Driving south: A multi-gene phylogeny of the brown algal family Fucaceae reveals relationships and recent drivers of a marine radiation

BMC Evolutionary Biology

Volumn 11, Issue 1, 2011, Pages

  Cánovas, Fernando G ^a   Mota, Catarina F ^a   Serrão, Ester A ^a   Pearson, Gareth A ^a  

^a UNIVERSITY OF ALGARVE   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTIVE RADIATION; BIOLOGICAL INVASION; BROWN ALGA; CLADISTICS; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC DIFFERENTIATION; GLACIATION; HABITAT TYPE; HERMAPHRODITE; MARINE ENVIRONMENT; MIOCENE; PHYLOGENY; PLEISTOCENE; PLIOCENE; POLYMORPHISM; PROTEIN; RADIATION BALANCE; RESOLUTION; SPECIATION (BIOLOGY); TOPOLOGY;

ATLANTIC OCEAN; ATLANTIC OCEAN (NORTH); PACIFIC OCEAN; PACIFIC OCEAN (NORTH);

ALGAE; FUCACEAE; FUCUS; PHAEOPHYCEAE;

COMPLEMENTARY DNA;

ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; BROWN ALGA; CLASSIFICATION; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENETICS; MOLECULAR GENETICS; PHYLOGENY; SPECIES DIFFERENTIATION; STATISTICAL MODEL;

BAYES THEOREM; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENETIC SPECIATION; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHAEOPHYTA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 84857783307     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-11-371     Document Type: Article

References (94)

