. doi request reprint Generation of divergent uroplakin tetraspanins and their partners during vertebrate evolution: identification of novel uroplakins
    Rob DeSalle
    Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
    BMC Evol Biol 14:13. 2014
  2. pmc Determination of enriched histone modifications in non-genic portions of the human genome
    Jeffrey A Rosenfeld
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    BMC Genomics 10:143. 2009
  3. pmc Finishing genomes with limited resources: lessons from an ensemble of microbial genomes
    Niranjan Nagarajan
    Computational and Mathematical Biology, Genome Institute of Singapore 127726, Singapore
    BMC Genomics 11:242. 2010
  4. pmc Polytene chromosomes as indicators of phylogeny in several species groups of Drosophila
    P M O'Grady
    Division of Invertebrate Zoology, American Museum of Natural History, New York, USA
    BMC Evol Biol 1:6. 2001
  5. pmc Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics
    Indra Neil Sarkar
    MBLWHOI Library, Marine Biological Laboratory, Woods Hole, MA, USA
    BMC Bioinformatics 9:103. 2008
  6. doi request reprint Evolution of cysteine patterns in the large extracellular loop of tetraspanins from animals, fungi, plants and single-celled eukaryotes
    Rob DeSalle
    Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
    Mol Phylogenet Evol 56:486-91. 2010
  7. ncbi request reprint The evolution of HOM-C homeoboxes in the Dipteran family Drosophilidae
    R DeSalle
    Division of Invertebrates, American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
    Insect Mol Biol 12:345-51. 2003
  8. ncbi request reprint Crossroads, milestones and landmarks in insect development and evolution: implications for systematics
    R DeSalle
    Department of Entomology, American Museum of Natural History, New York 10024, USA
    Aliso 14:305-21. 1996
  9. doi request reprint An even "newer" animal phylogeny
    Rob DeSalle
    American Museum of Natural History, New York, Sackler Institute for Comparative Genomics, New York, NY 10024, USA
    Bioessays 30:1043-7. 2008
  10. ncbi request reprint Species discovery versus species identification in DNA barcoding efforts: response to Rubinoff
    Rob DeSalle
    Division of Invertebrates, American Museum of Natural History, New York, NY 10024, USA
    Conserv Biol 20:1545-7. 2006

Research Grants

Detail Information

Publications101 found, 100 shown here

  1. doi request reprint Generation of divergent uroplakin tetraspanins and their partners during vertebrate evolution: identification of novel uroplakins
    Rob DeSalle
    Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
    BMC Evol Biol 14:13. 2014
    ....
  2. pmc Determination of enriched histone modifications in non-genic portions of the human genome
    Jeffrey A Rosenfeld
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    BMC Genomics 10:143. 2009
    ..Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) has recently been used to identify the modification patterns for the methylation and acetylation of many different histone tails in genes and enhancers...
  3. pmc Finishing genomes with limited resources: lessons from an ensemble of microbial genomes
    Niranjan Nagarajan
    Computational and Mathematical Biology, Genome Institute of Singapore 127726, Singapore
    BMC Genomics 11:242. 2010
    ....
  4. pmc Polytene chromosomes as indicators of phylogeny in several species groups of Drosophila
    P M O'Grady
    Division of Invertebrate Zoology, American Museum of Natural History, New York, USA
    BMC Evol Biol 1:6. 2001
    ..We place the classical Drosophila evolutionary biology tools of polytene chromosome inversion analysis in a phylogenetic context and assess their utility in comparison to nucleotide sequences...
  5. pmc Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics
    Indra Neil Sarkar
    MBLWHOI Library, Marine Biological Laboratory, Woods Hole, MA, USA
    BMC Bioinformatics 9:103. 2008
    ..A significant bottleneck in the analysis of genomic-scale views of the tree of life is the time required for manual curation of genomic data into multi-gene phylogenetic matrices...
  6. doi request reprint Evolution of cysteine patterns in the large extracellular loop of tetraspanins from animals, fungi, plants and single-celled eukaryotes
    Rob DeSalle
    Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
    Mol Phylogenet Evol 56:486-91. 2010
    ..Our study provides a framework to better understand tetraspanin formation, diversification and the evolutionary history of these important proteins...
  7. ncbi request reprint The evolution of HOM-C homeoboxes in the Dipteran family Drosophilidae
    R DeSalle
    Division of Invertebrates, American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
    Insect Mol Biol 12:345-51. 2003
    ..In addition, different patterns of codon bias were detected in homeoboxes interrupted with introns when compared to homeoboxes that are uninterrupted...
  8. ncbi request reprint Crossroads, milestones and landmarks in insect development and evolution: implications for systematics
    R DeSalle
    Department of Entomology, American Museum of Natural History, New York 10024, USA
    Aliso 14:305-21. 1996
    ..Both approaches will aid greatly in expanding our understanding of homology in particular, and insect development in general...
