Publications


In Press

Kurt Lienau E, Desalle R. Evidence, Content and Corroboration and the Tree of Life. Acta Biotheor

2009

Rosenfeld JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ. 2009. Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics. 10:143.

Egan M, Lee EK, Chiu JC, Coruzzi G, Desalle R. 2009. Gene Orthology Assessment with OrthologID. Methods Mol Biol 537:23-38.

Perkins SL, Austin CC. Four new species of Plasmodium from New Guinea lizards: Integrating morphology and molecules. J Parasitol 95(2): 424-433.

Perkins SL, Kerwin AS, Rothschild AD. 2009. Patterns of infection of the lizard malaria parasite, Plasmodium floridense, in invasive brown anoles (Anolis sagrei) in Southwestern Florida. Parasitol Res 104(5): 1191-1196.

Schierwater B, Eitel M, Jakob W, Osigus HJ, Hadrys H, Dellaporta SL, Kolokotronis SO, Desalle R. 2009. Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis. PLoS Biol 7(1):e1000020.

Almeida FC, Desalle R. Orthology, Function, and Evolution of Accessory Gland Proteins in the Drosophila repleta Group. 2009. Genetics 181:235-245.

Chen Z, Desalle R, Schiffman M, Herrero R, Burk RD. 2009. Evolutionary dynamics of human papillomavirus types 18, 45 and 97 variant genomes. J Virol. 83(3):1443-55.

Eaton MJ, Martin A, Thorbjarnarson J, Amato G. 2009. Species-level diversification of African dwarf crocodiles (Genus Osteolaemus): A geographic and phylogenetic perspective. Mol Phylogenet Evol 50(3):496-506.

Schierwater B, de Jong D, Desalle R. 2009. Placozoa and the evolution of Metazoa and intrasomatic cell differentiation. Int J Biochem Cell Biol 41(2):370-379.

Beadell JS, Covas R, Gebhard C, Ishtiaq F, Melo M, Schmidt BK, Perkins SL, Graves GR, Fleischer RC. 2009. Host associations and evolutionary relationships of avian blood parasites from West Africa. Int J Parasitol 39(2):257.-266

Lemke MJ, Lienau EK, Rothe J, Pagioro TA, Rosenfeld J, Desalle R. 2009. Description of freshwater bacterial assemblages from the Upper Paraná river floodpulse system, Brazil. Microb Ecol 57(1):94-103.

2008

Almeida FC, Leszczyniecka M, Fisher PB, Desalle R. 2008. Examining Ancient Inter-domain Horizontal Gene Transfer. Evol Bioinform Online 4:109-19.

Rosenfeld JA, DeSalle R, Lee EK, O'Grady P. 2008. Using whole genome presence/absence data to untangle function in 12 Drosophila genomes. Fly (Austin). 2(6):291-9.

Cibrián-Jaramillo A, Marler TE, DeSalle R, Brenner ED. 2008. Development of EST-microsatellites from the cycad Cycas rumphii, and their use in the recently endangered Cycas micronesica. Conserv Genet 9(4):1051-1054.

Krause J, Unger T, Noçon A, Malaspinas AS, Kolokotronis SO, Stiller M, Soibelzon L, Spriggs H, Dear PH, Briggs AH, Bray SE, O'Brien SJ, Rabeder G, Matheus P, Cooper A, Slatkin M, Pääbo S, Hofreiter M. (2008) Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evolutionary Biology 8:220.

Wyatt KB, Campos PF, Gilbert MTP, Kolokotronis S-O, Hynes WH, DeSalle R, Daszak P, MacPhee RD, Greenwood AD. 2008. Historical Mammal Extinction on Christmas Island (Indian Ocean) Correlates with Introduced Infectious Disease. PLoS ONE 3(11):e3602.

DeSalle R, Schierwater B. 2008. An even "newer" animal phylogeny. Bioessays 30(11-12):1043-7.

