PHYLAPHID B@se

How to use this website?

We have made this website as easy for you to use as possible and included help bubbles to most functions.

There are lots of features on this website and we hope you’ll enjoy exploring it!

Hereafter we provide some guidance on how you may use it.



1. Looking for information about species?

To search or browse the list of species included in the website, click «

Search on taxa » on the navigation banner.

A search interface as well as the full list of species then appears.

You may then either:

  • Use the interface to search for a species you are interested in (type all or part of its name)
  • Browse the list
  • Once you have found your favourite species, just click on its name to move to its dedicated web page, which contains info about its taxonomy, biology, distribution etc. as well as some pictures.



    2. Looking for information about specimens?

    To search on specimens included in the website, simply click « Search on specimens » on the navigation banner.

    A search interface then appears.

    You can search on specimens using (part of) their collection number, the taxon they belong to or their sampling locality.

    Once your search is completed simply click on the name of the specimen to move to its dedicated webpage, which contains info about its taxonomy, sampling locality (link to Google Earth) etc. as well as some pictures and link to available DNA sequences



    3. Want to access and export data from several specimens?

    First you need to check the box next to the specimens you are interested in (to select all specimens check the box next to the column headers). Then click « List » (just above the column headers), « Add selection to list » and press « OK » in the popup window.

    It is possible to include more specimens to the current list by searching on other criteria, select resulting specimens and again « Add [your new] selection to list »

    Once your list is created click on « List » > « List Management ».

    A window appears on which you can select the information you are interested in, just move the items from the left to the right table by clicking the arrows. Once you are happy with your selection, press « Next ». You can export the data in word or excel format.

    To visualise sampling localities of several specimens on a single map: Select the specimens you are interested (check box) then click « Export data » (above the column headers of the table of results) then « Show Map for Field » and « Geographic coordinates ». A window appears on which you can see a Google Earth map showing the sampling locality of the specimens.



    4. Want to use the molecular identification tool (BLAST / Tree)?

    This tool allows to compare your query sequence to all sequences present in our database (including those that are not yet published). You can perform a BLAST of a query sequence against the pool of reference sequences included in our database. It is also possible to view the query sequence embedded within a phylogenetic tree (distance methods, e.g. Neighbor joining) and check to which sequences of the database it is the most closely related.



    Requirements

    The barcode gene used for PhylAphid@base is a 648 base-pair region in the mitochondrial cytochrome c oxidase 1 gene (“COI”, standard barcode fragment http://www.barcodeoflife.org). To use the identification tool you therefore need to get sequences for the same gene region.

    PCR primers and protocols are available in these two publications:

    Foottit RG, Maw HEL, Von Dohlen CD, Hebert PDN (2008) Species identification of aphids (Insecta: Hemiptera: Aphididae) through DNA barcodes. Molecular Ecology Resources 8, 1189-1201.

    Coeur d’acier A., Cruaud A., Robert V., Artige E., Genson G., Pierre E., Simon J-C., Jousselin E., Rasplus J-Y.(accepted) DNA barcoding and associate PhylAphidB@se website for the identification of European Aphids (Insecta: Hemiptera: Aphididae), PLOS ONE.

    Of course the longer and cleaner is the sequence, the more accurate the identification will be!



    Perform identification (BLAST / tree)

    Click « BLAST» on the navigation banner

    Paste your query sequence in the dedicated box

    Change BLAST parameters if needed (though default parameters must be adequate)

    Read the disclaimer… and check the box if you agree

    Then, Start the alignment

    Results are sorted by BLAST hits (best BLAST scores), i.e sequences included in the database that are the most similar (Similarity%) over a certain length of coverage (Overlap%) to your query sequences are on top.

    You can click on any specimen of the hit table to reach its specific webpage and then get further information on the species it belongs to.

    You can export the BLAST hits table is you whish to either excel of word files.

    Some details regarding BLAST algorithm: Using specific scoring matrices (derived from the pairwise sequence alignment parameters), the BLAST algorithm calculates similarity scores for local alignments (i.e. the most similar regions of the sequences) between your query sequence and sequences that are included in the database. The algorithm then returns a table which shows the best hits (matches) from the database sorted by BLAST Score. This table includes other information including e.g. the query coverage (percentage of the query sequence that overlaps the reference sequence), and the percentage of similarity between the query and reference sequences over the length of the coverage area.

    For further information you may have a look to the NCBI Handbook



    It is also possible to view the query sequence embedded within a phylogenetic tree (distance methods, e.g. Neighbor joining) and check to which sequences of the database the query is the most closely related.

    To do so, click Draw Tree (above the BLAST hits table) and choose the method you want to use. On the resulting tree, your query sequence is labelled as « My Data ». Here again, you can click on any specimen of the tree to be redirected to its specific webpage.



    Interpret results.

    Be careful when interpreting the results. A high percentage of similarity over a long alignment length does not necessarily means your query sequence belongs to the same species as the specimen from which the reference sequence has been obtained. Some cases of mitochondrial introgression have been reported in certain groups; some species are in fact species complexes, which are difficult to distinguish genetically.

    This is why, in many cases, we provided sequences of other gene fragments to allow a more accurate identification.

    In the case of aphids, intra-specific divergence is generally very low (close to 0) and inter-specific divergences are much higher.

    We recommend considering identification as valid only if the percentage of similarity (Similarity%) is equal or higher than 99% and the percentage of overlap (Overlap%) reaches at least 90%.

    Numerous species groups are known in aphids. These groups are morphologically and genetically very close, though they are biologically well characterized. BLAST may be non-informative in those cases. Indeed, BLAST of your query sequence may result in high and similar scores with specimens belonging to different species (all belonging to the same species group). If you have some data about host plants it could be possible to refine the results of the identification. Anyway, if you obtain such a result, we highly recommend to read the webpage dedicated to the species to get more information on them and have a look to the companion paper of this website:

    Coeur d’acier A., Cruaud A., Robert V. Artige E., Genson G., Pierre E., SimonJ-C., Jousselin E., Rasplus J-Y.(accepted) DNA barcoding and associate PhylAphidB@se website for the identification of European Aphids (Insecta: Hemiptera: Aphididae), PLOS ONE.