2022 |
Cunha RL, Nicastro KR, Zardi GI, et al. Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus. PeerJ. 2022;10:e13953. doi:10:e13953 https://doi.org/10.7717/peerj.13953 |
2022 |
Almeida SC, Neiva J, Sousa F, et al. A low‐latitude species pump: Peripheral isolation, parapatric speciation and mating‐system evolution converge in a marine radiationAbstract. Molecular Ecology. 2022;31(18):4797 - 4817. doi:10.1111/mec.v31.1810.1111/mec.16623 |
2021 |
Pes K, Friese A, Cox CJ, Laizé V, Fernández I. Biochemical and molecular responses of the Mediterranean mussel (Mytilus galloprovincialis) to short-term exposure to three commonly prescribed drugs. Marine Environmental Research. 2021;168:105309. doi:10.1016/j.marenvres.2021.105309 |
2020 |
Egger C, Neusser TP, Norenburg J, et al. Uncovering the shell game with barcodes: diversity of meiofaunal Caecidae snails (Truncatelloidea, Caenogastropoda) from Central America. ZooKeys. 2020;968:1 - 42. doi:10.3897/zookeys.968.52986 |
2020 |
Sousa F, Civán P, Brazão J, Foster PG, Cox CJ. The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models,. PeerJ. 2020;8:e8995. doi:10.7717/peerj.899510.7717/peerj.8995/fig-110.7717/peerj.8995/fig-210.7717/peerj.8995/table-110.7717/peerj.8995/supp-110.7717/peerj.8995/supp-210.7717/peerj.8995/supp-310.7717/peerj.8995/supp-4 |
2020 |
Sousa F, Civán P, Foster PG, Cox CJ. The Chloroplast Land Plant Phylogeny: Analyses Employing Better-Fitting Tree- and Site-Heterogeneous Composition ModelsDataSheet_1.pdfDataSheet_2.pdf. Frontiers in Plant Science. 2020;11. doi:10.3389/fpls.2020.0106210.3389/fpls.2020.01062.s00110.3389/fpls.2020.01062.s002 |
2020 |
Carlier JD, Ettamimi S, Cox CJ, Hammani K, Ghazal H, Costa MClara. Prokaryotic diversity in stream sediments affected by acid mine drainage. Extremophiles. 2020. doi:10.1007/s00792-020-01196-8 |
2019 |
Fernández I, Fernandes JMO, Roberto VP, et al. Circulating small non-coding RNAs provide new insights into vitamin K nutrition and reproductive physiology in teleost fish. Biochimica et Biophysica Acta (BBA) - General Subjects. 2019;1863(1):39-51. doi:10.1016/j.bbagen.2018.09.017 |
2019 |
Ettamimi S, Carlier JD, Cox CJ, et al. A meta-taxonomic investigation of the prokaryotic diversity of water bodies impacted by acid mine drainage from the São Domingos mine in southern Portugal. Extremophiles. 2019. doi:10.1007/s00792-019-01136-1 |
2019 |
Williams TA, Cox CJ, Foster PG, Szöllősi GJ, T. Embley M. Phylogenomics provides robust support for a two-domains tree of life. Nature Ecology & Evolution. 2019. doi:10.1038/s41559-019-1040-x |
2019 |
de Sousa CBruno, Cox CJ, Brito L, et al. Improved phylogeny of brown algae Cystoseira (Fucales) from the Atlantic-Mediterranean region based on mitochondrial sequences. PloS one. 2019;14:e0210143. |
2019 |
Karimi E, Keller-Costa T, Slaby BM, et al. Genomic blueprints of sponge-prokaryote symbiosis are shared by low abundant and cultivatable Alphaproteobacteria. Scientific reports. 2019;9:1999. |
2019 |
Louro B, De Moro G, Garcia C, et al. A haplotype-resolved draft genome of the European sardine (Sardina pilchardus). GigaScience. 2019;8. doi:10.1093/gigascience/giz059 |
2019 |
Sousa F, Foster PG, Donoghue PCJ, Schneider H, Cox CJ. Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.). New Phytologist. 2019;222(1):565 - 575. doi:10.1111/nph.2019.222.issue-110.1111/nph.15587 |
