Winding up the molecular clock in the genus Carabus (Coleoptera: Carabidae): Assessment of methodological decisions on rate and node age estimation

BMC Evolutionary Biology

Volumn 12, Issue 1, 2012, Pages

  Andújar, Carmelo ^a   Serrano, José ^a   Gámez Zurita, Jesús ^b  

^a UNIVERSITY OF MURCIA   (Spain)

^b INSTITUTE OF EVOLUTIONARY BIOLOGY CSIC UNIVERSITAT POMPEU FABRA   (Spain)

Author keywords

Carabus; Clock model; Coleoptera; Deep node ages; Gblocks; Mitochondrial genes; Molecular clock; Nuclear genes; Outgroup selection; Partitioning model; Rates of molecular evolution

Indexed keywords

MITOCHONDRIAL DNA;

AGE; BEETLE; CALIBRATION; CLADISTICS; DATA SET; ECOLOGICAL MODELING; ESTIMATION METHOD; GENE EXPRESSION; GENETIC DIFFERENTIATION; GENETIC MARKER; MIOCENE; MITOCHONDRIAL DNA; MOLECULAR ANALYSIS; NUMERICAL MODEL; OLIGOCENE; PHYLOGENY; SELECTION;

ANIMAL; ARTICLE; BAYES THEOREM; BEETLE; BIOLOGICAL MODEL; BIOLOGY; DNA SEQUENCE; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT;

ANIMALS; BASE SEQUENCE; BAYES THEOREM; BEETLES; COMPUTATIONAL BIOLOGY; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENETICS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

CARABIDAE; COLEOPTERA;

EID: 84861872394     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-12-40     Document Type: Article

References (65)