  9. doi request reprint An even "newer" animal phylogeny
    Rob DeSalle
    American Museum of Natural History, New York, Sackler Institute for Comparative Genomics, New York, NY 10024, USA
    Bioessays 30:1043-7. 2008
    ..First, the methods used by the authors to generate their phylogenetic hypotheses call for close examination. Second, the relationships of animal taxa in their resultant trees also prompt further discussion...
  10. ncbi request reprint Species discovery versus species identification in DNA barcoding efforts: response to Rubinoff
    Rob DeSalle
    Division of Invertebrates, American Museum of Natural History, New York, NY 10024, USA
    Conserv Biol 20:1545-7. 2006
  11. ncbi request reprint The expansion of conservation genetics
    Rob DeSalle
    American Museum of Natural History, New York, New York 10024, USA
    Nat Rev Genet 5:702-12. 2004
    ..Such expansion will allow for more precise conservation decisions to be made and, more importantly, will allow conservation genetics to contribute to area- and landscape-based decision-making processes...
  12. pmc The unholy trinity: taxonomy, species delimitation and DNA barcoding
    Rob DeSalle
    Division of Invertebrate Zoology, American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
    Philos Trans R Soc Lond B Biol Sci 360:1905-16. 2005
    ....
  13. ncbi request reprint What's in a character?
    Rob DeSalle
    Division of Invertebrates and the Molecular Systematics Laboratories, American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
    J Biomed Inform 39:6-17. 2006
    ....
  14. pmc The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data
    Jose Eduardo de la Torre-Bárcena
    Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
    PLoS ONE 4:e5764. 2009
    ..Although most recent studies support the notion that gymnosperms and angiosperms are monophyletic and sister groups, they differ on the topological arrangements within each major group...
  15. doi request reprint Catching the phylogenic history through the ontogenic hourglass: a phylogenomic analysis of Drosophila body segmentation genes
    Amir Yassin
    Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th St at Central Park West, NY 10024, USA
    Evol Dev 12:288-95. 2010
    ..We suggest that simultaneous character-based analyses give better macroevolutionary support to the hourglass model of the developmental constraints on genome evolution than pairwise phenetic comparisons...
  16. pmc A functional phylogenomic view of the seed plants
    Ernest K Lee
    Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
    PLoS Genet 7:e1002411. 2011
    ..Our approach takes advantage of genomic data to define orthologs, reconstruct relationships, and narrow down candidate genes involved in plant evolution within a phylogenomic view of species' diversification...
  17. pmc Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution
    Angélica Cibrián-Jaramillo
    Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
    Genome Biol Evol 2:225-39. 2010
    ....
  18. doi request reprint A whole-genome phylogeny of the family Pasteurellaceae
    Maria Pia Di Bonaventura
    Sackler Institute of Comparative Genomics, American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
    Mol Phylogenet Evol 54:950-6. 2010
    ..We show that a very large number of concatenated gene sequences (>160) are needed to reliably obtain the same topology as the overall analysis...
  19. pmc Orthology, function and evolution of accessory gland proteins in the Drosophila repleta group
    Francisca C Almeida
    Department of Biology, New York University, New York, NY 10003, USA
    Genetics 181:235-45. 2009
    ..We found that positive selection is a strong force in the early divergence of these gene pairs...
  20. ncbi request reprint OrthologID: automation of genome-scale ortholog identification within a parsimony framework
    Joanna C Chiu
    Department of Biology, New York University, New York, NY 10003, USA
    Bioinformatics 22:699-707. 2006
    ..In contrast, orthology determination within a character-based phylogenetic framework has not been utilized on a genomic scale owing to the lack of efficiency and automation...
  21. doi request reprint The phylogenetic relationships of cynopterine fruit bats (Chiroptera: Pteropodidae: Cynopterinae)
    Francisca C Almeida
    American Museum of Natural History, Division of Vertebrate Zoology, Department of Mammalogy, Central Park West at 79th Street, New York, NY 10024, USA
    Mol Phylogenet Evol 53:772-83. 2009
    ..Biogeographic analyses indicate a Sundaland origin of the Cynopterinae and divergence date estimates suggest different timing of diversification of the two major cynopterine clades...
  22. pmc ESTimating plant phylogeny: lessons from partitioning
    Jose E B de la Torre
    Department of Biology, New York University, 100 Washington Sq East, New York, NY 10003, USA
    BMC Evol Biol 6:48. 2006
    ....
  23. pmc Evolutionary relationships of the old world fruit bats (Chiroptera, Pteropodidae): another star phylogeny?
    Francisca C Almeida
    American Museum of Natural History, Division of Vertebrate Zoology, Department of Mammalogy, Central Park West at 79th Street, New York, NY 10024, USA
    BMC Evol Biol 11:281. 2011
    ....
  24. ncbi request reprint ORFcurator: molecular curation of genes and gene clusters in prokaryotic organisms
    Jeffrey A Rosenfeld
    Division of Invertebrate Zoology, Central Park West, 79th Street, American Museum of Natural History, New York, NY 10024, USA
    Bioinformatics 20:3462-5. 2004
    ..AVAILABILITY: ORFcurator and all associated scripts are freely available as supplementary information. SUPPLEMENTARY INFORMATION: http://www.genomecurator.org/ORFcurator/..
  25. ncbi request reprint Animal phylogenomics: multiple interspecific genome comparisons
    Rob DeSalle
    Department of Interbrate Zoology, American Museum of Natural History, New York, New York 10024, USA
    Methods Enzymol 395:104-33. 2005
    ..Finally, genome-enabled technologies that are affecting comparative biology are also discussed...
  26. ncbi request reprint Reciprocal illumination in the gene content tree of life
    E Kurt Lienau
    American Museum of Natural History, Molecular Laboratories, Central Park West at 79th Street, P J P, New York, New York 10024, USA
    Syst Biol 55:441-53. 2006
    ..It also can serve as a technique for identifying well-corroborated sets of homologous genes for functional genomic applications...
  27. ncbi request reprint Phylogenetic utility of different types of molecular data used to infer evolutionary relationships among stalk-eyed flies (Diopsidae)
    R H Baker
    Department of Entomology, American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
    Syst Biol 50:87-105. 2001
    ..In general, inclusion of the more rapidly evolving data consistently improves the congruence among partitions...
  28. pmc Lack of population genetic structure and host specificity in the bat fly, Cyclopodia horsfieldi, across species of Pteropus bats in Southeast Asia
    Kevin J Olival
    EcoHealth Alliance, New York, NY 10001, USA
    Parasit Vectors 6:231. 2013
    ..Old-World flies in the family Nycteribiidae are entirely wingless and depend on their hosts for long-distance dispersal; their population genetics has been unstudied to date...
  29. doi request reprint Testing taxonomic boundaries and the limit of DNA barcoding in the Siberian sturgeon, Acipenser baerii
    Vadim J Birstein
    Sturgeon Conservation International, New York, USA
    Mitochondrial DNA 20:110-8. 2009
    ..baerii at the species level. Although control region variation among subspecies was significant, diagnostic differences were not found for any of the subspecies...
  30. doi request reprint Evidence of adaptive evolution of accessory gland proteins in closely related species of the Drosophila repleta group
    Francisca C Almeida
    Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
    Mol Biol Evol 25:2043-53. 2008
    ..Among these, the ones with a conserved protein domain had positively selected sites within the functional region of the sequence. We also detected one instance of lineage-specific adaptive evolution in a clade formed by 2 sister species...
  31. pmc Random Addition Concatenation Analysis: a novel approach to the exploration of phylogenomic signal reveals strong agreement between core and shell genomic partitions in the cyanobacteria
    Apurva Narechania
    Sackler Institute for Comparative Genomics, American Museum of Natural History, USA
    Genome Biol Evol 4:30-43. 2012
    ..Our method also demonstrates that most emergent phylogenetic signal appears early in the concatenation process. The software is freely available at http://desalle.amnh.org...
  32. doi request reprint The genus Drosophila as a model for testing tree- and character-based methods of species identification using DNA barcoding
    Amir Yassin
    Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th St, New York, NY 10024, USA
    Mol Phylogenet Evol 57:509-17. 2010
    ..In conclusion, DNA barcoding of Drosophila shows no reason to alter the 250 years old tradition of character-based taxonomy, and many reasons to shy away from the alternatives...
  33. pmc Complete genome sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700
    Maria Pia Di Bonaventura
    Sackler Institute for Comparative Genetics, American Museum of Natural History, New York, NY 10024, USA
    J Bacteriol 191:4693-4. 2009
    ..This strain has a rough appearance, and its genome contains genes encoding a type VI secretion system and several factors that may participate in host colonization...
  34. ncbi request reprint Mitochondrial DNA extraction and sequencing of formalin-fixed archival snake tissue
    Mike Friedman
    Sackler Insitute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
    Mitochondrial DNA 19:433-7. 2008
    ..We reiterate previous caution about minimizing amplicon size and maximizing controls for contamination when working with formalin-preserved reptile tissues...
  35. ncbi request reprint Using whole genome presence/absence data to untangle function in 12 Drosophila genomes
    Jeffrey A Rosenfeld
    Department of Biology, New York University, New York, New York 10024, USA
    Fly (Austin) 2:291-9. 2008
    ..We propose that measures of phylogenetic congruence can be used as criteria to identify loci with related GO terms that have a significant impact on cladogenesis...
  36. doi request reprint An ancient icon reveals new mysteries: mummy DNA resurrects a cryptic species within the Nile crocodile
    Evon Hekkala
    Department of Biological Sciences, Fordham University, New York, NY, USA
    Mol Ecol 20:4199-215. 2011
    ..suchus is declining or extirpated throughout much of its distribution. Without proper recognition of this cryptic species, current sustainable use-based management policies for the Nile crocodile may do more harm than good. ..
