A database of avian
haemosporidian lineages
Plasmodium, Haemoproteus and Leucocytozoon, organized around lineages of the mitochondrial cytochrome b gene. Every table and the alignment come from the same versioned release.
The release in numbers
Lineages by parasite genus
lineages have no genus recorded and are not counted above.
How widely each genus has been sampled
Host taxa are counted per parasite genus. A host species can carry more than one genus, so these do not sum to the totals above.
Where the records come from
Number of published studies per country, by parasite genus, counting both host records and vector screening. Hover a country for its count.
of the countries in the database are shown. small island territories cannot be resolved at this map scale; they are in the tables, as are the studies reported only from them.
Host records by parasite genus
Data reports · release
Each report is generated from a single release and stays fixed to it, so a report you cite remains available.
Errors in the database?
Tables
Open a table to search it here, or download it whole. These come from release .
Not part of the release, and not versioned with it. Host names are matched against the eBird/Clements taxonomy of , as bundled in clootl for the McTavish et al. 2025 avian phylogeny, by malaviR . The eBird taxonomy is revised every year and this key follows it, so a name here can change while the MalAvi release does not.
Submit your data
MalAvi is built from data contributed by researchers.
The form runs on Google Forms, and it asks you to sign in with a Google account because it accepts file uploads. If you do not have one, or Google is not available where you are, send the template and the PDF to malaviadmin@gmail.com instead. Email is just as welcome as the form.
It is advisable to name new haplotypes and have them added to the MalAvi database, before a manuscript is accepted for publication and sequences submitted to GenBank. This ensures that the same lineage names will appear in the publication, GenBank and the MalAvi database.
Before you publish
Send your new lineage names and their sequences. They are checked, and you are told of any changes — so the same names end up in your paper, in GenBank and in MalAvi. Send the accession numbers once you have deposited.
The new review process for MalAvi is still being perfected; in the short term, processing of submissions will likely take a little longer than usual.
When it is accepted
Send the records: which lineage, in which host, where, and how many were tested. Plus the paper and its supplementary files if you can. A curator adds them, resolves any questions with you by email, and they appear in the next release.
What to send
The paper and its supplementary files are welcome too, and go through the same form. Both are encouraged, but only one is required. They are used only to check the records you submitted: they are shared with the curators as a colleague would share a reprint, are never posted anywhere and are not redistributed.
If your study is not yet published, let us know and we won't put your sequences into the next data release. But we will reserve your sequence names so they don't end up attached to a different sequence later.
The detail, if you want it
Stage 1: naming new lineages
A new lineage is a sequence that differs at one or more positions from the most similar sequence already in MalAvi.
- Names are a 5–6 letter acronym from the scientific name of the first host it was found in, plus a two-digit number: Alcippe poioicephala → ALCPOI02. The name must be unique for the database. Names already taken can be found in the Grand Lineage Summary on the Tables page, or with the name checker below.
- Fill the NewLineages sheet, one representative host species per lineage.
- Fill the Reference sheet. A preliminary title is enough.
- Give the sequences, on the Sequences sheet or as a FASTA file whose names match your proposed names.
- Send us the accession numbers once you have deposited in GenBank.
Please send the sequences themselves whether or not they are in GenBank. Accession numbers alone are not enough.
Stage 2: the records
- Hosts_and_Sites: one row per lineage / host species / site combination.
- Sites: latitude and longitude as degrees and decimal minutes, e.g. 11°28.20000', 076°07.80000'. Decimal degrees are fine too.
- Alt_Lineage_names: if your paper calls an existing MalAvi lineage by a different name. Please fill this in; it avoids substantial work reconciling names during curation.
- MorphoSpecies: if your study links a lineage to a morphologically described species (a new description or an identification). Put the species name here, not in the ParasiteGenus column.
- Vectors: if you screened arthropods.
Filling in the workbook
- Green columns
- Yours to fill.