1. Genetic Divergence, Reproductive Isolation, and Marine Speciation. Palumbi SR, Annual Review of Ecology and Systematics 1994 25 547 572 10.1146/annurev.es.25.110194.002555 (Pubitemid 24986131)
2. Phylogeography and historical ecology of the North Atlantic intertidal. Wares J, Cunningham C, Evolution 2001 55 2455 2469 11831661 (Pubitemid 34115678)
3. Evaluating signatures of glacial refugia for North Atlantic benthic marine taxa. Maggs C, Castilho R, Foltz D, Henzler C, Jolly M, Kelly J, Olsen J, Perez K, Stam W, Väinölä R, Viard F, Wares J, Ecology 2008 89 11 Suppl 108 22 19097488
4. Ecological causes of adaptive radiation. Schluter D, American Naturalist 1996 148 40 S64 10.1086/285901 (Pubitemid 27050107)
5. Rapid Speciation and Ecological Divergence in the American Seven-Spined Gobies (Gobiidae, Gobiosomatini) Inferred from a Molecular Phylogeny. Rüber L, Van Tassell J, Zardoya R, Evolution 2003 57 7 1584 1598 12940363 (Pubitemid 36953647)
6. Speciation along a depth gradient in a marine adaptive radiation Speciation along a depth gradient in a marine adaptive radiation. Ingram T, Proceedings of the Royal Society of London, series B 2011 278 613 618 10.1098/rspb.2010.1127
7. Marine radiations at small geographic scales: speciation in neotropical reef gobies (Elacatinus). Taylor M, Hellberg M, Evolution 2005 59 374 385 15807422 (Pubitemid 40356050)
8. Evolution in Littorina: ecology matters. Johannesson K, Journal of Sea Research 2003 49 107 117 10.1016/S1385-1101(02)00218-6 (Pubitemid 36261084)
9. Ecological speciation. Rundle H, Nosil P, Ecology Letters 2005 8 336 352 10.1111/j.1461-0248.2004.00715.x (Pubitemid 40393919)
10. Functional divergence in heat shock response following rapid speciation of Fucus spp. in the Baltic Sea. Lago-Leston A, Mota C, Kautsky L, Pearson G, Marine Biology 2010 157 683 688 10.1007/s00227-009-1348-1
11. Adaptive traits are maintained on steep selective gradients despite gene flow and hybridization in the intertidal zone. Zardi G, Nicastro K, Canovas F, Ferreira-Costa J, Serrão E, Pearson G, PloS one 2011
12. Sympatric, parapatric or allopatric: the most important way to classify speciation? Butlin R, Galindo J, Grahame J, Philosophical transactions of the Royal Society of London. Series B 2008 363 2997 3007 10.1098/rstb.2008.0076 18522915
13. Ecological speciation. Schluter D, Trends in Ecology and Evolution 2001 16 372 380 10.1016/S0169-5347(01)02198-X 11403870 (Pubitemid 32525778)
14. Marine speciation on a small planet. Palumbi SR, Trends in Ecology & Evolution 1992 7 4 114 118 10.1016/0169-5347(92)90144-Z 22194962 (Pubitemid 23395167)
15. Plant sex determination and sex chromosomes. Charlesworth D, Heredity 2002 88 94 101 10.1038/sj.hdy.6800016 11932767 (Pubitemid 34196701)
16. Is self-fertilization an evolutionary dead end? Revisiting an old hypothesis with genetic theories and a macroevolutionary approach. Takebayashi N, Morrell P, American Journal of Botany 2001 88 1143 1150 10.2307/3558325 11454614 (Pubitemid 33645022)
17. Evidence for an early opening of the Bering Strait. Marincovich L, Gladenkov A, Nature 1999 397 149 151 10.1038/16446 (Pubitemid 29050916)
18. A refined age for the earliest opening of Bering Strait. Gladenkov A, Oleinik A, Marincovich L, Barinov K, Palaeogeology, Palaeoclimatology and Palaeoecology 2002 183 321 328 10.1016/S0031-0182(02)00249-3 (Pubitemid 34744200)
19. The Bering Strait connection: dispersal and speciation in boreal macroalgae. Lindstrom SC, Journal of Biogeography 2001 28 243 251 (Pubitemid 32614482)
20. Recent history of the Bering Strait. Svitoch A, Taldenkova E, Oceanology 1994 34 400 404
21. Arctic climate change and its impacts on the ecology of the North Atlantic. Greene C, Pershing A, Cronin T, Ceci N, Ecology 2008 89 24 S38 10.1890/07-0550.1 19097482
22. Phylogeny and historical ecology of the Desmarestiaceae (Phaeophyceae) support a southern hemisphere origin. Peters A, van Oppen M, Wiencke C, Stam W, Olsen J, Journal of Phycology 1997 33 294 309 10.1111/j.0022-3646.1997.00294.x
23. Evolution of the Fucaceae (Phaeophyceae) inferred from nrDNA-ITS. Serrão E, Lawrence A, Brawley S, Journal of Phycology 1999 35 382 394 10.1046/j.1529-8817.1999.3520382.x (Pubitemid 29228865)
24. A mtDNA-based phylogeny of the brown algal genus Fucus (Heterokontophyta; Phaeophyta). Coyer J, Hoarau G, Oudot-Le Secq M, Stam WT, Olsen JL, Molecular Phylogenetics and Evolution 2006 39 209 222 10.1016/j.ympev.2006.01.019 16495086