2018 |
Cox CJ. Land Plant Molecular Phylogenetics: A Review with Comments on Evaluating Incongruence Among Phylogenies. Critical Reviews in Plant Sciences. 2018;37(2-3):113 - 127. doi:10.1080/07352689.2018.1482443 |
2018 |
Rosa J, Cox CJ, M. Cancela L, Laizé V. Identification of a fish short-chain dehydrogenase/reductase associated with bone metabolism. Gene. 2018;645:137 - 145. doi:10.1016/j.gene.2017.12.021 |
2018 |
Puttick MN, Morris JL, Williams TA, et al. The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte. Current Biology. 2018;28(5):733 - 745.e2. doi:10.1016/j.cub.2018.01.063 |
2018 |
Lu L, Cox CJ, Mathews S, Wang W, Wen J, Chen Z. Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae). Cladistics. 2018;34(1):57 - 77. doi:10.1111/cla.12191 |
2017 |
Califano G, Castanho S, Soares F, et al. Molecular Taxonomic Profiling of Bacterial Communities in a Gilthead Seabream (Sparus aurata) Hatchery. Frontiers in Microbiology. 2017;8. doi:10.3389/fmicb.2017.00204 |
2016 |
Marques CL, Fernández I, Viegas MN, et al. Comparative analysis of zebrafish bone morphogenetic proteins 2, 4 and 16: molecular and evolutionary perspectives. Cellular and Molecular Life Sciences. 2016;73(4):841-857. doi:10.1007/s00018-015-2024-x |
2016 |
Martínez-Garrido J, Serrão EA, Engelen AH, Cox CJ, García-Murillo P, Gonzalez-Wangüemert M. Multilocus genetic analyses provide insight into speciation and hybridization in aquatic grasses, genus Ruppia. Biological Journal of the Linnean Society. 2016;117(2):177 - 191. doi:10.1111/bij.12666 |
2016 |
Laenen B, Machac A, S. Gradstein R, et al. Increased diversification rates follow shifts to bisexuality in liverworts. New Phytologist. 2016;210(3):1121 - 1129. doi:10.1111/nph.13835 |
2016 |
A. Shaw J, Devos N, Liu Y, et al. Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss). Annals of Botany. 2016;118(2):185 - 196. doi:10.1093/aob/mcw086 |
2016 |
Civán P, Craig H, Cox CJ, Brown TA. Multiple domestications of Asian rice. Nature Plants. 2016;2(4):16037. doi:10.1038/nplants.2016.37 |
2016 |
Rathore OSingh, Faustino A, Prudêncio P, Van Damme P, Cox CJ, Martinho RGonçalo. Absence of N-terminal acetyltransferase diversification during evolution of eukaryotic organisms. Scientific Reports. 2016;6:21304. doi:10.1038/srep21304 |
2015 |
Civán P, Craig H, Cox CJ, Brown TA. Three geographically separate domestications of Asian rice. Nature Plants. 2015;1(11):15164. doi:10.1038/nplants.2015.164 |
2014 |
Li B, Lopes JS, Foster PG, Embley TM, Cox CJ. Compositional Biases among Synonymous Substitutions Cause Conflict between Gene and Protein Trees for Plastid Origins. Molecular Biology and Evolution. 2014;31(7):1697 - 1709. doi:10.1093/molbev/msu105 |
2014 |
Liu Y, Cox CJ, Wang W, Goffinet B. Mitochondrial Phylogenomics of Early Land Plants: Mitigating the Effects of Saturation, Compositional Heterogeneity, and Codon-Usage Bias. Systematic Biology. 2014;63(6):862 - 878. doi:10.1093/sysbio/syu049 |
2014 |
Hardoim CCP, Cardinale M, Cúcio ACB, et al. Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges. Frontiers in Microbiology. 2014;5. doi:10.3389/fmicb.2014.00611 |
2014 |
Civa P, Foster PG, Embley MT, Seneca A, Cox CJ. Analyses of Charophyte Chloroplast Genomes Help Characterize the Ancestral Chloroplast Genome of Land Plants. Genome Biology and Evolution. 2014;6(4):897 - 911. doi:10.1093/gbe/evu061 |