1. The modern molecular clock. Bromham L, Penny D, Nat Rev Genet 2003 4 216 224 10.1038/nrg1020 12610526 (Pubitemid 36277637)
2. Rapid morphological radiation and convergence among races of the butterfly Heliconius erat inferred from patterns of mitochondrial-DNA evolution. Brower AVZ, Proc Nat Acad Sci USA 1994 91 6491 6495 10.1073/pnas.91.14.6491 8022810 (Pubitemid 24200687)
3. Low substitution rates in mitochondrial DNA in Mediterranean carabid beetles. Pruser F, Mossakowski D, Insect Mol Biol 1998 7 121 128 10.1046/j.1365-2583.1998.72056.x 9535158 (Pubitemid 28107080)
4. The evolutionary history of the genus Timarch (Coleoptera, Chrysomelidae) inferred from mitochondrial COII Gene and partial 16S rDNA sequences. Gámez-Zurita J, Juan C, Petitpierre E, Mol Phylogenet Evol 2000 14 304 317 10.1006/mpev.1999.0712 10679162 (Pubitemid 30181339)
5. Molecular phylogeny of the tribe Sphodrini (Coleoptera: Carabidae) based on mitochondrial and nuclear markers. Ruiz C, Jordal B, Serrano J, Mol Phylogenet Evol 2009 50 44 58 10.1016/j.ympev.2008.09.023 18948213
6. Mitochondrial evolutionary rate and speciation in termites: data on European Reticulitermes taxa (Isoptera, Rhinotermitidae). Luchetti A, Marini M, Mantovani B, Insectes Soc 2005 52 218 221 10.1007/s00040-005-0806-5 (Pubitemid 41187582)
7. Evolution and diversification of the forest and hypogean ground-beetle genus Trechus in the Canary Islands. Contreras-Diaz HG, Moya O, Oromi P, Juan C, Mol Phylogenet Evol 2007 42 687 699 10.1016/j.ympev.2006.10.007 17116412 (Pubitemid 46330814)
8. Ancient origin of a Western Mediterranean radiation of subterranean beetles. Ribera I, Fresneda J, Bucur R, Izquierdo A, Vogler A, Salgado J, Cieslak A, BMC Evol Biol 2010 10 29 10.1186/1471-2148-10-29 20109178
9. Revisiting the insect mitochondrial molecular clock: the mid-Aegean trench calibration. Papadopoulou A, Anastasiou I, Vogler A, Mol Biol Evol 2010 27 1659 1672 10.1093/molbev/msq051 20167609
10. Molecular clocks: four decades of evolution. Kumar S, Nat Rev Genet 2005 6 654 662 10.1038/nrg1659 16136655 (Pubitemid 41044303)
11. Evolutionary rates, divergence dates, and the performance of mitochondrial genes in bayesian phylogenetic analysis. Mueller RL, Syst Biol 2006 55 289 300 10.1080/10635150500541672 16611600
12. Nucleotide substitution rates for the full set of mitochondrial protein-coding genes in Coleoptera. Pons J, Ribera I, Bertranpetit J, Balke M, Mol Phylogenet Evol 2010 56 796 807 10.1016/j.ympev.2010.02.007 20152911
13. Variation in DNA substitution rates among lineages erroneously inferred from simulated clock-like data. Schwartz RS, Mueller RL, PLoS One 2010 5 9649 10.1371/journal.pone.0009649 20300176
14. Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Graur D, Martin W, Trends Genet 2004 20 80 86 10.1016/j.tig.2003.12.003 14746989 (Pubitemid 38121359)
15. Dating nodes on molecular phylogenies: a critique of molecular biogeography. Heads M, Cladistics 2005 21 62 78 10.1111/j.1096-0031.2005.00052.x (Pubitemid 40534295)
16. The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Inoue J, Donoghue PCJ, Yang Z, Syst Biol 2010 59 74 89 10.1093/sysbio/syp078 20525621
17. When trees grow too long: investigating the causes of highly inaccurate Bayesian branch-length estimates. Brown JM, Hedtke SM, Lemmon AR, Lemmon EM, Syst Biol 2010 59 145 161 10.1093/sysbio/syp081 20525627
18. Branch length estimation and divergence dating: estimates of error in Bayesian and maximum likelihood frameworks. Schwartz RS, Mueller RL, BMC Evol Biol 2010 10
19. Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. Aris-Brosou S, Yang Z, Syst Biol 2002 51 703 714 10.1080/10635150290102375 12396585 (Pubitemid 35294803)
20. Relaxed phylogenetics and dating with confidence. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A, Plos Biol 2006 4 699 710
21. Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals. Battistuzzi FU, Filipski A, Hedges SB, Kumar S, Mol Biol Evol 2010 27 1289 1300 10.1093/molbev/msq014 20093431
22. Fast and slow implementations of relaxed clock methods show similar patterns of accuracy in estimating divergence times. Battistuzzi FU, Billing-Ross P, Paliwal A, Kumar S, Mol Biol Evol 2011 28 2439 2442 10.1093/molbev/msr100 21498604