25. Fucus vesiculosus and spiralis species complex: a nested model of local adaptation at the shore level. Billard E, Serrão E, Pearson G, Destombe C, Valero M, Marine Ecology Progress Series 2010 405 163 174
26. Evolution and diversification within the intertidal brown macroalgae Fucus spiralis/Fucus vesiculosus species complex in the North Atlantic. Coyer J, Hoarau G, Costa J, Hogerdijk B, Serrão E, Billard E, Valero M, Pearson G, Olsen J, Molecular Phylogenetics and Evolution 2011 58 283 296 10.1016/j.ympev.2010.11.015 21111835
27. Rapid speciation in a newly opened postglacial marine environment, the Baltic Sea. Pereyra R, Bergström L, Kautsky L, Johannesson K, BMC Evolutionary Biology 2009 9 1 9 10.1186/1471-2148-9-1 19121213
28. Genetic isolation between three closely related taxa Fucus vesiculosus, F. spiralis and F. ceranoides. Billard E, Dauguin C, Pearson G, Serrão E, Engel C, Valero M, Journal of Phycology 2005 41 900 905 10.1111/j.0022-3646. 2005.04221.x (Pubitemid 41197177)
29. Genetic entities and mating system in hermaphroditic Fucus spiralis and its close dioecious relative F. vesiculosus (Fucaceae, Phaeophyceae). Engel C, Daguin C, Serrão E, Molecular Ecology 2005 14 2033 2046 10.1111/j.1365-294X.2005.02558.x 15910325 (Pubitemid 40778267)
30. Implications of mating system for genetic diversity of sister algal species Fucus spiralis and Fucus vesiculosus (Heterokontophyta, Phaeophyceae). Perrin C, Daguin C, Van De Vliet M, Engel C, Pearson G, Serrão E, European Journal of Phycology 2007 42 219 230 10.1080/09670260701336554 (Pubitemid 47295344)
31. Intriguing asexual life in marginal popu- lations of the brown seaweed Fucus vesiculosus. Tatarenkov A, Bergström L, Jönsson R, Serrão E, Kautsky L, Johannesson K, Molecular Ecology 2005 14 647 651 10.1111/j.1365-294X.2005.02425.x 15660953 (Pubitemid 40210691)
32. Trans-Pacific and trans-Arctic pathways of the intertidal macroalga Fucus distichus L. reveal multiple glacial refugia and colonizations from the North Pacific to the North Atlantic. Coyer J, Hoarau G, Van Schaik J, Luijckx P, Olsen JL, Journal of Biogeography 2010
33. Post-Ice age recolonization and differentiation of Fucus serratus L. (Fucaceae: Phaeophyta) populations in Northern Europe. Coyer J, Peters A, Stam W, Olsen J, Molecular Ecology 2003 12 1817 1829 10.1046/j.1365-294X.2003.01850.x 12803634 (Pubitemid 36815018)
34. Glacial refugia and recolonization pathways in the brown seaweed Fucus serratus. Hoarau G, Coyer J, Veldsink J, Stam W, Olsen J, Molecular Ecology 2007 16 17 3606 3616 10.1111/j.1365-294X.2007.03408.x 17845434 (Pubitemid 47383103)
35. Recent versus relic: discerning the genetic signature of Fucus vesiculosus(Heterokontophyta; Phaeophyceae) in the northwestern Atlantic. Muhlin J, Brawley S, Journal of Phycology 2009 45 828 837 10.1111/j.1529-8817.2009. 00715.x
36. Surfing the wave on a borrowed board: range expansion and spread of introgressed organellar genomes in the seaweed Fucus ceranoides L. Neiva J, Pearson G, Valero M, Serrão E, Molecular Ecology 2010 19 4812 4822 10.1111/j.1365-294X.2010.04853.x 20958817
37. Taylor T, Taylor E, Krings M, Paleobotany. The biology and evolution of fossil plants Elsevier 2009
38. A multi-locus time-calibrated phylogeny of the brown algae (Heterokonta, Ochrophyta, Phaeophyceae): Investigating the evolutionary nature of the "brown algal crown radiation". Silberfeld T, Leigh J, Verbruggen H, Cruaud C, de Reviers B, Rousseau F, Molecular phylogenetics and evolution 2010 56 2 659 74 10.1016/j.ympev.2010.04.020 20412862
39. Climate and atmospheric history of the past 420,000 years from the Vostok ice core, Antarctica. Petit J, Jouzel J, Raynaud D, Barkov N, Barnola J, Basile I, Bender M, Chappellaz J, Davis J, Delaygue G, Delmotte M, Kotlyakov V, Legrand M, Lipenkov V, Lorius C, Pépin L, Ritz C, Saltzman E, Stievenard M, Nature 1999 399 429 436 10.1038/20859 (Pubitemid 29258841)
40. Trends, rhythms, and aberrations in global climate 65 Ma to present. Zachos J, Pagani M, Sloan L, Thomas E, Billups K, Science 2001 292 686 693 10.1126/science.1059412 11326091 (Pubitemid 32385533)
41. A Pliocene-Pleistocene stack of 57 globally distributed benthic d18O records. Lisiecki L, Raymo M, Maureen E, Paleoceanography 2005 20
42. Alternative global Cretaceous paleogeography. Hay W, Deconto R, Wold C, Wilson K, Voigt S, Schulz M, Wold-Rossby A, Dullo WC, Ronov A, Balukhovsky A, Soeding E, The evolution of Cretaceous ocean/climate systems Geological Society of America Special Paper, Barrera E, Johnson C, 1999 1 47
43. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Yang Z, Rannala B, Molecular Biology and Evolution 1997 14 717 724 9214744 (Pubitemid 27287292)