2013 |
Hardoim CCP, Cox CJ, Peixoto RS, Rosado AS, Costa R, van Elsas JD. Diversity of the candidate phylum Poribacteria in the marine sponge Aplysina fulva. Brazilian Journal of Microbiology. 2013;44(1):329 - 334. doi:10.1590/S1517-83822013000100048 |
2013 |
Cox CJ, Foster PG. A 20-state empirical amino-acid substitution model for green plant chloroplasts. Molecular Phylogenetics and Evolution. 2013;68(2):218 - 220. doi:10.1016/j.ympev.2013.03.030 |
2013 |
Williams TA, Foster PG, Cox CJ, T. Embley M. An archaeal origin of eukaryotes supports only two primary domains of life. Nature. 2013;504(7479):231 - 236. doi:10.1038/nature12779 |
2012 |
Huttunen S, Bell N, Bobrova VK, et al. Disentangling knots of rapid evolution: origin and diversification of the moss order Hypnales. Journal of Bryology. 2012;34(3):187 - 211. doi:10.1179/1743282012Y.0000000013 |
2012 |
Williams TA, Foster PG, Nye TMW, Cox CJ, Embley TM. A congruent phylogenomic signal places eukaryotes within the Archaea. Proceedings of the Royal Society B: Biological Sciences. 2012;279(1749):4870 - 4879. doi:10.1098/rspb.2012.1795 |
2011 |
Forrest LL, Wickett N, Cox CJ, Goffinet B. Deep sequencing of Ptilidium (Ptilidiaceae) suggests evolutionary stasis in liverwort plastid genome structure. Plant Ecology and Evolution. 2011;144(1):1 - 15. doi:10.5091/plecevo.2011.535 |
2010 |
A. Shaw J, Devos N, Cox CJ, et al. Peatmoss (Sphagnum) diversification associated with Miocene Northern Hemisphere climatic cooling?. Molecular Phylogenetics and Evolution. 2010;55(3):1139 - 1145. doi:10.1016/j.ympev.2010.01.020 |
2010 |
Shaw AJ, Cox CJ, Buck WR, et al. Newly resolved relationships in an early land plant lineage: Bryophyta class Sphagnopsida (peat mosses). American Journal of Botany. 2010;97(9):1511 - 1531. doi:10.3732/ajb.1000055 |
2010 |
Conceição N, Cox CJ, Simões B, Viegas M, M. Cancela L. Comparative promoter analysis and its application to the identification of candidate regulatory factors of cartilage-expressed genes. Journal of Applied Ichthyology. 2010;26(2):245 - 250. doi:10.1111/jai.2010.26.issue-210.1111/j.1439-0426.2010.01415.x |
2010 |
Cox CJ, Goffinet B, Wickett NJ, Boles SB, Shaw AJ. Moss diversity: A molecular phylogenetic analysis of genera. Phytotaxa. 2010;9(1):175. doi:10.11646/phytotaxa.9.110.11646/phytotaxa.9.1.10 |
2009 |
Cock PJA, Antao T, Chang JT, et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009;25(11):1422 - 1423. doi:10.1093/bioinformatics/btp163 |
2009 |
Foster PG, Cox CJ, Embley TM. The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods. Philosophical Transactions of the Royal Society B: Biological Sciences. 2009;364(1527):2197 - 2207. doi:10.1098/rstb.2009.0034 |
2009 |
Waeschenbach A, Cox CJ, Littlewood DTJ, Porter JS, Taylor PD. First molecular estimate of cyclostome bryozoan phylogeny confirms extensive homoplasy among skeletal characters used in traditional taxonomy. Molecular Phylogenetics and Evolution. 2009;52(1):241 - 251. doi:10.1016/j.ympev.2009.02.002 |
2008 |
Shaw JA, Holz I, Cox CJ, Goffinet B. Phylogeny, Character Evolution, and Biogeography of the Gondwanic Moss Family Hypopterygiaceae (Bryophyta). Systematic Botany. 2008;33(1):21 - 30. doi:10.1600/036364408783887311 |
2006 |
James TY, Kauff F, Schoch CL, et al. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature. 2006;443(7113):818 - 822. doi:10.1038/nature05110 |
