taxonomy: Host taxonomy in the MalAvi dataset

In vincenzoaellis/malaviR: An R interface to MalAvi

Description

An object of class data.frame with the unique host species found in the MalAvi dataset (as of 14 September 2017) and their corresponding taxonomic classifications in the Jetz et al. phylogeny available on birdtree.org.

Usage

data("taxonomy")

Format

A data frame with 1415 observations on the following 3 variables.

species

a factor with levels equal to unique host species in the MalAvi dataset

Jetz.species

a factor with levels equal to the corresponding taxonomic classifications in the Jetz et al. dataset

match

a factor with levels no yes

Details

The factor Jetz.species has underscores which correspond to how those names are stored as tip labels in the phylogenies available on birdtree.org.

Two host species in the MalAvi dataset do not have corresponding species in the Jetz et al. phylogeny:

• Anas sp.

• Anthus cinnamomeus

And 27 pairs and 2 triplets of species in the MalAvi dataset are recorded as single species in the Jetz et al. phylogeny:

• Acrocephalus_arundinaceus == Acrocephalus arundinaceus / Acrocephalus orientalis

• Agelastes_niger == Agelastes niger / