Ecological Archives E095-240-A1

Jonathan P. Benstead, James M. Hood, Nathan V. Whelan, Michael R. Kendrick, Daniel Nelson, Amanda F. Hanninen, and Lee M. Demi. 2014. Coupling of dietary phosphorus and growth across diverse fish taxa: a meta-analysis of experimental aquaculture studies. Ecology 95:27682777. http://dx.doi.org/10.1890/13-1859.1

Appendix A. A description of the methods used to construct the phylogeny of fish species included in the meta-analysis and a plot of the resulting time-calibrated phylogeny.

Methods

We inferred a Bayesian time-calibrated phylogeny with all taxa in the analysis and additional species to increase phylogenetic robustness using the Cytochrome b (CytB) and Cytochrome coxidase I (COI) mitochondrial genes and an uncorrelated relaxed-clock model in the program BEAST 1.7.4 (Drummond et al. 2012). Gene sequences for each species analyzed were retrieved from GenBank (see Table A1 below). Partition Finder v1.0 (Lanfear et al. 2012) was used for model testing and to determine the partitioning scheme most appropriate for the data. Both genes were partitioned by codon position, and the GTR+Γ model was used for each partition except for the second COI position, where the HKY+Γ model was used. The starting tree used in the BEAST analysis was the majority rule consensus tree inferred from MrBayes 3.1.2 (Huelsenbeck and Ronquist 2001) using an identical partitioning scheme and two independent runs with 8 chains each. Node age calibration points of 200mya for Acipenser baerii (Grande and Bemis 1991) and 75mya for Salmonidae (Steinke et al. 2006) were defined with exponential priors. MCMC mixing and convergence was assessed with Tracer (Rambaut and Drummond 2007). The maximum clade credibility tree of three independent BEAST runs of 100,000,000 generations was used as the final phylogeny.

 

Literature cited

Drummond, A. J., M. A. Suchard, D. Xie, and A. Rambaut. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution 29:1969–1973.

Grande, L., and W. E. Bemis. 1991. Osteology and phylogenetic relationships of fossil and recent paddlefishes (Polydontidae) with comments on the interrelationships of Acipenseriformes. Journal of Vertebrate Paleontology 11:1–121.

Huelsenbeck, J. P., and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755.

Lanfear, R., B. Calcott, S. Y. W. Ho, and S. Guindon. 2012. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution 29:1695–1701.

Rambaut, A., and A. J. Drummond. 2007. Tracer v1.4. Available from http://beast.bio.ed.ac.uk/Tracer.

Steinke, D., W. Salzburger, and A. Meyer. 2006. Novel relationships among ten fish model species revealed based on a phylogenomic analysis using ESTs. Journal of Molecular Evolution 62:772–784.

 

Table A1. GenBank accession numbers for sequences used to construct the phylogeny for species included in the meta-analysis. E. calabaricus was used as the outgroup.

Species

COI Accession

CytB Accession

Acanthopagrus schlegelii

GU207325

GU131150

Acipenser baerii

FJ205563

JQ045341

Bidyanus bidyanus

EF609298

JQ769386

Catla catla

GU195054

JQ08787

Chanos chanos

EU752072

AY504825

Cichlasoma urophthalmus

EU751764

AY843427

Clarias gariepinus

JQ623925

AF475153

Coregonus lavaretus

AB034824

NC002646

Ctenopharyngodon idella

JN673561

HM237992

Cyprinus carpio

JN673560

HQ443697

Dicentrarchus labrax

JQ623929

EU492154

Epinephelus coioides

JN021298

JN980696

Epinephelus malabaricus

DQ107871

HQ141375

Erpetoichthys calabaricus

AY442348

AY442348

Heterobranchus bidorsalis

-

AF126825

Ictalurus punctatus

JN026912

AY184254

Larimichthys crocea

FJ595214

EU346930

Lateolabrax japonicus

NC018045

NC018045

Lates calcarifer

-

NC007439

Liza haematocheila

JQ343910

JQ060220

Melanogrammus aeglefinus

EU752122

DQ174055

Morone saxatilis

JN027262

AF240746

Myxocyprinus asiaticus

AY526869

AF036176

Nibea albifora

HQ890947

NC015205

Oncorhynchus keta

FJ998790

FJ435616

Oncorhynchus mykiss

NC001717

NC001717

Oreochromis aureus

DQ856611

GU477630

Oreochromis mossambicus

AY597335

DQ274052

Oreochromis niloticus

NC013663

GU477628

Paralichthys olivaceus

JF952803

NC00238

Pargus major

AP002949

GU131149

Pseudobagrus fulvidraco

HM641815

AY744502

Puntius tetrazona

JF915651

NC010110

Salmo salar

HM007799

FJ435618

Sebastes schlegelii

HM180869

DQ678481

Seriola quinqueradiata

NC016868

AB263290

Sparus aurata

JQ623999

DQ198005

 

FigA1

Fig. A1. Time-calibrated phylogeny inferred with BEAST. Time scale is in millions of years. Values before nodes are Bayesian posterior probabilities.


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