  37. pmc Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals
    Shaadi F Pooyaei Mehr
    The Graduate Center, Molecular, Cellular and Developmental Biology, City University of New York, New York, NY 10065, USA
    BMC Genomics 14:546. 2013
    ..Using an approach that combines next-generation sequencing, de novo transcriptome assembly, gene annotation and synthetic gene construction, we identify and cluster the protein families from Favia corals from the northern Red Sea...
  38. pmc Population genetics of the understory fishtail palm Chamaedorea ernesti-augusti in Belize: high genetic connectivity with local differentiation
    Angélica Cibrián-Jaramillo
    Department of Ecology, Evolution and Environmental Biology, Columbia University, 1200 Amsterdam Avenue, Mail Code 5557, New York, NY 10027, USA
    BMC Genet 10:65. 2009
    ..We use microsatellite markers to describe the population genetics of this species in Belize and test the effects of climate change and deforestation on its recent and historical effective population size...
  39. doi request reprint Integrating DNA barcode data and taxonomic practice: determination, discovery, and description
    Paul Z Goldstein
    Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
    Bioessays 33:135-47. 2011
    ..This paper examines the potential strengths and pitfalls of integrating DNA sequence data, specifically in the form of DNA barcodes as they are currently generated and analyzed, with taxonomic practice...
  40. pmc A novel analytical framework for dissecting the genetic architecture of behavioral symptoms in neuropsychiatric disorders
    Anthony J Deo
    Department of Biology, New York University, New York, New York, United States of America
    PLoS ONE 5:e9714. 2010
    ....
  41. ncbi request reprint Preparation of samples for comparative studies of arthropod chromosomes: visualization, in situ hybridization, and genome size estimation
    Rob DeSalle
    Department of Invertebrate Zoology, American Museum of Natural History, New York, New York 10024, USA
    Methods Enzymol 395:460-88. 2005
    ..As well, advances in Genome size measurement and theory are described herein...
  42. ncbi request reprint Genetic assessment of a white-collared x red-fronted lemur hybrid zone at Andringitra, Madagascar
    Yael M Wyner
    Department of Entomology, American Museum of Natural History, New York, New York 10024, USA
    Am J Primatol 57:51-66. 2002
    ..f. rufus populations. The remaining three individuals were found to contain only markers for E. albocollaris. These results indicate that the population at Andringitra is a hybrid population between E. albocollaris and E.f. rufus...
  43. ncbi request reprint An automated phylogenetic key for classifying homeoboxes
    I Neil Sarkar
    Department of Medical Informatics, Columbia University College of Physicians and Surgeons, New York, NY, USA
    Mol Phylogenet Evol 24:388-99. 2002
    ..Using a subset of homeobox protein sequences as a test case, we show that our method approximates classification based on full-scale phylogenetic analysis with very high accuracy in a tiny fraction of the time...
  44. ncbi request reprint The origin of polynucleotide phosphorylase domains
    Magdalena Leszczyniecka
    Division of Invertebrates, American Museum of Natural History, New York, NY 10024, USA
    Mol Phylogenet Evol 31:123-30. 2004
    ..This result suggests that RPH experienced different evolutionary divergence patterns than the PNPase domains, consistent with the linked nature of the two PNPase domains...
  45. ncbi request reprint The Widespread Colonization Island of Actinobacillus actinomycetemcomitans
    Paul J Planet
    Department of Microbiology, College of Physicians and Surgeons, Columbia University, 701 West 168th Street, New York, New York 10032, USA
    Nat Genet 34:193-8. 2003
    ..We present evidence for a specific horizontal transfer event leading to the establishment of this region as a determinant of disease...
  46. ncbi request reprint Multiple sources of character information and the phylogeny of Hawaiian drosophilids
    R H Baker
    Department of Entomology, American Museum of Natural History, 79th Street at Central Park West, New York, New York 10024, USA
    Syst Biol 46:654-73. 1997
    ..We present a new method, partitioned Bremer support, for examining the contribution of a particular data partition to the topological support of the simultaneous analysis tree...
  47. ncbi request reprint A molecular phylogeny of Costaceae (Zingiberales)
    C D Specht
    Department of Biology, New York University, New York, New York 10003, USA
    Mol Phylogenet Evol 21:333-45. 2001
    ..This represents the first detailed investigation into intrageneric and interspecific evolutionary relationships within the family Costaceae and presents some novel evolutionary trends with respect to floral morphology and biogeography...
  48. ncbi request reprint The evolution and development of dipteran wing veins: a systematic approach
    J Stark
    Department of Biology, New York University, New York 10003, USA
    Annu Rev Entomol 44:97-129. 1999
    ..We argue that further developmental evolutionary studies, and the interpretation of data therefrom, must be conducted within the context of a well-supported phylogeny of the organisms under study...
  49. ncbi request reprint Molecular genetic analysis among subspecies of two Eurasian sturgeon species, Acipenser baerii and A. stellatus
    P Doukakis
    American Museum of Natural History, New York, NY 10024, USA
    Mol Ecol 8:S117-27. 1999
    ....
