Bioinformatics Vol. 19 no. 18 2003
pages 2496-2497
© 2003 Oxford University Press
Applications Note |
DnaSP, DNA polymorphism analyses by the coalescent and other methods
1 Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Diagonal 645, 08071 Barcelona, Spain and 2 Departament de Llenguatges i Sistemes Informàtics, Universitat Politècnica de Catalunya, Barcelona, Spain
Received on February 28, 2003
; revised on June 6, 2003
; accepted on July 8, 2003
Summary: DnaSP is a software package for the analysis of DNA polymorphism data. Present version introduces several new modules and features which, among other options allow: (1) handling big data sets (
5 Mb per sequence); (2) conducting a large number of coalescent-based tests by Monte Carlo computer simulations; (3) extensive analyses of the genetic differentiation and gene flow among populations; (4) analysing the evolutionary pattern of preferred and unpreferred codons; (5) generating graphical outputs for an easy visualization of results.
Availability: The software package, including complete documentation and examples, is freely available to academic users from: http://www.ub.es/dnasp
Contact: jrozas{at}ub.edu
* To whom correspondence should be addressed.
Present address: Departament de Tecnología, Universitat Pompeu Fabra, Barcelona, Spain.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  L. M. Mullen, S. N. Vignieri, J. A. Gore, and H. E. Hoekstra Adaptive basis of geographic variation: genetic, phenotypic and environmental differences among beach mouse populations Proc R Soc B, November 7, 2009; 276(1674): 3809 - 3818. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P.-C. Liao, T.-P. Lin, W.-C. Lan, J.-D. Chung, and S.-Y. Hwang Duplication of the class I cytosolic small heat shock protein gene and potential functional divergence revealed by sequence variations flanking the {alpha}-crystallin domain in the genus Rhododendron (Ericaceae) Ann. Bot., November 3, 2009; (2009) mcp272v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. J. Waine, D. Honeybourne, E. G. Smith, J. L. Whitehouse, and C. G. Dowson Cross-Sectional and Longitudinal Multilocus Sequence Typing of Pseudomonas aeruginosa in Cystic Fibrosis Sputum Samples J. Clin. Microbiol., November 1, 2009; 47(11): 3444 - 3448. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Nakamura, S. Kawai, F. Yukuhiro, S. Ito, T. Gotoh, R. Kisimoto, T. Yanase, Y. Matsumoto, D. Kageyama, and H. Noda Prevalence of Cardinium Bacteria in Planthoppers and Spider Mites and Taxonomic Revision of "Candidatus Cardinium hertigii" Based on Detection of a New Cardinium Group from Biting Midges Appl. Envir. Microbiol., November 1, 2009; 75(21): 6757 - 6763. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Hellborg and J. Piskur Complex Nature of the Genome in a Wine Spoilage Yeast, Dekkera bruxellensis Eukaryot. Cell, November 1, 2009; 8(11): 1739 - 1749. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Freire, A. Arias, J. Mendez, and A. Insua SEQUENCE VARIATION OF THE INTERNAL TRANSCRIBED SPACER (ITS) REGION OF RIBOSOMAL DNA IN CERASTODERMA SPECIES (BIVALVIA: CARDIIDAE) J. Mollus. Stud., October 30, 2009; (2009) eyp047v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. P. Foxe and S. I. Wright Signature of Diversifying Selection on Members of the Pentatricopeptide Repeat Protein Family in Arabidopsis lyrata Genetics, October 1, 2009; 183(2): 663 - 672. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Chattopadhyay, R. N. Paranjpye, D. E. Dykhuizen, E. V. Sokurenko, and M. S. Strom Comparative Evolutionary Analysis of the Major Structural Subunit of Vibrio vulnificus Type IV Pili Mol. Biol. Evol., October 1, 2009; 26(10): 2185 - 2196. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Ikeda, N. Fujii, and H. Setoguchi Application of the Isolation with Migration Model Demonstrates the Pleistocene Origin of Geographic Differentiation in Cardamine nipponica (Brassicaceae), an Endemic Japanese Alpine Plant Mol. Biol. Evol., October 1, 2009; 26(10): 2207 - 2216. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Jovelin Rapid Sequence Evolution of Transcription Factors Controlling Neuron Differentiation in Caenorhabditis Mol. Biol. Evol., October 1, 2009; 26(10): 2373 - 2386. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. J. Oswald, J. M. Grady, and J. M. Quattro Cytonuclear Patterns of Genetic Diversity and the Intricate Evolutionary History of the Inland Silverside (Menidia beryllina) J. Hered., September 1, 2009; 100(5): 526 - 532. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. G. Hoen, G. Margos, S. J. Bent, M. A. Diuk-Wasser, A. Barbour, K. Kurtenbach, and D. Fish Phylogeography of Borrelia burgdorferi in the eastern United States reflects multiple independent Lyme disease emergence events PNAS, September 1, 2009; 106(35): 15013 - 15018. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Slotte, H.-R. Huang, K. Holm, A. Ceplitis, K. St. Onge, J. Chen, U. Lagercrantz, and M. Lascoux Splicing Variation at a FLOWERING LOCUS C Homeolog Is Associated With Flowering Time Variation in the Tetraploid Capsella bursa-pastoris Genetics, September 1, 2009; 183(1): 337 - 345. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. J. White, C. Cheng, D. Sangare, N. F. Lobo, F. H. Collins, and N. J. Besansky The Population Genomics of Trans-Specific Inversion Polymorphisms in Anopheles gambiae Genetics, September 1, 2009; 183(1): 275 - 288. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. J. Eckert, J. L. Wegrzyn, B. Pande, K. D. Jermstad, J. M. Lee, J. D. Liechty, B. R. Tearse, K. V. Krutovsky, and D. B. Neale Multilocus Patterns of Nucleotide Diversity and Divergence Reveal Positive Selection at Candidate Genes Related to Cold Hardiness in Coastal Douglas Fir (Pseudotsuga menziesii var. menziesii) Genetics, September 1, 2009; 183(1): 289 - 298. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Gonzalez, J. M. Macpherson, and D. A. Petrov A Recent Adaptive Transposable Element Insertion Near Highly Conserved Developmental Loci in Drosophila melanogaster Mol. Biol. Evol., September 1, 2009; 26(9): 1949 - 1961. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Ferrer-Admetlla, M. Sikora, H. Laayouni, A. Esteve, F. Roubinet, A. Blancher, F. Calafell, J. Bertranpetit, and F. Casals A Natural History of FUT2 Polymorphism in Humans Mol. Biol. Evol., September 1, 2009; 26(9): 1993 - 2003. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Ramirez, A. Ojeda, A. Tomas, D. Gallardo, L.S. Huang, J.M. Folch, A. Clop, A. Sanchez, B. Badaoui, O. Hanotte, et al. Integrating Y-Chromosome, Mitochondrial, and Autosomal Data to Analyze the Origin of Pig Breeds Mol. Biol. Evol., September 1, 2009; 26(9): 2061 - 2072. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Giokas, D. Thomaz, V. Douris, R. lecanidou, and G. C. Rodakis 5000 YEARS OF MOLECULAR EVOLUTION IN A POPULATION OF THE LAND SNAIL ALBINARIA CAERULEA TRANSPORTED BY HUMANS J. Mollus. Stud., August 18, 2009; (2009) eyp041v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. I. Hersch-Green and R. Cronn Tangled trios?: Characterizing a hybrid zone in Castilleja (Orobanchaceae) Am. J. Botany, August 1, 2009; 96(8): 1519 - 1531. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Legrand, M. I. Tenaillon, P. Matyot, J. Gerlach, D. Lachaise, and M.-L. Cariou Species-Wide Genetic Variation and Demographic History of Drosophila sechellia, a Species Lacking Population Structure Genetics, August 1, 2009; 182(4): 1197 - 1206. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Takano-Kai, H. Jiang, T. Kubo, M. Sweeney, T. Matsumoto, H. Kanamori, B. Padhukasahasram, C. Bustamante, A. Yoshimura, K. Doi, et al. Evolutionary History of GS3, a Gene Conferring Grain Length in Rice Genetics, August 1, 2009; 182(4): 1323 - 1334. