Archive 04/01/2022.

# Standardized Test Sets for evaluating Software/Methods

BrianFoley

A 2010 PLOS publication by Linder et al provides test data sets for phylogenetics and metagenomics.

At the HIV Databses we have gathered and organized several data sets which are useful for comparing analysis methods or developing new methods. The Phylogenetic Handbook contains sample data sets for each chapter along with the tutorials of how to use the phylogenetic software. Neither of these sites were specifically set up for providing test data sets, but they could be useful.

I am sure there are other such sets available, and it would be nice to list some of the better ones here in the PhyloBabble site.

ematsen

This paper:

uses a data set (available on TreeBase) that seems to have become the designated test data set for Bayesian analyses (e.g. Hohna and Drummond, Larget 2013, etc).

BrianFoley

The Lakner paper discusses several data sets, but in TreeBase it is only easy to find one data matrix; that of the wingless gene, 378 bases long. The table 1 in the paper lists several other matrices such as rDNA, internal transcribed spacer (ITS) M767 of 1082 bases, but I don’t see how to download that alignment matrix in TreeBase. Am I missing something here?

BrianFoley

In my opinion, the long and short branch lengths in this tree built from the 398 bases in the wingless matrix, is due to the sequences being too short, rather than true differences in rates of evolution.

ematsen

I believe that there’s been a change in the TreeBASE numbering scheme. Here are I believe the latest numbers, courtesy of @cwhidden:

|  Data | Sp | Nt   | Type of data                           | TreeBASE |
|-------+----+------+----------------------------------------+----------|
|  DS1  | 27 | 1949 | rRNA; 18s                              | M2017    |
|  DS2  | 29 | 2520 | rDNA; 18s                              | M2131    |
|  DS3  | 36 | 1812 | mtDNA; COII (1–678); cytb (679-1812)   | M127     |
|  DS4  | 41 | 1137 | rDNA; 18s                              | M487     |
|  DS5  | 50 | 378  | Nuclear protein coding; wingless       | M2907    |
|  DS6  | 50 | 1133 | rDNA; 18s                              | M220     |
|  DS7  | 59 | 1824 | mtDNA; COII; and cytb                  | M2449    |
|  DS8  | 64 | 1008 | rDNA; 28s                              | M2261    |
|  DS9  | 67 | 955  | Plastid ribosomal protein; s16 (rps16) | M2389    |
|  DS10 | 67 | 1098 | rDNA; 18s                              | M2152    |
|  DS11 | 71 | 1082 | rDNA; internal transcribed spacer      | M2274    |

cwhidden

@ematsen @BrianFoley Yes, those are the new numbers. Note that I followed the data set numbering from Hohna and Drummond (2012). The Lakner et al. paper had one more dataset with 43 taxa as DS5 so DS5-DS11 in this table are DS6-DS12 in Lakner et al.

TreeBASE actually maintains the old IDs in a “description” field but you cannot search this field with the regular search bar. There is an advanced search option with a query language that might work, but I actually matched these up by searching for the number of taxa and characters and then verified with the description field. Dataset 5 from Lakner et al appears to have changed from M932 to M2359.

BrianFoley

I poked around this set a bit more, and I am not sure why it would be considered a good set for testing software. In my opinion, a good test set would have a phylogeny that was known by other criteria, such as the fossil record, morphology (in a type of organism where morphology can be well used to follow evolution), etc. I don’t see this set of insect data being ideal. The insects have shared a common ancestor some 400 million years ago, so even in conserved genes encoded in the nucleus there are many issues with molecular evolution. The butterflies are just a subset of insects and their most recent common ancestor was closer to 280 million years ago.

Many researchers who are using this type of data, with protein-coding genes which have been under hundreds of millions of years of selection pressures, are being careful to use only subsets of the data such as first and second position of each codon, and thus throwing away the sites which contribute more noise and misinformation (due to base composition bias, codon use bias, etc) than true phylogenetic signal.

Surely there must be good data sets which present particular types of problems, such as known shifts in codon use bias (GC:AT ratio has been shown to change rather rapidly as species adapt to high and low temperature environments), or a “long branches attract” problem (human, gorilla, mouse, rat, dozens of carnivors and ungulates), sets where there are well documented changes in rates of evolution between lineages, etc.

Each data set might be appropriate for only a small range of phylogenetic analyses. The set that tests how well a given program can resist the “long branches attract” problem will not be the same set that can test population genetics questions.

rob_lanfear

Weighing in late here. I have been assembling a collection of datasets here:

Happy to take suggestions of new datasets, corrections, suggestions for changes to format etc. (NB: if you have a dataset you’d like on there, send it along. Only requirement is that it’s published and you’re happy to make the dataset open access).

Please don’t email me directly about the collection, instead raise all suggestions/corrections as issues on the repo itself, so that I can keep track:

Cheers,

Rob

BrianFoley

The github repository by Rob Lanfear currently seems to list the data sets by author_year. I only recognize one or two of the authors. It would be very nice if I could find data sets for “mammals”, or “primates” or “vertebrates”. Or maybe find sets with at least 3,000 bases of DNA and not more than 40 taxa.

For purposes of “test driving” various phylogenetic methods to compare one to another, it seems the ideal data set(s) would be one that is backed up by a solid fossil record and/or other data. For example a set of mammal mitochiondrial genomes plus some marsupials for outgroup. Or if that is “too easy” so all methods produce the “correct tree”, maybe something tougher like a few dozen tetrapod mitochondrial genomes with fish for the outgroup.

rob_lanfear

Hi Brian,

There’s a summary.csv file in the repo that will allow you to do what you want, i.e. select datasets based on any attribute or combination of attributes.

Rob

BrianFoley

Nice! The .csv file was very helpful indeed. I found the Kjer2007 complete mitochondrial genomes of mammals, plus marsupial outgroup was exactly what I was looking for. I used the data to illustrate what the use of partitions does for the trees, here.

BrianFoley

Another great data set for your archive:

A molecular phylogeny of living primates. Perelman P, Johnson WE, Roos C, Seuánez HN, Horvath JE, Moreira MA, Kessing B, Pontius J, Roelke M, Rumpler Y, Schneider MP, Silva A, O’Brien SJ, Pecon-Slattery J. PLoS Genet. 2011 Mar;7(3):e1001342. doi: 10.1371/journal.pgen.1001342. Epub 2011 Mar 17. PMID: 21436896

The final, post-GBLOCK, edited, annotated PAUP* nexus alignment of the 54 concatenated genes used for this study is publicly available .

The file is a compressed zip file that can be viewed in either a generic text editor, PAUP*, or alignment programs that read large nexus format files.

My “quick and dirty” neighbor-joing tree from the data:

Transitions and transversions vs F84 distances for the data set:

BrianFoley

The nuclear gene data stands in nice contrast to complete mitochondrial genomes from primates, such as the set from Kistler et al. Mitochondria evolve roughly ten-fold faster than nuclear DNA so the mitochondria are reaching saturation with mutations within the primates.

Also, note the extreme transition:transversion bias in mitochondrial evolution, relative to nuclear genes. The Ts rate is more than 10-fold faster than Tv in the primate mitochondria.

BrianFoley

Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science. 2006 Mar 3;311(5765):1283-7. Erratum in: Science. 2006 May 5;312(5774):697. PubMed PMID: 16513982.

The supplementary information includes the complete data matrix (Amino acid sequences) and a table for converting the taxon names from short numbers (they used the NCBI taxonomy table code for each species) to “Genus species” names. TreeOfLife2006ScienceSupplTreePDF.pdf (17.6 KB)