  50. ncbi request reprint Evolution of endogenous retrovirus-like elements of the woolly mammoth (Mammuthus primigenius) and its relatives
    A D Greenwood
    Division of Vertebrate Zoology, American Museum of Natural History, New York, New York 10024 5192, USA
    Mol Biol Evol 18:840-7. 2001
    ....
  51. ncbi request reprint Character congruence of multiple data partitions and the origin of the Hawaiian Drosophilidae
    J Remsen
    Department of Entomology, American Museum of Natural History, New York, New York 10024, USA
    Mol Phylogenet Evol 9:225-35. 1998
    ....
  52. ncbi request reprint Captive breeding, reintroduction, and the conservation genetics of black and white ruffed lemurs, Varecia variegata variegata
    Y M Wyner
    Department of Biology, New York University, NY 10003 6688, USA
    Mol Ecol 8:S107-15. 1999
    ..This study demonstrates the utility of combining genetic information with a consideration of conservation priorities in evaluating the implementation of management strategies...
  53. pmc Phylogenetic analysis of glucosyltransferases and implications for the coevolution of mutans streptococci with their mammalian hosts
    Silvia Argimon
    Department of Cariology and Comprehensive Care, New York University College of Dentistry, New York, New York, United States of America
    PLoS ONE 8:e56305. 2013
    ..Thus, the acquisition and diversification of S. mutans Gtfs predates modern humans and is unrelated to the increase in dietary sucrose consumption...
  54. doi request reprint Assessing biodiversity funding during the sixth extinction
    George Amato
    Sackler Institute for Comparative Genomics, American Museum of Natural History New York, NY, USA
    Bioessays 34:658-60. 2012
    ..A true solution to the biodiversity crisis will require greater attention from governmental and international funding agencies...
  55. pmc Evolutionary dynamics of variant genomes of human papillomavirus types 18, 45, and 97
    Zigui Chen
    Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
    J Virol 83:1443-55. 2009
    ....
  56. pmc Evidence, content and corroboration and the Tree of Life
    E Kurt Lienau
    Department of Biology, New York University, New York, NY 10003, USA
    Acta Biotheor 57:187-99. 2009
    ..Discussion of this "total evidence" approach leads to several interesting conclusions about generating ToL hypotheses...
  57. ncbi request reprint An application of tissue and DNA banking for genomics and conservation: the Ambrose Monell Cryo-Collection (AMCC)
    Angelique Corthals
    American Museum of Natural History, New York, NY, 10024, USA
    Syst Biol 54:819-23. 2005
  58. ncbi request reprint Relationships among characiform fishes inferred from analysis of nuclear and mitochondrial gene sequences
    Daniela Calcagnotto
    Division of Vertebrate Zoology, American Museum of Natural History, Central Park West at 79th St, New York, NY 10024 5192, USA
    Mol Phylogenet Evol 36:135-53. 2005
    ....
  59. ncbi request reprint Patterns of mitochondrial versus nuclear DNA sequence divergence among nymphalid butterflies: the utility of wingless as a source of characters for phylogenetic inference
    A V Brower
    Department of Entomology, American Museum of Natural History, New York, NY, USA
    Insect Mol Biol 7:73-82. 1998
    ..We suggest that wg will be a useful source of characters for phylogenetic studies of butterflies, and perhaps other insect taxa, with divergence times up to 60 million years ago...
  60. doi request reprint DNA barcodes for globally threatened marine turtles: a registry approach to documenting biodiversity
    Eugenia Naro-Maciel
    Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
    Mol Ecol Resour 10:252-63. 2010
    ..DNA barcoding of marine turtles is a powerful tool for species identification and wildlife forensics, which also provides complementary data for conservation genetic research...
  61. doi request reprint Taking the conservation biology perspective to secondary school classrooms
    Yael Wyner
    Secondary Education, City College of New York, New York, NY 10031, USA
    Conserv Biol 24:649-54. 2010
    ..Nevertheless, if the research is placed in the context of larger ecological processes that are being taught, students can gain a better understanding of ecology and a better understanding of their effect on the world...
  62. doi request reprint PERMANENT GENETIC RESOURCES: Development of microsatellite markers of the Mexican understorey palm Chamaedorea elegans, cross-species genotyping, and amplification in congeners
    Angélica Cibrián-Jaramillo
    Department of Ecology, Evolution, and Environmental Biology, Columbia University, 1200 Amsterdam Avenue, MC5557, New York, NY 10027, USA, Department of Biology, Georgetown University, 37th and O Streets, NW, Washington, D C 20057, USA, Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
    Mol Ecol Resour 8:322-4. 2008
    ..All nine multiplexing loci amplified in other five congeneric species, which will facilitate comparisons within the genus and contribute to the conservation of its genetic resources...