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Guirao-Rico and M. Aguade Positive Selection Has Driven the Evolution of the Drosophila Insulin-Like Receptor (InR) at Different Timescales Mol. Biol. Evol., August 1, 2009; 26(8): 1723 - 1732. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. D. Leache, M. S. Koo, C. L. Spencer, T. J. Papenfuss, R. N. Fisher, and J. A. McGuire From the Cover: Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex (Phrynosoma) PNAS, July 28, 2009; 106(30): 12418 - 12423. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Loaiza, M. Scott, E. Bermingham, J. Rovira, O. Sanjur, and J. E. Conn Anopheles darlingi (Diptera: Culicidae) in Panama Am J Trop Med Hyg, July 1, 2009; 81(1): 23 - 26. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. T. Monaghan, R. Wild, M. Elliot, T. Fujisawa, M. Balke, D. J.G. Inward, D. C. Lees, R. Ranaivosolo, P. Eggleton, T. G. Barraclough, et al. Accelerated Species Inventory on Madagascar Using Coalescent-Based Models of Species Delineation Syst Biol, July 1, 2009; (2009) syp027v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A.-A. Saidou, C. Mariac, V. Luong, J.-L. Pham, G. Bezancon, and Y. Vigouroux Association Studies Identify Natural Variation at PHYC Linked to Flowering Time and Morphological Variation in Pearl Millet Genetics, July 1, 2009; 182(3): 899 - 910. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Svetec, P. Pavlidis, and W. Stephan Recent Strong Positive Selection on Drosophila melanogaster HDAC6, a Gene Encoding a Stress Surveillance Factor, as Revealed by Population Genomic Analysis Mol. Biol. Evol., July 1, 2009; 26(7): 1549 - 1556. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Burzynski and B. Smietanka Is Interlineage Recombination Responsible for Low Divergence of Mitochondrial nad3 Genes in Mytilus galloprovincialis? Mol. Biol. Evol., July 1, 2009; 26(7): 1441 - 1445. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Bataille, A. A. Cunningham, V. Cedeno, L. Patino, A. Constantinou, L. D. Kramer, and S. J. Goodman Natural colonization and adaptation of a mosquito species in Galapagos and its implications for disease threats to endemic wildlife PNAS, June 23, 2009; 106(25): 10230 - 10235. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. D. Quang, S. Ikeda, and K. Harada Patterns of Nucleotide Diversity at the Methionine Synthase Locus in Fragmented and Continuous Populations of a Wind-Pollinated Tree, Quercus mongolica var. crispula J. Hered., June 16, 2009; (2009) esp036v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Tian, N. M. Stevens, and E. S. Buckler IV Colloquium Papers: Tracking footprints of maize domestication and evidence for a massive selective sweep on chromosome 10 PNAS, June 16, 2009; 106(Supplement_1): 9979 - 9986. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Livingstone and S. Anderson Patterns of Variation in the Evolution of Carotenoid Biosynthetic Pathway Enzymes of Higher Plants J. Hered., June 11, 2009; (2009) esp026v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Librado and J. Rozas DnaSP v5: a software for comprehensive analysis of DNA polymorphism data Bioinformatics, June 1, 2009; 25(11): 1451 - 1452. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Ikeda, N. Fujii, and H. Setoguchi Molecular Evolution of Phytochromes in Cardamine nipponica (Brassicaceae) Suggests the Involvement of PHYE in Local Adaptation Genetics, June 1, 2009; 182(2): 603 - 614. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. L. Strasburg, C. Scotti-Saintagne, I. Scotti, Z. Lai, and L. H. Rieseberg Genomic Patterns of Adaptive Divergence between Chromosomally Differentiated Sunflower Species Mol. Biol. Evol., June 1, 2009; 26(6): 1341 - 1355. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. J. Stewart, C. R. Young, and C. M. Cavanaugh Evidence for Homologous Recombination in Intracellular Chemosynthetic Clam Symbionts Mol. Biol. Evol., June 1, 2009; 26(6): 1391 - 1404. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. D. Findlay, M. J. MacCoss, and W. J. Swanson Proteomic discovery of previously unannotated, rapidly evolving seminal fluid genes in Drosophila Genome Res., May 1, 2009; 19(5): 886 - 896. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. E. Smith and H. S. Malik The apolipoprotein L family of programmed cell death and immunity genes rapidly evolved in primates at discrete sites of host-pathogen interactions Genome Res., May 1, 2009; 19(5): 850 - 858. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Yasukochi, S. Nishida, S.-H. Han, T. Kurosaki, M. Yoneda, and H. Koike Genetic Structure of the Asiatic Black Bear in Japan Using Mitochondrial DNA Analysis J. Hered., May 1, 2009; 100(3): 297 - 308. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. R. Haag, S. J. McTaggart, A. Didier, T. J. Little, and D. Charlesworth Nucleotide Polymorphism and Within-Gene Recombination in Daphnia magna and D. pulex, Two Cyclical Parthenogens Genetics, May 1, 2009; 182(1): 313 - 323. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. R. Omilian and M. Lynch Patterns of Intraspecific DNA Variation in the Daphnia Nuclear Genome Genetics, May 1, 2009; 182(1): 325 - 336. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. C. Li, J. C. Davis, K. Lenkov, B. Bolival, M. T. Fuller, and D. A. Petrov Molecular Evolution of the Testis TAFs of Drosophila Mol. Biol. Evol., May 1, 2009; 26(5): 1103 - 1116. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Mukherjee, N. Sarkar-Roy, D. K. Wagener, and P. P. Majumder Signatures of natural selection are not uniform across genes of innate immune system, but purifying selection is the dominant signature PNAS, April 28, 2009; 106(17): 7073 - 7078. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Ishida, M. Welker, G. Christiansen, S. Cadel-Six, C. Bouchier, E. Dittmann, C. Hertweck, and N. Tandeau de Marsac Plasticity and Evolution of Aeruginosin Biosynthesis in Cyanobacteria Appl. Envir. Microbiol., April 1, 2009; 75(7): 2017 - 2026. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T.-Y. Wei, J.-G. Yang, F.-L. Liao, F.-L. Gao, L.-M. Lu, X.-T. Zhang, F. Li, Z.-J. Wu, Q.-Y. Lin, L.-H. Xie, et al. Genetic diversity and population structure of rice stripe virus in China J. Gen. Virol., April 1, 2009; 90(4): 1025 - 1034. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Jovelin, J. P. Dunham, F. S. Sung, and P. C. Phillips High Nucleotide Divergence in Developmental Regulatory Genes Contrasts With the Structural Elements of Olfactory Pathways in Caenorhabditis Genetics, April 1, 2009; 181(4): 1387 - 1397. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Nadachowska and W. Babik Divergence in the Face of Gene Flow: The Case of Two Newts (Amphibia: Salamandridae) Mol. Biol. Evol., April 1, 2009; 26(4): 829 - 841. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. G. McCracken, M. Bulgarella, K. P. Johnson, M. K. Kuhner, J. Trucco, T. H. Valqui, R. E. Wilson, and J. L. Peters Gene Flow in the Face of Countervailing Selection: Adaptation to High-Altitude Hypoxia in the {beta}A Hemoglobin Subunit of Yellow-Billed Pintails in the Andes Mol. Biol. Evol., April 1, 2009; 26(4): 815 - 827. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Wlasiuk, S. Khan, W. M. Switzer, and M. W. Nachman A History of Recurrent Positive Selection at the Toll-Like Receptor 5 in Primates Mol. Biol. Evol., April 1, 2009; 26(4): 937 - 949. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. P. Foxe, T. Slotte, E. A. Stahl, B. Neuffer, H. Hurka, and S. I. Wright Recent speciation associated with the evolution of selfing in Capsella PNAS, March 31, 2009; 106(13): 5241 - 5245. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y.-L. Guo, J. S. Bechsgaard, T. Slotte, B. Neuffer, M. Lascoux, D. Weigel, and M. H. Schierup Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck PNAS, March 31, 2009; 106(13): 5246 - 5251. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. A. Medina, F. Torres-Perez, H. Galeno, M. Navarrete, P. A. Vial, R. E. Palma, M. Ferres, J. A. Cook, and B. Hjelle Ecology, Genetic Diversity, and Phylogeographic Structure of Andes Virus in Humans and Rodents in Chile J. Virol., March 15, 2009; 83(6): 2446 - 2459. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Boessenkool, J. J Austin, T. H Worthy, P. Scofield, A. Cooper, P. J Seddon, and J. M Waters Relict or colonizer? Extinction and range expansion of penguins in southern New Zealand Proc R Soc B, March 7, 2009; 276(1658): 815 - 821. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. F. Demarest, H. Amrine-Madsen, D. M. Irlbeck, K. M. Kitrinos, and on behalf of the CCR102881 Clinical Study Team Virologic Failure in First-Line Human Immunodeficiency Virus Therapy with a CCR5 Entry Inhibitor, Aplaviroc, plus a Fixed-Dose Combination of Lamivudine-Zidovudine: Nucleoside Reverse Transcriptase Inhibitor Resistance Regardless of Envelope Tropism Antimicrob. Agents Chemother., March 1, 2009; 53(3): 1116 - 1123. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. M. Kitrinos, H. Amrine-Madsen, D. M. Irlbeck, J. M. Word, J. F. Demarest, and on behalf of the CCR100136 Study Team Virologic Failure in Therapy-Naive Subjects on Aplaviroc plus Lopinavir-Ritonavir: Detection of Aplaviroc Resistance Requires Clonal Analysis of Envelope Antimicrob. Agents Chemother., March 1, 2009; 53(3): 1124 - 1131. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. van der Loo, J. Abrantes, and P. J. Esteves Sharing of Endogenous Lentiviral Gene Fragments among Leporid Lineages Separated for More than 12 Million Years J. Virol., March 1, 2009; 83(5): 2386 - 2388. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Bilhere, P. M. Lucas, O. Claisse, and A. Lonvaud-Funel Multilocus Sequence Typing of Oenococcus oeni: Detection of Two Subpopulations Shaped by Intergenic Recombination Appl. Envir. Microbiol., March 1, 2009; 75(5): 1291 - 1300. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. S. Wondji, H. Irving, J. Morgan, N. F. Lobo, F. H. Collins, R. H. Hunt, M. Coetzee, J. Hemingway, and H. Ranson Two duplicated P450 genes are associated with pyrethroid resistance in Anopheles funestus, a major malaria vector Genome Res., March 1, 2009; 19(3): 452 - 459. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. E. Janes, T. Ezaz, J. A. Marshall Graves, and S. V. Edwards Recombination and Nucleotide Diversity in the Sex Chromosomal Pseudoautosomal Region of the Emu, Dromaius novaehollandiae J. Hered., March 1, 2009; 100(2): 125 - 136. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. C. S. Ramos, J. P. De Lemos-Filho, and M. B. Lovato Phylogeographical Structure of the Neotropical Forest Tree Hymenaea courbaril (Leguminosae: Caesalpinioideae) and Its Relationship with the Vicariant Hymenaea stigonocarpa from Cerrado J. Hered., March 1, 2009; 100(2): 206 - 216. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Edh, B. Widen, and A. Ceplitis Molecular Population Genetics of the SRK and SCR Self-Incompatibility Genes in the Wild Plant Species Brassica cretica (Brassicaceae) Genetics, March 1, 2009; 181(3): 985 - 995. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B.-H. Song, A. J. Windsor, K. J. Schmid, S. Ramos-Onsins, M. E. Schranz, A. J. Heidel, and T. Mitchell-Olds Multilocus Patterns of Nucleotide Diversity, Population Structure and Linkage Disequilibrium in Boechera stricta, a Wild Relative of Arabidopsis Genetics, March 1, 2009; 181(3): 1021 - 1033. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. D. Marshall, M. W. Coulson, and S. M. Carr Near Neutrality, Rate Heterogeneity, and Linkage Govern Mitochondrial Genome Evolution in Atlantic Cod (Gadus morhua) and Other Gadine Fish Mol. Biol. Evol., March 1, 2009; 26(3): 579 - 589. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Johnsen, M. Teschke, P. Pavlidis, B. M. McGee, D. Tautz, D. Ginsburg, and J. F. Baines Selection on cis-Regulatory Variation at B4galnt2 and Its Influence on von Willebrand Factor in House Mice Mol. Biol. Evol., March 1, 2009; 26(3): 567 - 578. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Parsch, Z. Zhang, and J. F. Baines The Influence of Demography and Weak Selection on the McDonald-Kreitman Test: An Empirical Study in Drosophila Mol. Biol. Evol., March 1, 2009; 26(3): 691 - 698. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. L. Kelley, K. Turkheimer, M. Haney, and W. J. Swanson Targeted resequencing of two genes, RAGE and POLL, confirms findings from a genome-wide scan for adaptive evolution and provides evidence for positive selection in additional populations Hum. Mol. Genet., February 15, 2009; 18(4): 779 - 784. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Ah-You, L. Gagnevin, P. A. D. Grimont, S. Brisse, X. Nesme, F. Chiroleu, L. Bui Thi Ngoc, E. Jouen, P. Lefeuvre, C. Verniere, et al. Polyphasic characterization of xanthomonads pathogenic to members of the Anacardiaceae and their relatedness to species of Xanthomonas Int J Syst Evol Microbiol, February 1, 2009; 59(2): 306 - 318. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Deletoile, D. Decre, S. Courant, V. Passet, J. Audo, P. Grimont, G. Arlet, and S. Brisse Phylogeny and Identification of Pantoea Species and Typing of Pantoea agglomerans Strains by Multilocus Gene Sequencing J. Clin. Microbiol., February 1, 2009; 47(2): 300 - 310. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. S. Baucom, J. C. Estill, J. Leebens-Mack, and J. L. Bennetzen Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome Genome Res., February 1, 2009; 19(2): 243 - 254. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Alvarez-Ponce, M. Aguade, and J. Rozas Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12 Drosophila genomes Genome Res., February 1, 2009; 19(2): 234 - 242. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Carneiro, N. Ferrand, and M. W. Nachman Recombination and Speciation: Loci Near Centromeres Are More Differentiated Than Loci Near Telomeres Between Subspecies of the European Rabbit (Oryctolagus cuniculus) Genetics, February 1, 2009; 181(2): 593 - 606. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Touzet and L. F. Delph The Effect of Breeding System on Polymorphism in Mitochondrial Genes of Silene Genetics, February 1, 2009; 181(2): 631 - 644. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. N. Balakrishnan and S. V. Edwards Nucleotide Variation, Linkage Disequilibrium and Founder-Facilitated Speciation in Wild Populations of the Zebra Finch (Taeniopygia guttata) Genetics, February 1, 2009; 181(2): 645 - 660. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. S. Caldwell and R. W. Michelmore Arabidopsis thaliana Genes Encoding Defense Signaling and Recognition Proteins Exhibit Contrasting Evolutionary Dynamics Genetics, February 1, 2009; 181(2): 671 - 684. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. J. Balbi, E. P.C. Rocha, and E. J. Feil The Temporal Dynamics of Slightly Deleterious Mutations in Escherichia coli and Shigella spp. Mol. Biol. Evol., February 1, 2009; 26(2): 345 - 355. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. H. Hur, K. Van Doninck, M. L. Mandigo, and M. Meselson Degenerate Tetraploidy Was Established Before Bdelloid Rotifer Families Diverged Mol. Biol. Evol., February 1, 2009; 26(2): 375 - 383. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Wu, J. M. Comeron, H. S. Yoon, and D. Bhattacharya Unexpected Dynamic Gene Family Evolution in Algal Actins Mol. Biol. Evol., February 1, 2009; 26(2): 249 - 253. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Reina, E. Grego, L. Bertolotti, D. De Meneghi, and S. Rosati Genome Analysis of Small-Ruminant Lentivirus Genotype E: a Caprine Lentivirus with Natural Deletions of the dUTPase Subunit, vpr-Like Accessory Gene, and 70-Base-Pair Repeat of the U3 Region J. Virol., January 15, 2009; 83(2): 1152 - 1155. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Vanlaere, A. Baldwin, D. Gevers, D. Henry, E. De Brandt, J. J. LiPuma, E. Mahenthiralingam, D. P. Speert, C. Dowson, and P. Vandamme Taxon K, a complex within the Burkholderia cepacia complex, comprises at least two novel species, Burkholderia contaminans sp. nov. and Burkholderia lata sp. nov. Int J Syst Evol Microbiol, January 1, 2009; 59(1): 102 - 111. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Andrew, T.L. Peever, and B.M. Pryor An expanded multilocus phylogeny does not resolve morphological species within the small-spored Altemrnaria species complex. Mycologia, January 1, 2009; 101(1): 95 - 109. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Chen, P. L. Morrell, V. E. T. M. Ashworth, M. de la Cruz, and M. T. Clegg Tracing the Geographic Origins of Major Avocado Cultivars J. Hered., January 1, 2009; 100(1): 56 - 65. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Rodriguez, S. Hammer, T. Perez, F. Suchentrunk, R. Lorenzini, J. Michallet, N. Martinkova, J. Albornoz, and A. Dominguez Cytochrome b Phylogeography of Chamois (Rupicapra spp.). Population Contractions, Expansions and Hybridizations Governed the Diversification of the Genus J. Hered., January 1, 2009; 100(1): 47 - 55. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. E. Alter, S. F. Ramirez, S. Nigenda, J. U. Ramirez, L. R. Bracho, and S. R. Palumbi Mitochondrial and Nuclear Genetic Variation across Calving Lagoons in Eastern North Pacific Gray Whales (Eschrichtius robustus) J. Hered., January 1, 2009; 100(1): 34 - 46. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. A. Anderson, W. D. Gilliland, and C. H. Langley Molecular Population Genetics and Evolution of Drosophila Meiosis Genes Genetics, January 1, 2009; 181(1): 177 - 185. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Aguade Nucleotide and Copy-Number Polymorphism at the Odorant Receptor Genes Or22a and Or22b in Drosophila melanogaster Mol. Biol. Evol., January 1, 2009; 26(1): 61 - 70. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. N. Lau, L. Peng, H. Goto, L. Chemnick, O. A. Ryder, and K. D. Makova Horse Domestication and Conservation Genetics of Przewalski's Horse Inferred from Sex Chromosomal and Autosomal Sequences Mol. Biol. Evol., January 1, 2009; 26(1): 199 - 208. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. B. Wells, G. Zhang, Z. Harley, and H. Vaziri Genetic Hypervariability in Two Distinct Deuterostome Telomerase Reverse Transcriptase Genes and their Early Embryonic Functions Mol. Biol. Cell, January 1, 2009; 20(1): 464 - 480. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Kurata, T. Jaffre, and H. Setoguchi Genetic diversity and geographical structure of the pitcher plant Nepenthes vieillardii in New Caledonia: A chloroplast DNA haplotype analysis Am. J. Botany, December 1, 2008; 95(12): 1632 - 1644. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. R. Linnen and B. D. Farrell Comparison of Methods for Species-Tree Inference in the Sawfly Genus Neodiprion (Hymenoptera: Diprionidae) Syst Biol, December 1, 2008; 57(6): 876 - 890. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. E. Palme, M. Wright, and O. Savolainen Patterns of Divergence among Conifer ESTs and Polymorphism in Pinus sylvestris Identify Putative Selective Sweeps Mol. Biol. Evol., December 1, 2008; 25(12): 2567 - 2577. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. A. Tennessen and M. S. Blouin Balancing Selection at a Frog Antimicrobial Peptide Locus: Fluctuating Immune Effector Alleles? Mol. Biol. Evol., December 1, 2008; 25(12): 2669 - 2680. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. C. Verrelli, C. M. Lewis Jr, A. C. Stone, and G. H. Perry Different Selective Pressures Shape the Molecular Evolution of Color Vision in Chimpanzee and Human Populations Mol. Biol. Evol., December 1, 2008; 25(12): 2735 - 2743. [Abstract] [Full Text] [PDF]
|
|