23. Accommodating heterogenous rates of evolution in molecular divergence dating methods: an example using intercontinental dispersal of Plestiodon (Eumeces) Lizards. Brandley MC, Wang Y, Guo X, Montes de Oca AN, Fería Ortiz M, Hikida T, Ota H, Syst Biol 2011 6 3 15
24. Taxon sampling effects in molecular clock dating: An example from the African Restionaceae. Linder HP, Hardy CR, Rutschmann F, Mol Phylogenet Evol 2005 35 569 582 10.1016/j.ympev.2004.12.006 15878126 (Pubitemid 40607950)
25. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Lemmon AR, Brown JM, Stanger-Hall K, Lemmon EM, Syst Biol 2009 58 130 145 10.1093/sysbio/syp017 20525573
26. Origin and diversification of hindwingless Damaster ground beetles within the Japanese islands as deduced from mitochondrial ND5 gene sequences (Coleoptera, Carabidae). Su ZH, Tominaga O, Okamoto M, Osawa S, Mol Biol Evol 1998 15 1026 1039 9718730 (Pubitemid 28364456)
27. Formation of the Japanese carabina fauna inferred from a phylogenetic tree of mitochondrial ND5 gene sequences (Coleoptera, Carabidae). Tominaga O, Su ZH, Kim CG, Okamoto M, Imura Y, Osawa S, J Mol Evol 2000 50 541 549 10835484 (Pubitemid 30429951)
28. Illustrated Catalogue of the Genus Carabus of the World (Coleoptera: Carabidae. Deuve T, Sofia-Moscow: PENSOFT 2004
29. Phylogeny and life-history evolution in Carabus (subtribe Carabina: Coleoptera, Carabidae) based on sequences of two nuclear genes. Sota T, Ishikawa R, Biol J Linn Soc 2004 81 135 149 10.1111/j.1095-8312.2004.00277.x (Pubitemid 38106582)
30. Phylogeny. Arndt E, Brücker M, Marciniak K, Mossakowski D, Prüser F, The genus Carabus L. in Europe, a synthesis Sofía-Moscow- Leiden: PENSOFT & European Invertebrate Survey, Turin H, Penev L, 2003 307 325
31. Incongruence of mitochondrial and nuclear gene trees in the Carabid beetles Ohomopterus. Sota T, Vogler AP, Syst Biol 2001 50 39 59 12116593
32. MEGA4: Molecular evolutionary genetics analysis (MEGA). Tamura K, Dudley J, Nei M, Kumar S, Mol Biol Evol 2007 24 1596 1599 10.1093/molbev/msm092 17488738 (Pubitemid 47236692)
33. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Katoh K, Misawa K, Kuma K, Miyata T, Nucleic Acids Res 2002 30 3059 3066 10.1093/nar/gkf436 12136088 (Pubitemid 34851225)
34. Multiple alignment of DNA sequences with MAFFT. Katoh K, Asimenos G, Toh H, Bioinf DNA Seq Anal 2009 537 39 64 10.1007/978-1-59745-251-9-3
35. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Castresana J, Mol Biol Evol 2000 17 540 552 10742046 (Pubitemid 30210700)
36. Testing significance of incongruence. Farris JS, Kallersjo M, Kluge AG, Bult C, Cladistics 1994 10 315 319 10.1111/j.1096-0031.1994.tb00181.x
37. The phylogeny of the extant chelicerate orders. Wheeler WC, Hayashi CY, Cladistics 1998 14 173 192 10.1111/j.1096-0031.1998.tb00331.x (Pubitemid 128369214)
38. PAUP*. Swofford DL, Phylogenetic Analysis Using Parsimony (*and Other Methods) Sunderland, Massachusetts: Sinauer Associates 2000
39. MrBayes: Bayesian inference of phylogenetic trees. Huelsenbeck JP, Ronquist F, Bioinformatics 2001 17 754 755 10.1093/bioinformatics/17.8.754 11524383 (Pubitemid 32851390)
40. MrBayes 3: Bayesian phylogenetic inference under mixed models. Ronquist F, Huelsenbeck JP, Bioinformatics 2003 19 1572 1574 10.1093/bioinformatics/ btg180 12912839 (Pubitemid 37038874)
41. jModelTest: Phylogenetic model averaging. Posada D, Mol Biol Evol 2008 25 1253 1256 10.1093/molbev/msn083 18397919 (Pubitemid 351882013)
42. Tracer v1.5 2007. Rambaut A, Drummond AJ, http://beast.bio.ed.ac.uk/ Tracer
43. FigTree v.1.1.2 2008. Rambaut A, http://tree.bio.ed.ac.uk/software/ figtree/
44. BEAST: Bayesian evolutionary analysis by sampling trees. Drummond AJ, Rambaut A, BMC Evol Biol 2007 7
45. A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Pagel M, Meade A, Syst Biol 2004 53 571 581 10.1080/10635150490468675 15371247 (Pubitemid 39290200)