  63. ncbi request reprint Testing dispersal hypotheses in foraging green sea turtles (Chelonia mydas) of Brazil
    Eugenia Naro-Maciel
    the Center for Biodiversity and Conservation and the Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th St, New York, NY 10024, USA
    J Hered 98:29-39. 2007
    ..The results are consistent with a model of juvenile natal homing impacted by other factors. Effective protection of turtles foraging along the extensive Brazilian coast may enhance breeding populations thousands of kilometers away...
  64. doi request reprint caos software for use in character-based DNA barcoding
    Indra Neil Sarkar
    MBLWHOI Library, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA, Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street at CPW, New York, NY 10024, USA
    Mol Ecol Resour 8:1256-9. 2008
    ..The software is publicly available from http://sarkarlab.mbl.edu/CAOS...
  65. doi request reprint DNA barcoding of an invasive mammal species, the small Indian mongoose (Herpestes javanicus; E. Geoffroy Saint-Hillaire 1818) in the Caribbean and Hawaiian Islands
    Chanda E Bennett
    Center for Biodiversity and Conservation, American Museum of Natural History, New York, USA
    Mitochondrial DNA 22:12-8. 2011
    ..Although the small Indian mongoose is recognized as Herpestes javanicus, this nomenclature has been used interchangeably with Herpestes auropunctatus...
  66. ncbi request reprint Gene family evolution and homology: genomics meets phylogenetics
    J W Thornton
    Department of Biological Sciences and Center for Environmental Research and Conservation, Columbia University, New York, New York 10027, USA
    Annu Rev Genomics Hum Genet 1:41-73. 2000
    ..A marriage of the principles of phylogenetic systematics with the copious data generated by genomics promises unprecedented insights into the nature of biological organization and the historical processes that created it...
  67. ncbi request reprint How the fruit fly changed (some of) its spots
    P M O'Grady
    Division of Invertebrates, American Museum of Natural History, New York 10024, USA
    Curr Biol 10:R75-7. 2000
    ..While several genes have been shown to play a role in melanization, changes in a single gene - the one encoding tyrosine hydroxylase - are sufficient to generate novel pigmentation patterns...
  68. ncbi request reprint Molecular evolution of the synapsin gene family
    H T Kao
    Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, New York 10021, USA
    J Exp Zool 285:360-77. 1999
    ..This was accompanied by the emergence of an additional conserved domain, termed A. J. Exp. Zool. ( Mol. Dev. Evol. ) 285:360-377, 1999...
  69. ncbi request reprint Genetic divergence within the Drosophila mayaguana subcluster, a closely related triad of Caribbean species in the repleta species group
    P M O'Grady
    American Museum of Natural History, Division of Invertebrate Zoology, Central Park West 79th St, New York, NY 10024, USA
    Hereditas 136:240-5. 2002
    ..straubae from D. parisiena, highlighting the importance of examining a diverse array of data (morphological, molecular, ecological, and behavioral) when defining species limits...
  70. ncbi request reprint The effect of differential reproductive success on population genetic structure: correlations of life history with matrilines in humpback whales of the gulf of maine
    H C Rosenbaum
    Molecular Systematics Laboratory, American Museum of Natural History, 79th Street and CPW, New York, NY 10024, USA
    J Hered 93:389-99. 2002
    ..These results indicate that population structure can be influenced by interactions or associations between reproductive success, genetic structure, and environmental factors in a natural population of long-lived mammals...
  71. ncbi request reprint Hierarchical structure in the Drosophila mojavensis cluster (Diptera: Drosophilidae)
    D C S G Oliveira
    Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
    Hereditas 139:223-7. 2003
    ..arizonae. Our results suggest that either these taxa are still undergoing differentiation at the molecular level or have experienced gene flow in the recent past...
  72. doi request reprint Random roots and lineage sorting
    Jeffrey A Rosenfeld
    IST High Performance and Research Computing, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA
    Mol Phylogenet Evol 64:12-20. 2012
    ..Likelihood tends to stabilize incongruence as outgroups get further and further away from the ingroup. In one extreme case, likelihood overcompensates for sequence divergence but increases random rooting causing long branch repulsion...
  73. doi request reprint Mycobacterium tuberculosis spoligotypes that may derive from mixed strain infections are revealed by a novel computational approach
    Luiz Claudio O Lazzarini
    Institute of Thoracic Disease, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
    Infect Genet Evol 12:798-806. 2012
    ....
  74. pmc The COBRA family of putative GPI-anchored proteins in Arabidopsis. A new fellowship in expansion
    Francois Roudier
    Department of Biology, New York University, New York, NY 10003, USA
    Plant Physiol 130:538-48. 2002
    ..Together, these results indicate that COB family members are likely to be important new players at the plasma membrane-cell wall interface...
  75. ncbi request reprint Falsifications and corroborations: Karl Popper's influence on systematics
    Kevin G Helfenbein
    American Museum of Natural History, Department of Invertebrate Zoology, Central Park West at 79th Street, New York, NY 10024, USA
    Mol Phylogenet Evol 35:271-80. 2005
    ..We begin by presenting a synopsis of Popper's philosophical views to allow those views to be placed in the context of systematics...