44. Properties of phylogenetic trees generated by Yule-type speciation models. Steel M, McKenzie A, Mathematical Bioscience 2001 170 91 112 10.1016/S0025-5564(00)00061-4 (Pubitemid 32230649)
45. GENIE: estimating demographic history from molecular phylogenies. Pybus O, Rambaut A, Bioinformatics 2002 18 1404 1405 10.1093/bioinformatics/18.10.1404 12376389 (Pubitemid 35244201)
46. Assigning morphological variants of Fucus (Fucales, Phaeophyceae) in Canadian waters to recognized species using DNA barcoding. Kucera H, Saunders G, Botany 2008 86 1065 1079 10.1139/B08-056
47. Travelling in time with networks: Revealing present day hybridization versus ancestral polymorphism between two species of brown algae, Fucus vesiculosus and F. spiralis. Moalic Y, Arnaud-Haond S, Perrin C, Pearson G, Serrão E, BMC Evolutionary Biology 2011
48. Inbreeding depression and its evolutionary consequences. Charlesworth D, Charlesworth B, Annual Review of Ecology and Systematics 1987 18 237 268 10.1146/annurev.es.18.110187.001321
49. Revisiting synchronous gamete release by fucoid algae in the intertidal zone: fertilization success and beyond? Int Comp Biol 2006, 46: 587-597. Pearson G, Serrão E, International Comparative Biology 2006 46 587 597 10.1093/icb/icl030 (Pubitemid 44597664)
50. Recent evolution in Baltic Fucus vesiculosus: reduced tolerance to emersion stresses compared to intertidal (North Sea) populations. Pearson G, Kautsky L, Serrão E, Marine Ecology Progress Series 2000 202 67 79
51. Analysis of sexual phenotype and prezygotic fertility in natural populations of Fucus spiralis, F. vesiculosus (Fucaceae, Phaeophyceae) and their putative hybrids. Billard E, Serrão E, Pearson G, Engel CR, Destombe C, Valero M, European Journal of Phycology 2005 40 4 397 407 10.1080/ 09670260500334354 (Pubitemid 41759251)
52. Sex chromosomes in flowering plants. Ming R, Wang J, Moore P, Paterson A, American Journal of Botany 2007 94 141 150 10.3732/ajb.94.2.141 21642216 (Pubitemid 46955031)
53. Baker's law revisited: reproductive assurance in a metapopulation. Pannell J, Barrett S, Evolution 1998 52 657 668 10.2307/2411261 (Pubitemid 28324496)
54. Stebbins G, Variation and evolution in plants New York: Columbia University Press 1950
55. Stebbins G, Flowering plants. Evolution above the species level Cambridge: Belknap Press of Harvard University Press 1974
56. Simple and rapid RNA extraction from freeze-dried tissue of brown algae and seagrasses. Pearson G, Lago-Leston A, Valente M, Serrão E, European Journal of Phycology 2006 41 97 104 10.1080/09670260500505011 (Pubitemid 43379207)
57. An Expressed Sequence Tag Analysis of the Intertidal Brown Seaweeds Fucus serratus (L.) and F. vesiculosus (L.) (Heterokontophyta, Phaeophyceae) in Response to Abiotic Stressors. Pearson G, Hoarau G, Lago-leston A, Coyer J, Marine Biotechnology 2010 12 195 213 10.1007/s10126-009-9208-z 19609612
58. Primer3 on the WWW for general users and for biologist programmers. Rozen S, Skaletsky H, Krawetz S, Misener S, Methods in Molecular Biology 2000 365 386
59. Phylogenetic relationships within the Fucales (Phaeophyceae) assessed by the photosystem I coding psaA sequences. Cho G, Rousseau F, de Reviers B, Boo S, Phycologia 2006 45 5 512 519 10.2216/05-48.1 (Pubitemid 44360085)
60. Multiple alignment of DNA sequences with MAFFT. Katoh K, Asimenos G, Toh H, Bioinformatics for DNA sequence analysis New York, USA: Humana Press, Posada D, 2009 39 64
61. SeaView and Phylo-win, two graphic tools for sequence alignment and molecular phylogeny. Galtier N, Gouy M, Gautier C, Computer Applications in the Biosciences 1996 12 543 548 9021275
62. MrModeltest v2. Nylander J, Xxxx 2004
63. Dating the human-ape split by a molecular clock of mitochondrial DNA. Hasegawa M, Kishino H, Yano T, Journal of Molecular Evolution 1985 22 160 174 10.1007/BF02101694 3934395 (Pubitemid 16227864)
64. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Kimura M, Journal of Molecular Evolution 1980 16 111 120 10.1007/BF01731581 7463489 (Pubitemid 11166431)
65. Estimation of evolutionary distances between nucleotide sequences. Zharkikh A, Journal of Molecular Evolution 1994 39 315 329 10.1007/BF00160155 7932793 (Pubitemid 24283347)
66. The general stochasstic model of nucletide substitution. Rodriguez F, Oliver JL, Marin A, Medina JR, Journal of Theoretical Biology 1990 142 485 501 10.1016/S0022-5193(05)80104-3 2338834 (Pubitemid 20108270)
67. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Guindon S, Gascuel O, Systematic Biology 2003 52 696 704 10.1080/10635150390235520 14530136 (Pubitemid 37365050)
68. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Bremer K, Evolution 1988 42 795 803 10.2307/2408870
69. Multiple sources of character information and the phylogeny of Hawaiian Drosophilids. Baker R, DeSalle R, Systematic Biology 1997 46 654 673 10.1093/sysbio/46.4.654 11975337 (Pubitemid 127366000)
70. Assessing the relative contribution of molecular and morphological characters in simultaneous analysis trees. Baker R, Yu X, DeSalle R, Molecular Phylogenetics and Evolution 1998 9 427 436 10.1006/mpev.1998.0519 9667991 (Pubitemid 128351477)
71. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Ronquist F, Huelsenbeck P, Bioinformatics 2003 19 1572 1574 10.1093/bioinformatics/btg180 12912839 (Pubitemid 37038874)
72. Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Altekar G, Dwarkadas S, Huelsenbeck J, Ronquist F, Bioinformatics 2004 20 407 415 10.1093/bioinformatics/btg427 14960467 (Pubitemid 38262773)
73. Non-calcareous marine algae from California Miocene deposits. Parker B, Dawson E, Nova Hedwigia 1965 10 273 295
74. Eine Blätter-Flora des Egerien (Ober-Oligozän) aus marinen Sedimenten der Zentralen Paratethys im Linzer Raum (sterreich). Kovar J, Beiträge zur Paläontologie von sterreich 1982 9 1 209 19387542
75. The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages. Wolf Y, Novichkov P, Karev G, Koonin E, Lipman D, Proceedings of the National Academy of Science of USA 2009 106 18 7273 7280 10.1073/pnas.0901808106
76. Evolution of genes and taxa: a primer. Doyle J, Gaut B, Plant Molecular Biology 2000 42 1 23 10.1023/A:1006349518932 10688128 (Pubitemid 30096110)
77. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Shapiro B, Rambaut A, Drummond AJ, Molecular Biology and Evolution 2006 23 7 9 16177232 (Pubitemid 41785947)
78. BEAST: Bayesian evolutionary analysis by sampling trees. Drummond A, Rambaut A, BMC Evolutionary Biology 2007 8 1 8
79. R Development Core Team, R: A language and environment for statistical computing Vienna, Austria 2009
80. Paradis E, Analysis of phylogenetics and evolution with R New York: Springer Science+Business Media 2006
81. On phylogenetic tests of irreversible evolutionEvo. Goldberg E, Igi B, Evolution 2008 62 2727 2741 10.1111/j.1558-5646.2008.00505.x 18764918
82. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Pagel M, Proceedings of the Royal Society of London, series B 1994 255 37 45 10.1098/rspb.1994.0006 (Pubitemid 24044170)
83. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Pagel M, Systematic Biology 1999 48 612 622 10.1080/106351599260184 (Pubitemid 129479567)
84. A likelihood approach to estimating phylogeny from discrete morphological character data. Lewis P, Systematic Biology 2001 50 913 925 10.1080/106351501753462876 12116640
85. Phylogenetic inference of reciprocal effects between geographic range evolution and diversification. Goldberg E, Lancaster L, Ree R, Systematic Biology 2011 60 451 465 10.1093/sysbio/syr046 21551125
86. Estimating a binary character's effect on speciation and extinction. Maddison W, Midford P, Otto S, Systematic Biology 2007 56 701 710 10.1080/10635150701607033 17849325 (Pubitemid 47402904)
87. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. Fitzjohn R, Maddison W, Otto S, Systematic Biology 2009 58 595 611 10.1093/sysbio/syp067 20525612
88. A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Ree R, Moore B, Webb C, Donoghue M, Evolution 2005 59 2299 2311 16396171 (Pubitemid 41752644)
89. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Ree R, Smith S, Systematic Biology 2008 57 4 14 18253896
90. Prospects and challenges for parametric models in historical biogeographical inference. Ree R, Sanmartn I, Journal of Biogeography 2009 36 1211 1220 10.1111/j.1365-2699.2008.02068.x
91. Gradstein F, Ogg J, Smith A, Geologic time scale 2004 UK: Cambridge University Press 2005
92. Prospects for inferring very large phylogenies by using the neighbor-joining method. Tamura K, Nei M, Kumar S, Proceedings of the National Academy of Science of USA 2004 101 11030 11035 10.1073/pnas.0404206101 (Pubitemid 38989579)
93. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Tamura K, Dudley J, Nei M, Kumar S, Molecular Biology and Evolution 2007 24 1596 1599 10.1093/molbev/msm092 17488738 (Pubitemid 47236692)
94. A reassessment of species boundaries in Cystoseira and Halidrys (Phaeophyceae, Fucales) along the North American West coast. Harvey J, Goff L, Journal of Phycology 2006 42 707 720 10.1111/j.1529-8817.2006.00215.x (Pubitemid 43807275)