2006 |
Goffinet B, Wickett NJ, Werner O, Ros RM, Shaw AJ, Cox CJ. Distribution and Phylogenetic Significance of the 71-kb Inversion in the Plastid Genome in Funariidae (Bryophyta). Annals of Botany. 2006;99(4):747 - 753. doi:10.1093/aob/mcm010 |
2005 |
A. Shaw J, Cox CJ, Boles SB. Phylogeny, Species Delimitation, and Recombination in Sphagnum Section Acutifolia. Systematic Botany. 2005;30(1):16 - 33. doi:10.1600/0363644053661823 |
2005 |
A. Shaw J, Melosik I, Cox CJ, Boles SB. Divergent and Reticulate Evolution in Closely Related Species of Sphagnum Section Subsecunda. The Bryologist. 2005;108(3):363 - 376. doi:10.1639/0007-2745(2005)108[0363:DAREIC]2.0.CO;2 |
2005 |
Shaw AJ, Cox CJ. Variation in "biodiversity value" of peatmoss species in Sphagnum section Acutifolia (Sphagnaceae). American Journal of Botany. 2005;92(11):1774 - 1783. doi:10.3732/ajb.92.11.1774 |
2004 |
Vanderpoorten A, Shaw AJ, Cox CJ. Evolution of multiple paralogous adenosine kinase genes in the moss genus Hygroamblystegium: phylogenetic implications. Molecular Phylogenetics and Evolution. 2004;31(2):505 - 516. doi:10.1016/j.ympev.2003.09.020 |
2004 |
Hedderson TA, Murray DJ, Cox CJ, Nowell TL. Phylogenetic Relationships of Haplolepideous Mosses (Dicranidae) Inferred from rps4 Gene Sequences. Systematic Botany. 2004;29(1):29 - 41. doi:10.1600/036364404772973960 |
2004 |
Buck WR, Cox CJ, A. Shaw J, Goffinet B. Ordinal relationships of pleurocarpous mosses, with special emphasis on the Hookeriales. Systematics and Biodiversity. 2004;2(2):121 - 145. doi:10.1017/S1477200004001410 |
2004 |
Shaw J, Cox CJ, Boles SB. Phylogenetic Relationships Among Sphagnum Sections: Hemitheca, Isocladus, and Subsecunda. The Bryologist. 2004;107(2):189 - 196. doi:10.1639/0007-2745(2004)107[0189:PRASSH]2.0.CO;2 |
2004 |
Goffinet B, Shaw AJ, Cox CJ. Phylogenetic inferences in the dung-moss family Splachnaceae from analyses of cpDNA sequence data and implications for the evolution of entomophily. American Journal of Botany. 2004;91(5):748 - 759. doi:10.3732/ajb.91.5.748 |
2004 |
Diezmann S, Cox CJ, Schonian G, Vilgalys RJ, Mitchell TG. Phylogeny and Evolution of Medical Species of Candida and Related Taxa: a Multigenic Analysis. Journal of Clinical Microbiology. 2004;42(12):5624 - 5635. doi:10.1128/JCM.42.12.5624-5635.2004 |
2004 |
Cox CJ, Goffinet B, A. Shaw J, Boles SB. Phylogenetic Relationships among the Mosses Based on Heterogeneous Bayesian Analysis of Multiple Genes from Multiple Genomic Compartments. Systematic Botany. 2004;29(2):234 - 250. doi:10.1600/036364404774195458 |
2004 |
Lutzoni F, Kauff F, Cox CJ, et al. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. American Journal of Botany. 2004;91(10):1446 - 1480. doi:10.3732/ajb.91.10.1446 |
2004 |
Schneider H, Russell SJ, Cox CJ, et al. Chloroplast Phylogeny of Asplenioid Ferns based on rbcL and trnL-F Spacer Sequences (Polypodiidae, Aspleniaceae) and its Implications for Biogeography. Systematic Botany. 2004;29(2):260 - 274. doi:10.1600/036364404774195476 |
2003 |
Pedersen N, Cox CJ, Hedenäs L. Phylogeny of the Moss Family Bryaceae Inferred from Chloroplast DNA Sequences and Morphology. Systematic BotanySystematic Botany. 2003;28(3):471 - 482. http://www.bioone.org/doi/abs/10.1043/02-46.1. |
2003 |