46. Phylogeny and classification of the tribe Hydaticini (Coleoptera: Dytiscidae): partition choice for Bayesian analysis with multiple nuclear and mitochondrial protein-coding genes. Miller KB, Bergsten J, Whiting MF, Zool Scr 2009 38 591 615 10.1111/j.1463-6409.2009.00393.x
47. Time-dependent rates of molecular evolution. Ho SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, Cooper A, Mol Ecol 2011 20 3087 3101 10.1111/j.1365-294X.2011.05178.x 21740474
48. TreeStat v1.6.1: tree statistic calculation tool. Rambaut A, Drummond AJ, 2010
49. Evolution of the Arctic-North Atlantic and the Western Tethy. Ziegler PA, Tulsa, OK: American Association of Petroleum Geologists Memoir 1988
50. Turin H, Penev L, Casale A, The Genus Carabus in Europe. A synthesis Sofía-Moscow-Leiden: PENSOFT & European Invertebrate Survey 2003
51. Phylogeny and evolution of Digitulati ground beetles (Coleoptera, Carabidae) inferred from mitochondrial ND5 gene sequences. Su ZH, Imura Y, Okamoto M, Kim CG, Zhou HZ, Paik JC, Osawa S, Mol Phylogenet Evol 2004 30 152 166 10.1016/S1055-7903(03)00163-5 15022766 (Pubitemid 38092526)
52. Mode of morphological differentiation in the Latitarsi-ground beetles (Coleoptera, Carabidae) of the world inferred from a phylogenetic tree of mitochondrial ND5 gene sequences. Su ZH, Imura Y, Zhou HZ, Okamoto M, Osawa S, Genes Genet Syst 2003 78 53 70 10.1266/ggs.78.53 12655138 (Pubitemid 36362534)
53. Slightly deleterious mutant substitutions in evolution. Ohta T, Nature 1973 246 96 98 10.1038/246096a0 4585855
54. Agabus alexandrae sp n. from Morocco, with a molecular phylogeny of the Western Mediterranean species of the A. guttatus group (Coleoptera: Dytiscidae). Ribera I, Hernando C, Aguilera P, Insect Syst Evol 2001 32 253 262 10.1163/187631201X00191 (Pubitemid 33380049)
55. Recent diversification rates in North American tiger beetles estimated from a dated mtDNA phylogenetic tree. Barraclough TG, Vogler AP, Mol Biol Evol 2002 19 1706 1716 10.1093/oxfordjournals.molbev.a003993 12270897
56. Speciation of Iberian diving beetles in Pleistocene refugia (Coleoptera, Dytiscidae). Ribera I, Vogler AP, Mol Ecol 2004 13 179 193 10.1046/j.1365-294X. 2003.02035.x 14653798 (Pubitemid 38106483)
57. Molecular phylogenetics and evolutionary analysis of body shape in the genus Cyrtonus (Coleoptera, Chrysomelidae). Gámez-Zurita J, Garneria I, Petitpierre E, J Zool Syst Evol Res 2007 45 317 328 10.1111/j.1439-0469.2006. 00393.x (Pubitemid 47620468)
58. Ancient associations of aquatic beetles and tank bromeliads in the Neotropical forest canopy. Balke M, Gámez-Zurita J, Ribera I, Viloria A, Zillikens A, Steiner J, Garcia M, Hendrich L, Vogler AP, Proc Nat Acad Sci USA 2008 105 6356 6361 10.1073/pnas.0710368105 18434549 (Pubitemid 351758350)
59. The evolution of unisexuality in Calligrapha leaf beetles: Molecular and ecological insights on multiple origins via interspecific hybridization. Gámez-Zurita J, Funk DJ, Vogler AP, Evolution 2006 60 328 347 16610324 (Pubitemid 44804557)
60. Late Miocene diversification of the genus Hydrochus (Coleoptera, Hydrochidae) in the west Mediterranean area. Hidalgo-Galiana A, Ribera I, Mol Phylogenet Evol 2011 59 377 385 10.1016/j.ympev.2011.01.018 21354316
61. Phylogenetic relationships of Western Mediterranean subterranean Trechini groundbeetles (Coleoptera: Carabidae). Faille A, Casale A, Ribera I, Zool Scr 2011 40 282 295 10.1111/j.1463-6409.2010.00467.x
62. The importance of data partitioning and the utility of bayes factors in Bayesian phylogenetics. Brown JM, Lemmon AR, Syst Biol 2007 56 643 655 10.1080/10635150701546249 17661232
63. Exploring patterns and extent of bias in estimating divergence time from mitochondrial DNA sequence data in a particular lineage: A case study of salamanders (Order Caudata). Zheng Y, Peng R, Kuro-o M, Zeng X, Mol Biol Evol 2011 28 2521 2535 10.1093/molbev/msr072 21422243
64. Cryptic failure of partitioned Bayesian phylogenetic analyses: Lost in the land of long trees. Marshall DC, Syst Biol 2010 59 108 117 10.1093/sysbio/syp080 20525623
65. Mind the gaps: Evidence of bias in estimates of multiple sequence alignments. Golubchik T, Wise MJ, Easteal S, Jermiin LS, Mol Biol Evol 2007 24 2433 2442 10.1093/molbev/msm176 17709332 (Pubitemid 350060444)