Naro-Maciel E, Le M, Fitzsimmons NN, Amato G. 2008. Evolutionary relationships of marine turtles: A molecular phylogeny based on nuclear and mitochondrial genes. Mol Phylogenet Evol 49(2):659-662.

Laufer AS, Siddall ME, Graf J. 2008. Characterization of the Digestive-Tract Microbiota of Hirudo orientalis, a European Medicinal Leech. Appl Environ Microbiol 74(19):6151-6154.

Gatesy J, Amato G. 2008. The rapid accumulation of consistent molecular support for intergeneric crocodylian relationships. Mol Phylogenet Evol 48(3):1232-1237.

Almeida FC, Desalle R. 2008. Evidence of adaptive evolution of accessory gland proteins in closely related species of the Drosophila repleta group. Mol Biol Evol 25(9):2043–53.

Rach J, Desalle R, Sarkar IN, Schierwater B, Hadrys H. 2008. Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata. Proc Biol Sci 275(1632):237-247.

Sarkar IN, Egan MG, Coruzzi G, Lee EK, DeSalle R. 2008. Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics. BMC Bioinformatics 9:103.

Martinsen ES, Perkins SL, Schall JJ. 2008. A three-genome phylogeny of malaria parasites (Plasmodium and closely related genera): evolution of life-history traits and host switches. Mol Phylogenet Evol 47(1):261-273.

Baillie GJ, Kolokotronis SO, Waltari E, Maffei JG, Kramer LD, Perkins SL. 2008. Phylogenetic and evolutionary analyses of St. Louis encephalitis virus genomes. Mol Phylogenet Evol 47(2):717-728.

Borda E, Oceguera-Figueroa A, Siddall ME. 2008. On the classification, evolution and biogeography of terrestrial haemadipsoid leeches (Hirudinida: Arhynchobdellida: Hirudiniformes). Mol Phylogenet Evol 46(1):142-154.

Fontanella FM, Feldman CR, Siddall ME, Burbrink FT. 2008. Phylogeography of Diadophis punctatus: extensive lineage diversity and repeated patterns of historical demography in a trans-continental snake. Mol Phylogenet Evol 46(3):1049-1070.

Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, Sørensen MV, Haddock SH, Schmidt-Rhaesa A, Okusu A, Kristensen RM, Wheeler WC, Martindale MQ, Giribet G. 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452(7188):745-749.

Zink R, Barrowclough GF. 2008. Mitochondrial DNA under siege in avian phylogeography. Mol Ecol 17(9):2107-2121.

Mendez M, Rosenbaum HC, Bordino P. 2008. Conservation genetics of the franciscana dolphin in Northern Argentina: population structure, by-catch impacts, and management implications. Conserv Genet 9(2):419-435.

Ji X, Wu X, Yan P, Amato G. 2008. Complete sequence and gene organization of the mitochondrial genome of Siamensis Crocodile (Crocodylus siamensis). Mol Biol Rep 35(2):133-138.

Garcia-España A, Chung PJ, Sarkar IN, Stiner E, Sun TT, Desalle R. 2008. Appearance of new tetraspanin genes during vertebrate evolution. Genomics 91(4):326-334.

O'Grady P, Desalle R. 2008. Out of Hawaii: the origin and biogeography of the genus Scaptomyza (Diptera: Drosophilidae). Biol Lett 4(2):195-199.

Cibrián-Jaramillo A, Hahn WJ, DeSalle R. 2008. Development of microsatellite markers of the Mexican understory palm Chamaedorea elegans, cross-species genotyping, and amplification in congeners. Mol Ecol Notes 8(2):322-324.

Wheeler WC, Pickett KM. 2008. Topology-Bayes versus clade-Bayes in phylogenetic analysis. Mol Biol Evol 25(2):447-453.

Kao HT, Sturgis S, DeSalle R, Tsai J, Davis D, Gruber DF, Pieribone VA. 2008. Dynamic regulation of fluorescent proteins from a single species of coral. Mar Biotechnol 9(6):733-746.