Cox CJ, Hedderson TAJ. Phylogenetic relationships within the moss family Bryaceae based on chloroplast DNA evidence. Journal of Bryology. 2003;25(1):31 - 40. doi:10.1179/037366803125002635 |
2003 |
Shaw AJ, Cox CJ, Boles SB. Polarity of peatmoss (Sphagnum) evolution: who says bryophytes have no roots?. American Journal of Botany. 2003;90(12):1777 - 1787. doi:10.3732/ajb.90.12.1777 |
2003 |
A. Shaw J, Cox CJ, Boles SB. Global patterns in peatmoss biodiversity. Molecular Ecology. 2003;12(10):2553 - 2570. doi:10.1046/j.1365-294X.2003.01929.x |
2003 |
Shaw AJ, Cox CJ, Goffinet B, Buck WR, Boles SB. PHYLOGENETIC EVIDENCE OF A RAPID RADIATION OF PLEUROCARPOUS MOSSES (BRYOPHYTA). Evolution. 2003;57(10):2226 - 2241. doi:10.1111/evo.2003.57.issue-1010.1111/j.0014-3820.2003.tb00235.x |
2003 |
Vanderpoorten A, Goffinet B, Hedenäs L, Cox CJ, Shaw AJ. A taxonomic reassessment of the Vittiaceae (Hypnales, Bryopsida): evidence from phylogenetic analyses of combined chloroplast and nuclear sequence data. Plant Systematics and Evolution. 2003;241(1-2):1 - 12. doi:10.1007/s00606-003-0032-z |
2002 |
Vanderpoorten A, Hedenäs L, Cox CJ, Shaw AJ. Phylogeny and Morphological Evolution of the Amblystegiaceae (Bryopsida). Molecular Phylogenetics and Evolution. 2002;23(1):1 - 21. doi:10.1006/mpev.2001.1067 |
2002 |
Vanderpoorten A, Hedenäs L, Cox CJ, A. Shaw J, Hedenäs L. Circumscription, Classification, and Taxonomy of Amblystegiaceae (Bryopsida) Inferred from Nuclear and Chloroplast DNA Sequence Data and Morphology. Taxon. 2002;51(1):115. doi:10.2307/1554968 |
2002 |
Pinter I, Bakker F, Cox C, et al. Phylogenetic and biosystematic relationships in four highly disjunct polyploid complexes in the subgenera and in (Aspleniaceae). Organisms Diversity & Evolution. 2002;2(4):299 - 311. doi:10.1078/1439-6092-00050 |
2002 |
Buck WR, A. Shaw J, Cox CJ. A new species of Leskeodon (Daltoniaceae) from Ecuador. Brittonia. 2002;54(3):178 - 180. doi:10.1663/0007-196X(2002)054[0178:ANSOLD]2.0.CO;2 |
2001 |
Goffinet B, Cox CJ, A. Shaw J, Hedderson TA. The Bryophyta (Mosses): Systematic and Evolutionary Inferences from an rps4 Gene (cpDNA) Phylogeny. Annals of Botany. 2001;87(2):191 - 208. doi:10.1006/anbo.2000.1318 |
2000 |
Cox CJ, Goffinet B, Newton AE, A. Shaw J, Hedderson TAJ. Phylogenetic Relationships Among the Diplolepideous-alternate Mosses (Bryidae) Inferred from Nuclear and Chloroplast DNA Sequences. The Bryologist. 2000;103(2):224 - 241. doi:10.1639/0007-2745(2000)103[0224:PRATDA]2.0.CO;2 |
2000 |
Goffinet B, Cox CJ. Phylogenetic Relationships Among Basal-most Arthrodontous Mosses with Special Emphasis on the Evolutionary Significance of the Funariineae. The Bryologist. 2000;103(2):212 - 223. doi:10.1639/0007-2745(2000)103[0212:PRABMA]2.0.CO;2 |
2000 |
Newton AE, Cox CJ, Duckett JG, et al. Evolution of the Major Moss Lineages: Phylogenetic Analyses Based on Multiple Gene Sequences and Morphology. The Bryologist. 2000;103(2):187 - 211. doi:10.1639/0007-2745(2000)103[0187:EOTMML]2.0.CO;2 |
1999 |
Hedderson TA, Cox CJ, J. Gibbings G. Phylogenetic Relationships of the Wardiaceae (Musci); Evidence from 18s rRNA and rps4 Gene Sequences. The Bryologist. 1999;102(1):26. doi:10.2307/3244455 |
1999 |
Vogel JC, Rumsey FJ, Russell SJ, et al. Genetic structure, reproductive biology and ecology of isolated populations of Asplenium csikii (Aspleniaceae, Pteridophyta). Heredity. 1999;83(5):604 - 612. doi:10.1038/sj.hdy.6886120 |