 |
|
This section presents information related to the DNA component of our studies. We have listed here some bee DNA sequences from recent publications for public download. |
|
|
|
The purpose of making our DNA sequences freely available here, is to better enable researchers to: |
|
|
|
(i) |
incorporate our data with theirs for comparative analyses (e.g. dating analyses); |
|
(ii) |
re-analyse our data using different approaches (e.g. ML versus BI, varying levels of partitioning/parameterization, etc.); |
|
(iii) |
explore patterns in our data sets that have not been explored or anticipated by us (e.g. evolution of base composition bias - there appear to be some patterns here). |
|
|
|
|
| FILE NAME |
FILE TYPE |
PUBLICATION |
 |
|
 |
|
fuller et al 2005 |
.nex |
.sit |
... |
FULLER, S, Tierney, SM, & Schwarz, MP. (2005) Phylogenetics of the allodapine bee genus Braunsapis: implications for across sea dispersal of bees. Journal of Biogeography 32(12):2135 |
schwarz et al 2006 |
.nex |
.sit |
... |
SCHWARZ, MP, Fuller, S, Tierney, SM, & Cooper, SJB. (2006) Molecular phylogenetics of the exoneurine allodapine bees reveal an ancient and puzzling dispersal from Africa to Australia. Systematic Biology 55(1):31-45 |
|
|
 |
|
 |
|
|
|
|
.nex files |
NEXUS format
Excecutable in PAUP*
Exportable to MrBayes, MacClade, Mesquite, and others. |
|
|
.sit files |
StuffIt 5.0 format via Mac Classic
Should preserve line break definitions which can otherwise become corrupted, making execution problematic under some platforms, (then requiring careful use of a text editor). |
|
|
|
|
|
|
All our DNA sequence files have been written and manipulated using Mac Classic or MacOSX. If you have any problems accessing these files, contact MPS or trevl (the web author). |
|
|
|
| GENE / CODON POSITION DESIGNATION |
|
|
Genes and codon positions are indicated using nexus commands after the data matrix. |
|
|
|
All sequences in our publications are available from GenBank, and accession numbers are available from our publications. However, the sequences here are easier to use since they are already aligned and are in taxon blocks with nexus run commands. You can save yourself a lot of time by using our aligned sequences rather than those from GenBank. HOWEVER, GenBank remains the definitive source for sequence data. Over time, our sequences here will have accession numbers added to them so that if you use them, it will be easy to refer to them via GenBank numbers whilst still making use of our easily executable files. |
|
|
|
| ARRANGEMENT / CONTENT OF FILES |
|
|
At present we are providing sequence files according to our publications. For example, we provide the original nexus files used in Schwarz et al. (2006) (see publications list in our web pages) and other recent publications. Sequence files are therefore arranged under publication titles and years. Over time, we will provide more comprehensive files arranged according to taxa (families, tribes, genera). |
|
|
|
Files are provided in the format used for our published analyses. For different papers, the accompanying files may or may not include introns or may have slightly different start/stop positions. When included in PAUP files introns have been bracketed out with [...]. Over time we will rectify this so that all files have equivalent formats so they can be mixed and matched into any one analysis without any need for editing. |
|
|
|
|
|
|
|