2007

Olival KJ, Stiner EO, Perkins SL. 2007. Detection of Hepatocystis sp. in southeast Asian flying foxes (Pteropodidae) using microscopic and molecular methods. J Parasitol 93(6):1538-1540.

Ponnerassery S, Crane S, Cain KD, Strom M. 2007. Sortase inhibitor phenyl vinyl sulfone inhibits Renibacterium salmoninarum adherence and invasion of host cells. Dis Aquat Org 78(2):115-127.

Ho SYW, Kolokotronis SO, Allaby RG. 2007. Elevated substitution rates estimated from ancient DNA sequences. Biol Lett 3(6):702-705.

DeSalle R, Schierwater B. 2007. Key transitions in animal evolution. Integr Comp Biol 47(5):667-669.

Schierwater B, DeSalle R. 2007. Can we ever identify the Urmetazoan? Integr Comp Biol 47(5):670-676.

Sears KE, Goswami A, Flynn JJ, Niswander LA. 2007. The correlated evolution of Runx2 tandem repeats and facial length in Carnivora. Evol Dev 9(6): 555-565.

Rodriguez JP,...Mendez M et al. 2007. The globalization of conservation: a view from the South. Science 317(5839):755-756.

Baldo L, Prendini L, Corthals A, Werren JH. 2007. Wolbachia are present in southern african scorpions and cluster with supergroup F. Curr Microbiol 55(5):367-373.

Finarelli JA, Flynn JJ. 2007. The evolution of encephalization in caniform carnivorans. Evolution 61(7):1758-1772.

Mendez M, Waller T, Micucci P, Alvarenga E, and Morales JC. 2007. Genetic population structure of the yellow anaconda (Eunectes notaeus) in Northern Argentina: management implications. In: Biology of the Boas and Pythons. Henderson RW & Powel R, Eds. Eagle Mountain Publishing, LC.

Ribas CC, Moyle RG, Miyaki CY, Cracraft J. 2007. The assembly of montane biotas: linking Andean tectonics and climatic oscillations to independent regimes of diversification in Pionus parrots. Proc Biol Sci 274(1624):2399-2408.

Reddy S, Cracraft J. 2007. Old World shrike-babblers (Pteruthius) belong with New World vireos (Vireonidae). Mol Phylogenet Evol 44(3):1352-1357.

Wheeler WC. 2007. Chromosomal character optimization. Mol Phylogenet Evol 44(3):1130-1140.

Waltari E, Hijmans RJ, Peterson AT, Nyari AS, Perkins SL, Guralnick RP. 2007. Locating Pleistocene refugia: comparing phylogeographic and ecological niche model predictions. PLoS ONE 2:e563.

Russello MA, Amato G. 2007. On the horns of a dilemma: molecular approaches refine ex situ conservation in crisis. Mol Ecol 16(12):2405-2406.

Gatesy J, DeSalle R, Wahlberg N. 2007. How many genes should a systematist sample? Conflicting insights from a phylogenomic matrix characterized by replicated incongruence. Syst Biol 56(2):355-363.

Pellens R, D'Haese CA, Bellés X, Piulachs MD, Legendre F, Wheeler WC, Grandcolas P. 2007. The evolutionary transition from subsocial to eusocial behaviour in Dictyoptera: phylogenetic evidence for modification of the "shift-in-dependent-care" hypothesis with a new subsocial cockroach. Mol Phylogenet Evol 43(2):616-626.

Waltari E, Hoberg EP, Lessa EP, Cook JA. 2007. Eastward Ho: phylogeographical perspectives on colonization of hosts and parasites across the Beringian nexus. J Biogeogr 34(4):561-574.

Kolokotronis SO, MacPhee RDE, Greenwood AD. 2007. Detection of mitochondrial insertions in the nucleus (NuMts) of Pleistocene and modern muskoxen. BMC Evol Biol 7:67.