  76. ncbi request reprint Key transitions in animal evolution
    Rob DeSalle
    American Museum of Natural History, New York, Division of Invertebrate Zoology 79 St at Central Park West, New York, NY 10024 ITZ, Ecology and Evolution, TiHo Hannover, Bünteweg 17d, D 30559 Hannover, Germany
    Integr Comp Biol 47:667-9. 2007
    ..In order to address this subject further and to assess progress in the examination of animal origins and transitions, an international group of scientists was convened at the Society for Comparative Biology meeting in January 2007...
  77. ncbi request reprint Can we ever identify the Urmetazoan?
    Bernd Schierwater
    ITZ, Ecology and Evolution, TiHo Hannover, Bünteweg 17d, D 30559 Hannover, Germany American Museum of Natural History, Division of Invertebrate Zoology 79 St at Central Park West, New York, NY 10024, USA
    Integr Comp Biol 47:670-6. 2007
    ..Even considerable amounts of recent molecular data have not provided a generally accepted answer. Here, we review the major problems of this phylogenetic conundrum and provide some directions for solving it...
  78. doi request reprint An introduction to a novel population genetic approach for HIV characterization
    Beatriz Perez-Sweeney
    American Museum of Natural History, Sackler Institute for Comparative Genomics, New York, NY, USA
    Infect Genet Evol 10:1155-64. 2010
    ..This strategy may prove to be a helpful way to characterize HIV genetic variation among hosts with suspected selection pressure differences, like progressors versus non-progressors...
  79. ncbi request reprint flp-1, the first representative of a new pilin gene subfamily, is required for non-specific adherence of Actinobacillus actinomycetemcomitans
    S C Kachlany
    Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
    Mol Microbiol 40:542-54. 2001
    ..actinomycetemcomitans. The duplication and divergence of flp genes in bacteria may be important to the diversification of the colonization properties of these organisms...
  80. pmc Phylogeny of genes for secretion NTPases: identification of the widespread tadA subfamily and development of a diagnostic key for gene classification
    P J Planet
    Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
    Proc Natl Acad Sci U S A 98:2503-8. 2001
    ..This molecular key-based method can be applied to other gene superfamilies and represents a valuable tool for genome analysis...
  81. ncbi request reprint The Trichoplax PaxB gene: a putative Proto-PaxA/B/C gene predating the origin of nerve and sensory cells
    Thorsten Hadrys
    ITZ, Ecology and Evolution, Hannover, Germany
    Mol Biol Evol 22:1569-78. 2005
    ..While PaxB, Pax2/5/8, and Pax6 genes have been linked to nerve cell and sensory system/organ development in virtually all animals investigated so far, our study suggests that Pax genes predate the origin of nerve and sensory cells...
  82. ncbi request reprint Is the evolution of Cnox-2 Hox/ParaHox genes "multicolored" and "polygenealogical?"
    Bernd Schierwater
    ITZ, Ecology and Evolution, TiHo Hannover, Bünteweg 17d, D 30559 Hannover, Germany
    Mol Phylogenet Evol 24:374-8. 2002
    ..The existing data on possible gene functions also reveal a quite heterogeneous picture. It seems conceivable that part of the "multicolored" picture relates to a "polygenealogical" origin of the Cnox-2 gene...
  83. ncbi request reprint Combined support for wholesale taxic atavism in gavialine crocodylians
    John Gatesy
    Department of Biology, University of California, Riverside, California 92521, USA
    Syst Biol 52:403-22. 2003
    ..Remaining inconsistencies in minimum length trees, including concentrated hierarchical patterns of homoplasy and extensive gaps in the fossil record, indicate where future work in crocodylian systematics should be directed...
  84. ncbi request reprint Phylogenetic and expression analysis of the glutamate-receptor-like gene family in Arabidopsis thaliana
    Joanna C Chiu
    Department of Biology, New York University, New York 10003, USA
    Mol Biol Evol 19:1066-82. 2002
    ..The three AtGLR clades do not show distinct clade-specific organ expression patterns. All 20 AtGLR genes are expressed in the root. Among them, five of the nine clade-II genes are root-specific in 8-week-old Arabidopsis plants...
  85. ncbi request reprint Origin of the tetraspanin uroplakins and their co-evolution with associated proteins: implications for uroplakin structure and function
    Antonio Garcia-Espana
    Unitat de Recerca, University Hospital Joan XXIII, Universitat Rovira i Virgili, 46007 Tarragona, Spain
    Mol Phylogenet Evol 41:355-67. 2006
    ..The structure and function of uroplakins, which are also expressed in Xenopus kidney, oocytes and fat body, are much more versatile than hitherto appreciated...
  86. ncbi request reprint Phylogeny and age of diversification of the planitibia species group of the Hawaiian Drosophila
    James Bonacum
    Department of Biology, University of Illinois at Springfield, 62703 5407, USA
    Mol Phylogenet Evol 37:73-82. 2005
    ....
