TY - JOUR AU - Zink, R. M. AU - Barrowclough, G. F. PY - 2008 DA - 2008// TI - Mitochondrial DNA under siege in avian phylogeography JO - Mol Ecol VL - 17 UR - https://doi.org/10.1111/j.1365-294X.2008.03737.x DO - 10.1111/j.1365-294X.2008.03737.x ID - Zink2008 ER - TY - JOUR AU - Edwards, S. AU - Bensch, S. PY - 2009 DA - 2009// TI - Looking forwards or looking backwards in avian phylogeography? A comment on Zink and Barrowclough 2008 JO - Mol Ecol VL - 18 UR - https://doi.org/10.1111/j.1365-294X.2009.04270.x DO - 10.1111/j.1365-294X.2009.04270.x ID - Edwards2009 ER - TY - JOUR AU - Lee, J. Y. AU - Edwards, S. V. PY - 2008 DA - 2008// TI - Divergence across Australia's Carpentarian barrier: statistical phylogeography of the red-backed fairy wren (Malurus melanocephalus) JO - Evolution VL - 62 UR - https://doi.org/10.1111/j.1558-5646.2008.00543.x DO - 10.1111/j.1558-5646.2008.00543.x ID - Lee2008 ER - TY - JOUR AU - Kuhner, M. K. PY - 2006 DA - 2006// TI - LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btk051 DO - 10.1093/bioinformatics/btk051 ID - Kuhner2006 ER - TY - JOUR AU - Hey, J. AU - Nielsen, R. PY - 2007 DA - 2007// TI - Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics JO - Proc Natl Acad Sci USA VL - 104 UR - https://doi.org/10.1073/pnas.0611164104 DO - 10.1073/pnas.0611164104 ID - Hey2007 ER - TY - JOUR AU - Corander, J. AU - Marttinen, P. PY - 2006 DA - 2006// TI - Bayesian identification of admixture events using multilocus molecular markers JO - Mol Ecol VL - 15 UR - https://doi.org/10.1111/j.1365-294X.2006.02994.x DO - 10.1111/j.1365-294X.2006.02994.x ID - Corander2006 ER - TY - JOUR AU - Pritchard, J. K. AU - Stephens, M. AU - Donnelly, P. PY - 2000 DA - 2000// TI - Inference of population structure using multilocus genotype data JO - Genetics VL - 155 ID - Pritchard2000 ER - TY - JOUR AU - Rosenblum, E. B. AU - Belfiore, N. M. AU - Moritz, C. PY - 2006 DA - 2006// TI - Anonymous nuclear markers for the eastern fence lizard, Sceloporus undulatus JO - Mol Ecol Notes VL - 7 UR - https://doi.org/10.1111/j.1471-8286.2006.01547.x DO - 10.1111/j.1471-8286.2006.01547.x ID - Rosenblum2006 ER - TY - JOUR AU - Fujita, M. K. AU - Engstrom, T. N. AU - Starkey, D. E. AU - Shaffer, H. B. PY - 2004 DA - 2004// TI - Turtle phylogeny: insights from a novel nuclear intron JO - Mol Phylogenet Evol VL - 31 UR - https://doi.org/10.1016/j.ympev.2003.09.016 DO - 10.1016/j.ympev.2003.09.016 ID - Fujita2004 ER - TY - JOUR AU - Willows-Munro, S. AU - Robinson, T. J. AU - Matthee, C. A. PY - 2005 DA - 2005// TI - Utility of nuclear DNA intron markers at lower taxonomic levels: phylogenetic resolution among nine Tragelaphus spp JO - Mol Phylogenet Evol VL - 35 UR - https://doi.org/10.1016/j.ympev.2005.01.018 DO - 10.1016/j.ympev.2005.01.018 ID - Willows-Munro2005 ER - TY - JOUR AU - Berrebi, P. AU - Boissin, E. AU - Fang, F. AU - Cattaneo-Berrebi, G. PY - 2005 DA - 2005// TI - Intron polymorphism (EPIC-PCR) reveals phylogeographic structure of Zacco platypus in China: a possible target for aquaculture development JO - Heredity VL - 94 UR - https://doi.org/10.1038/sj.hdy.6800660 DO - 10.1038/sj.hdy.6800660 ID - Berrebi2005 ER - TY - JOUR AU - Chow, S. AU - Nakadate, M. PY - 2004 DA - 2004// TI - PCR primers for fish