Janies D, Hill AW, Guralnick R, Habib F, Waltari E, Wheeler WC. 2007. Genomic analysis and geographic visualization of the spread of avian influenza (H5N1). Syst Biol 56(2):321-329.

Ramirez MJ, Coddington JA, Maddison WP, Midford PE, Prendini L, Miller J, Griswold CE, Hormiga G, Sierwald P, Scharff N, Benjamin SP, Wheeler WC. 2007. Linking of digital images to phylogenetic data matrices using a morphological ontology. Syst Biol 56(2):283-294.

Li Y, Wu X, Ji X, Yan P, Amato G. 2007. The complete mitochondrial genome of salt-water crocodile (Crocodylus porosus) and phylogeny of crocodilians. J Genet Genomics 34(2):119-128.

Siddall ME, Trontelj P, Utevsky SY, Nkamany M, Macdonald III, KS. 2007. Diverse molecular data demonstrate that commercially available medicinal leeches are not Hirudo medicinalis. Proc R Soc Lond B Biol Sci 274(1617):1481-1487

Rousset V, Pleijel F, Rouse GW, Erséus C, Siddall ME. 2007. A molecular phylogeny of annelids. Cladistics 23(1):41-63.

Smith WL, Sparks JS. 2007. Gobius lagocephalus: The world's most widespread nomen dubium. Mol Phylogenet Evol 43(2):696-698.

Naro-Maciel E, Becker JH, Lima EH, Marcovaldi MA, DeSalle R. 2007. Testing dispersal hypotheses in foraging green sea turtles (Chelonia mydas) of Brazil. J Hered 98(1):29-39.

Dávalos LM. 2007. Short-faced bats (Phyllostomidae: Stenodermatina): a Caribbean radiation of strict frugivores. J Biogeogr 34(2):364-375.

Chen Z, Schiffman M, Herrero R, DeSalle R, Burk RD. 2007. Human papillomavirus (HPV) types 101 and 103 isolated from cervicovaginal cells lack an E6 open reading frame (ORF) and are related to gamma-papillomaviruses. Virology 360(2):447-453.

Almeida FC, Cordeiro-Estrela P, Bonvicino BR 2007. Phylogeny and temporal diversification of Calomys (Rodentia, Sigmodontinae): implications for the biogeography of an endemic genus of the open/dry biomes of South America. Mol Phylogenet Evol 42(2):449-466.

Perkins SL, Sarkar IN, Carter R. 2007. The phylogeny of rodent malaria parasites: simultaneous analysis across three genomes. Infect Genet Evol 7(1):74-83.

2006

Amato G, Ryder OA, Rosenbaum HC, DeSalle R [Editors]. 2006. Conservation Genetics in the Age of Genomics. Columbia University Press, New York.

Ji XF, Wu XB, Li Y, Yan P, Amato G. 2006. The mitochondrial genome of Crocodylus niloticus with implications for phylogenetic relationships among crocodilians. Acta Zoolog Sin 52(4):810-818.

Kretzman M, Mentzer L, DiGiovanni R, Leslie MS, Amato G. 2006. Microsatellite diversity and fitness in stranded juvenile harp seals (Phoca groenlandica). J Hered 97(6):555-560.

Giannini NP, Almeida FC, Simmons NB, DeSalle R. 2006. Phylogenetic relationships of the enigmatic Harpy fruit bat, Harpyionycteris (Mammalia: Chiroptera: Pteropodidae). Am Mus Novit 3533.

Vinh le S, Varón A, Wheeler WC. 2006. Pairwise alignment with rearrangements. Genome Inform 17(2):141-151.

DeSalle R. 2006. Species discovery versus species identification in DNA barcoding efforts: response to Rubinoff. Conserv Biol 20(5):1545-1547.

Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, Depamphilis C, DeSalle R et al. 2006. Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS 10(2):231-237.

Burk RD, DeSalle R. 2006. The tango and tangle of human papillomavirus and the human genome. J Natl Cancer Inst 98(15):1026-1027.