  87. ncbi request reprint How many genes should a systematist sample? Conflicting insights from a phylogenomic matrix characterized by replicated incongruence
    John Gatesy
    Department of Biology, University of California Riverside, Spieth Hall, Riverside, California 92521, USA
    Syst Biol 56:355-63. 2007
  88. ncbi request reprint Phenetic and DNA taxonomy; a comment on Waugh
    Rob DeSalle
    Bioessays 29:1289-90. 2007
  89. ncbi request reprint Calibrating phylogenetic species formation in a threatened insect using DNA from historical specimens
    Paul Z Goldstein
    Division of Insects, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
    Mol Ecol 12:1993-8. 2003
    ..Implications for the phylogenetic species criterion and for the reintroduction of individuals to formerly occupied sites are discussed...
  90. pmc Out of Hawaii: the origin and biogeography of the genus Scaptomyza (Diptera: Drosophilidae)
    Patrick O'Grady
    Department of Environmental Science, Policy and Management, 117 Hilgard Hall, University of California, Berkeley, Berkeley, CA 94720, USA
    Biol Lett 4:195-9. 2008
    ..We propose that a combination of small body size, rapid generation time and unique ecological and physiological adaptations have allowed this genus to effectively disperse and diversify...
  91. ncbi request reprint Tumor outbreaks in marine turtles are not due to recent herpesvirus mutations
    Larry Herbst
    Curr Biol 14:R697-9. 2004
  92. pmc Diversifying selection in human papillomavirus type 16 lineages based on complete genome analyses
    Zigui Chen
    Department of Microbiology and Immunology, Albert Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    J Virol 79:7014-23. 2005
    ..Whether response to selective pressure upon the E5 and E6 ORFs contributes to the biological success of HPV16, its specific biological niche, and/or its oncogenic potential remains to be established...
  93. pmc Phylogenetic incongruence among oncogenic genital alpha human papillomaviruses
    Apurva Narechania
    Department of Microbiology, Albert Einstein College of Medicine, Ullman Building, Room 515, 1300 Morris Park Ave, Bronx, NY 10461, USA
    J Virol 79:15503-10. 2005
    ..These data indicate that the phylogeny of the oncogenic HPVs is complex and that their evolution may not be monophyletic across all genes...
  94. ncbi request reprint Resolution of a supertree/supermatrix paradox
    John Gatesy
    Department of Biology, University of California, Riverside, California 92521, USA
    Syst Biol 51:652-64. 2002
  95. doi request reprint Appearance of new tetraspanin genes during vertebrate evolution
    Antonio Garcia-Espana
    Research Unit, Universitat Rovira i Virgili, Hospital Joan XXIII, Pere Virgily Institute, Tarragona 43007, Spain
    Genomics 91:326-34. 2008
    ....
  96. pmc Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)
    Jim Leebens-Mack
    Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
    OMICS 10:231-7. 2006
    ..Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors...
  97. ncbi request reprint Lack of the canonical pRB-binding domain in the E7 ORF of artiodactyl papillomaviruses is associated with the development of fibropapillomas
    Apurva Narechania
    Department of Microbiology and Immunology, Albert Einstein Cancer Center, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    J Gen Virol 85:1243-50. 2004
    ....
  98. pmc Human papillomavirus (HPV) types 101 and 103 isolated from cervicovaginal cells lack an E6 open reading frame (ORF) and are related to gamma-papillomaviruses
    Zigui Chen
    Department of Microbiology and Immunology, Albert Einstein Cancer Center, Albert Einstein College of Medicine of Yeshiva University, NY 10461, USA
    Virology 360:447-53. 2007
    ..Moreover, this is the first report of HPVs lacking an E6 ORF and phylogenetic evidence suggests this occurred subsequent to their emergence from the gamma-/pi-PVs...
  99. ncbi request reprint In vitro assessment of chemokine receptor-ligand interactions mediating mouse eosinophil migration
    Michael T Borchers
    Mayo Clinic Scottsdale, Scottsdale, Arizona 85259, USA
    J Leukoc Biol 71:1033-41. 2002
    ..Collectively, these observations reveal physiologically relevant distinctions in mechanisms mediating human and mouse eosinophil migration that potentially reflect evolutionary disparities between these species...
  100. ncbi request reprint Dynamic regulation of fluorescent proteins from a single species of coral
    Hung Teh Kao
    Department of Psychiatry and Human Behavior, Division of Biology and Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
    Mar Biotechnol (NY) 9:733-46. 2007
    ..These findings have implications for current hypotheses regarding the properties and natural function of fluorescent proteins...
  101. ncbi request reprint The carcinogenicity of human papillomavirus types reflects viral evolution
    Mark Schiffman
    Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MA, USA
    Virology 337:76-84. 2005
    ..These results present several clear clues and research directions in our ongoing efforts to understand HPV carcinogenesis...

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