- Amber columns
- Optional but helpful.
- Red columns
- Not required. These were database index numbers and are now filled in by the curator. The exception is HOST_SPECIES_ID, which you may take from the NCBI taxonomy browser.
- Comment columns
- Use them to specify details that might be of interest, e.g. voucher numbers, mixed infections, etc.
- Reference key
- Use the same string on every sheet, e.g., Gupta et al. 2019.
- Prevalence
- Number found and number tested, where your study reports them. Found must not exceed tested.
- Minimum length
- 470 bp of unambiguous sequence within the 479 bp window. If your sequences are shorter than 470 bp, please email the curators before submitting.
Every header in the workbook carries a note explaining it; you can read it by hovering your mouse over the cell in Excel.
If you only have a paper
Send the PDF and its supplementary tables and tell us what they contain: host-parasite associations, localities, prevalence, vector records. We will do the extraction.
Older papers are also welcome. If you find any older papers that were missed in previous versions of MalAvi, please send them (and the supplementary materials if appropriate) to us either using the form or email.
Check a sequence
One sequence at a time. Paste it plain or with a Fasta header. This tells you whether it is already in MalAvi, which genus it looks like, and whether it is long enough to be named as new. It also runs the quality checks a curator would: how much of the barcode region you have, whether it reads through in frame, and whether any base sits where no other lineage has one. If it does look new, it will help you work out the name.
A curator confirms every new lineage and its name.
Check a name
No sequence needed. Give the host species your new lineage came from and this shows which numbers its acronym has already used — both in the release and in submissions that are still in the queue.
Or give a lineage name to see whether it is already in MalAvi, or claimed by a submission in the queue.
The MalAvi toolkit
Software and reports built around the database.
R packages
Apps
Reports
Where the records come from
Every sampling site with coordinates in the database. Choose a host species, a parasite genus, or both, and the map shows the sites where records match; each point opens to the lineages, studies and prevalence reported there.
The queue
Every submission is reviewed by a curator before anything enters the database. This page shows the current status of submissions. If one has been waiting longer than expected, please contact the curators.
Contributors
Contributors are listed here if they wish to be; indicate this on the submission form.
About MalAvi
A database of avian malaria parasites and related haemosporidians (Plasmodium, Haemoproteus and Leucocytozoon), organized around lineages of the mitochondrial cytochrome b gene.
Avian malaria parasites Plasmodium and related haemosporidians (Haemoproteus and Leucocytozoon) multiply as haploid clones in avian hosts and undergo a sexual phase in dipteran vectors. Understanding their ecology and evolution requires detailed records of their host ranges and geographic distributions. The MalAvi database provides that service.
Please note that a molecular finding of a cytochrome b lineage by PCR is no guarantee that the species is a competent host. This requires microscopic examination of thin blood films confirming presence of gametocytes, or ultimately by controlled infection experiments.
For images of the parasites, see the P. B. Šivickis Laboratory of Parasitology in Vilnius.
Found an error?
Corrections to any record are welcome. Email the curators with the lineage, host or reference concerned.
Know of a study we missed?
Send the paper and its supplementary materials through the data submission form. If you fill out the template, even better. But if you don't have time, we will extract the data from the documents you send.
The Curators
MalAvi is curated by the people below. Curators review incoming data submissions and add data from papers they find; the role is an editorial appointment and is listed here so it can be cited on a CV.
Listing recognizes sustained work, and curators remain listed for as long as they are active.
Curators
With thanks to
Citing MalAvi
Please cite the database paper, and the release you used. Each release is versioned so your analysis stays reproducible.
Bensch S, Hellgren O, Pérez-Tris J (2009). MalAvi: a public database of malaria parasites and related haemosporidians in avian hosts based on mitochondrial cytochrome b lineages. Molecular Ecology Resources 9: 1353–1358.
Known issues in this release
Issues or problems found in the current release are listed here. We will fix issues in later releases.