Barrowclough GF, Groth JG, Mertz LA. 2006. The RAG-1 exon in the avian order Caprimulgiformes: phylogeny, heterozygosity, and base composition. Mol Phylogenet Evol 41(1):238-248.

Lienau EK, DeSalle R, Rosenfeld JA, Planet PJ. 2006. Reciprocal illumination in the gene content tree of life. Syst Biol 55(3):441-453.

Garcia-Espana A, Chung PJ, Zhao X, Lee A, Pellicer A, Yu J, Sun TT, DeSalle R. 2006. Origin of the tetraspanin uroplakins and their co-evolution with associated proteins: implications for uroplakin structure and function. Mol Phylogenet Evol 41(2):355-367.

de la Torre JE, Egan MG, Katari M, Brenner ED, Stevenson DW, Coruzzi GM, DeSalle R. 2006. ESTimating plant phylogeny: lessons from partitioning. BMC Evol Biol 6(1):48

Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, DeSalle R. 2006. OrthologID: automation of genome-scale ortholog identification within a parsimony framework. Bioinformatics 22(6):699-707.

DeSalle R. 2006. What's in a character? J Biomed Inform 39(1):6-17.

Siddall ME, Aguado MT. 2006. Molecular phylogenetic evidence of a haplosporidian parasite infecting the polychaete Syllis nipponica (Imajima, 1966). Parasitol Res 99(3):309-312.

Sarkar IN. 2006. Phylogenetics in the modern era. J Biomed Inform 39(1):3-5.

Pomilla C & Rosenbaum HC. 2006. Estimates of relatedness in groups of humpback whales (Megaptera novaeangliae) on two wintering grounds of the Southern Hemisphere. Mol Ecol 15(9):2541-2555.

Amor DC, Kolokotronis SO, Medellín RA, Ramey Jr R, Ryder OA. 2006. Genética de la conservación. In: El Berrendo en México: Acciones de conservación. [The Pronghorn in Mexico: Conservation Actions]. (Valdes M, de la Cruz E, Peters E, and Pallares E, Eds.) Agrupación Sierra Madre - Instituto Nacional de Ecología (INE-SEMARNAT), México. pp 27-33.

Moyle RG, Cracraft J, Lakim M, Nais J, Sheldon FH. 2006. Reconsideration of the phylogenetic relationships of the enigmatic Bornean Bristlehead (Pityriasis gymnocephala). Mol Phylogenet Evol 39(3):893-898.

Dávalos LM. 2006. Earth history and the evolution of Caribbean bats. In: Evolution, Ecology, and Conservation of Island Bats. (Fleming, TH & Racey PA, Eds.) Chicago: University of Chicago Press.

Ochman H & Dávalos LM. 2006. The nature and dynamics of bacterial genomes. Science 311(5768):1730-1733.

Austin CC & Perkins SL. 2006. Parasites in a biodiversity hotspot: a survey of hematozoa and a molecular phylogenetic analysis of Plasmodium in New Guinea skinks. J Parasitol 92(4):770-777.

Charleston MA & Perkins SL. 2006. Traversing the tangle: algorithms and applications for cophylogenetic studies. J Biomed Inform 39:62-71.

Siddall ME & Aguado MT. 2006. Molecular phylogenetic evidence of a haplosporidian parasite infecting the polychaete Syllis nipponica (Imajima, 1966). Parasitol Res 99(3):309-312.

Smith WL & Wheeler WC. 2006. Venom evolution widespread in fishes: a phylogenetic road map for the bioprospecting of piscine venoms. J Hered 97(3):206-217.

Sparks JS & Smith WL. 2006. Sicyopterus lagocephalus: Widespread species, species complex, or neither? A critique on the use of molecular data for species identification. Mol Phylogenet Evol 40(3):900-902.

Steel M & Pickett KM. 2006. On the impossibility of uniform priors on clades. Mol Phylogenet Evol 39(2):585-586.

Last updated: 23 May 2008