G6PD gene intron and characterization of intron length variation in the albacore Thunnus alalunga JO - Mol Ecol Notes VL - 4 UR - https://doi.org/10.1111/j.1471-8286.2004.00662.x DO - 10.1111/j.1471-8286.2004.00662.x ID - Chow2004 ER - TY - JOUR AU - Palumbi, S. R. AU - Baker, C. S. PY - 1994 DA - 1994// TI - Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales JO - Mol Biol Evol VL - 11 ID - Palumbi1994 ER - TY - JOUR AU - Lessa, E. P. PY - 1992 DA - 1992// TI - Rapid surveying of DNA sequence variation in natural populations JO - Mol Biol Evol VL - 9 ID - Lessa1992 ER - TY - JOUR AU - Slade, R. W. AU - Moritz, C. AU - Heideman, A. AU - Hale, P. T. PY - 1993 DA - 1993// TI - Rapid assessment of single-copy nuclear DNA variation in diverse species JO - Mol Ecol VL - 2 UR - https://doi.org/10.1111/j.1365-294X.1993.tb00029.x DO - 10.1111/j.1365-294X.1993.tb00029.x ID - Slade1993 ER - TY - JOUR AU - Ishikawa, G. AU - Yonemaru, J. AU - Saito, M. AU - Nakamura, T. PY - 2007 DA - 2007// TI - PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and D genomes JO - BMC Genomics VL - 8 UR - https://doi.org/10.1186/1471-2164-8-135 DO - 10.1186/1471-2164-8-135 ID - Ishikawa2007 ER - TY - STD TI - Fredslund J, Madsen LH, Hougaard BK, Sandal N, Stougaard J, Bertioli D, Schauser L: GeMprospector--online design of cross-species genetic marker candidates in legumes and grasses. Nucleic Acids Res. 2006, W670-675. 10.1093/nar/gkl201. 34 Web Server ID - ref17 ER - TY - JOUR AU - Yang, L. AU - Jin, G. AU - Zhao, X. AU - Zheng, Y. AU - Xu, Z. AU - Wu, W. PY - 2007 DA - 2007// TI - PIP: a database of potential intron polymorphism markers JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm296 DO - 10.1093/bioinformatics/btm296 ID - Yang2007 ER - TY - JOUR AU - Backström, N. AU - Fagerberg, S. AU - Ellegren, H. PY - 2008 DA - 2008// TI - Genomics of natural bird populations: a gene-based set of reference markers evenly spread across the avian genome JO - Mol Ecol VL - 17 UR - https://doi.org/10.1111/j.1365-294X.2007.03551.x DO - 10.1111/j.1365-294X.2007.03551.x ID - Backström2008 ER - TY - JOUR AU - Edwards, S. V. PY - 2008 DA - 2008// TI - A smorgasbord of markers for avian ecology and evolution JO - Mol Ecol VL - 17 UR - https://doi.org/10.1111/j.1365-294X.2007.03644.x DO - 10.1111/j.1365-294X.2007.03644.x ID - Edwards2008 ER - TY - JOUR AU - Quattro, J. M. AU - Jones, W. J. AU - Oswald, K. J. PY - 2001 DA - 2001// TI - PCR primers for an aldolase-B intron in acanthopterygian fishes JO - BMC Evol Biol VL - 1 UR - https://doi.org/10.1186/1471-2148-1-9 DO - 10.1186/1471-2148-1-9 ID - Quattro2001 ER - TY - JOUR AU - Hassan, M. AU - Lemaire, C. AU - Fauvelot, C. AU - Bonhomme, F. PY - 2002 DA - 2002// TI - Seventeen new exon-primed intron-crossing polymerase chain reaction amplifiable introns in fish JO - Mol Eco Notes VL - 2 UR - https://doi.org/10.1046/j.1471-8286.2002.00236.x DO - 10.1046/j.1471-8286.2002.00236.x ID - Hassan2002 ER - TY - JOUR AU - Li, C. AU - Orti, G. AU - Zhang, G. AU - Lu, G. PY - 2007 DA - 2007// TI - A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study JO - BMC Evol Biol VL - 7 UR - https://doi.org/10.1186/1471-2148-7-44 DO - 10.1186/1471-2148-7-44 ID - Li2007 ER - TY - JOUR AU - Venkatesh, B. AU - Kirkness, E. F. AU - Loh, Y. H. AU - Halpern, A. L. AU - Lee, A. P. AU - Johnson, J. AU - Dandona, N. AU - Viswanathan, L. D. AU - Tay, A. AU - Venter, J. C. PY - 2007 DA - 2007// TI - Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome JO - PLoS Biol VL - 5 UR - https://doi.org/10.1371/journal.pbio.0050101 DO - 10.1371/journal.pbio.0050101 ID - Venkatesh2007 ER - TY - JOUR AU - Wiens, J. J. PY - 2007 DA - 2007// TI - Species delimitation: new approaches for discovering diversity JO - Syst Biol VL - 56 UR - https://doi.org/10.1080/10635150701748506 DO - 10.1080/10635150701748506 ID - Wiens2007 ER - TY - JOUR AU - Zhang, D. X. AU - Hewitt, G. M. PY - 2003 DA - 2003// TI - Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects JO - Mol Ecol VL - 12 UR - https://doi.org/10.1046/j.1365-294X.2003.01773.x DO - 10.1046/j.1365-294X.2003.01773.x ID - Zhang2003 ER - TY - JOUR AU - Moriyama, E. N. AU - Powell, J. R. PY - 1996 DA - 1996// TI - Intraspecific nuclear DNA variation in Drosophila JO - Mol Biol Evol VL - 13 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025563 DO - 10.1093/oxfordjournals.molbev.a025563 ID - Moriyama1996 ER - TY - JOUR AU - Jayashree, B. AU - Jagadeesh, V. T. AU - Hoisington, D. PY - 2007 DA - 2007// TI - CISprimerTOOL: software to implement a comparative genomics strategy for the development of conserved intron scanning (CIS) markers JO - Mol Ecol Notes VL - 8 UR - https://doi.org/10.1111/j.1471-8286.2007.02035.x DO - 10.1111/j.1471-8286.2007.02035.x ID - Jayashree2007 ER - TY - JOUR AU - Choi, H. -. K. AU - Luckow, M. A. AU - Doyle, J. AU - Cook, D. R. PY - 2006 DA - 2006// TI - Development of nuclear gene-derived molecular markers linked to legume genetic maps JO - Mol Gen Genomics VL - 276 UR - https://doi.org/10.1007/s00438-006-0118-8 DO - 10.1007/s00438-006-0118-8 ID - Choi2006 ER - TY - JOUR AU - Shaffer, H. B. AU - Thomson, R. C. PY - 2007 DA - 2007// TI - Delimiting species in recent radiations JO - Syst Biol VL - 56 UR - https://doi.org/10.1080/10635150701772563 DO - 10.1080/10635150701772563 ID - Shaffer2007 ER - TY - JOUR AU - Stephens, M. AU - Donnelly, P. PY - 2003 DA - 2003// TI - A comparison of bayesian methods for haplotype reconstruction from population genotype data JO - Am J Hum Genet VL - 73 UR - https://doi.org/10.1086/379378 DO - 10.1086/379378 ID - Stephens2003 ER - TY - JOUR AU - Creer, S. PY - 2007 DA - 2007// TI - Choosing and Using Introns in Molecular Phylogenetics JO - Evol Bioinform VL - 3 ID - Creer2007 ER - TY - JOUR AU - Margulies, M. AU - Egholm, M. AU - Altman, W. E. AU - Attiya, S. AU - Bader, J. S. AU - Bemben, L. A. AU - Berka, J. AU - Braverman, M. S. AU - Chen, Y. J. AU - Chen, Z. PY - 2005 DA - 2005// TI - Genome sequencing in microfabricated high-density picolitre reactors JO - Nature VL - 437 ID - Margulies2005 ER - TY - JOUR AU - Meyer, M. AU - Stenzel, U. AU - Myles, S. AU - Prufer, K. AU - Hofreiter, M. PY - 2007 DA - 2007// TI - Targeted high-throughput sequencing of tagged nucleic acid samples JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkm566 DO - 10.1093/nar/gkm566 ID - Meyer2007 ER - TY - JOUR AU - Cronn, R. AU - Liston, A. AU - Parks, M. AU - Gernandt, D. S. AU - Shen, R. AU - Mockler, T. PY - 2008 DA - 2008// TI - Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkn502 DO - 10.1093/nar/gkn502 ID - Cronn2008 ER - TY - JOUR AU - Binladen, J. AU - Gilbert, M. T. AU - Bollback, J. P. AU - Panitz, F. AU - Bendixen, C. AU - Nielsen, R. AU - Willerslev, E. PY - 2007 DA - 2007// TI - The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing JO - PLoS One VL - 2 UR - https://doi.org/10.1371/journal.pone.0000197 DO - 10.1371/journal.pone.0000197 ID - Binladen2007 ER - TY - JOUR AU - Altschul, S. F. AU - Gish, W. AU - Miller, W. AU - Myers, E. W. AU - Lipman, D. J. PY - 1990 DA - 1990// TI - Basic local alignment search tool JO - J Mol Biol VL - 215 UR - https://doi.org/10.1016/S0022-2836(05)80360-2 DO - 10.1016/S0022-2836(05)80360-2 ID - Altschul1990 ER - TY - JOUR AU - Thompson, J. D. AU - Higgins, D. G. AU - Gibson, T. J. PY - 1994 DA - 1994// TI - CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice JO - Nucleic Acids Res VL - 22 UR - https://doi.org/10.1093/nar/22.22.4673 DO - 10.1093/nar/22.22.4673 ID - Thompson1994 ER - TY - JOUR AU - Tamura, K. AU - Dudley, J. AU - Nei, M. AU - Kumar, S. PY - 2007 DA - 2007// TI - MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm092 DO - 10.1093/molbev/msm092 ID - Tamura2007 ER - TY - STD TI - Fredslund J, Schauser L, Madsen LH, Sandal N, Stougaard J: PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs. Nucleic Acids Res. 2005, W516-520. 10.1093/nar/gki425. 33 Web Server ID - ref40 ER - TY - JOUR AU - Rozen, S. AU - Skaletsky, H. PY - 2000 DA - 2000// TI - Primer3 on the WWW for general users and for biologist programmers JO - Methods Mol Biol VL - 132 ID - Rozen2000 ER - TY - CHAP AU - Peng, Z. AU - Diogo, R. AU - He, S. ED - Hedges, S. B. ED - Kumar, S. PY - 2009 DA - 2009// TI - Teleost fishes (Teleostei) BT - The timetree of life PB - Oxford University Press CY - New York ID - Peng2009 ER - TY - CHAP AU - Sambrook, J. AU - Fritsch, E. F. AU - Maniatis, T. PY - 1989 DA - 1989// BT - Molecular cloning: a laboratory manual PB - New York CY - Cold Spring Harbor Laboratory Press ID - Sambrook1989 ER - TY - CHAP AU - Nei, M. AU - Kumar, S. PY - 2000 DA - 2000// BT - Molecular Evolution and Phylogenetics PB - Oxford University Press CY - New York ID - Nei2000 ER - TY - JOUR AU - Li, C. AU - Lu, G. AU - Orti, G. PY - 2008 DA - 2008// TI - Optimal data partitioning and a test case for ray-finned fishes (actinopterygii) based on ten nuclear Loci JO - Syst Biol VL - 57 UR - https://doi.org/10.1080/10635150802206883 DO - 10.1080/10635150802206883 ID - Li2008 ER - TY - CHAP AU - Jobb, G. PY - 2008 DA - 2008// TI - TREEFINDER BT - Munich, Germany: Distributed by the author ID - Jobb2008 ER - TY - JOUR AU - Nylander, J. A. AU - Ronquist, F. AU - Huelsenbeck, J. P. AU - Nieves-Aldrey, J. L. PY - 2004 DA - 2004// TI - Bayesian phylogenetic analysis of combined data JO - Syst Biol VL - 53 UR - https://doi.org/10.1080/10635150490264699 DO - 10.1080/10635150490264699 ID - Nylander2004 ER - TY - JOUR AU - Huson, D. H. AU - Richter, D. C. AU - Rausch, C. AU - Dezulian, T. AU - Franz, M. AU - Rupp, R. PY - 2007 DA - 2007// TI - Dendroscope: An interactive viewer for large phylogenetic trees JO - BMC Bioinformatics VL - 8 UR - https://doi.org/10.1186/1471-2105-8-460 DO - 10.1186/1471-2105-8-460 ID - Huson2007 ER -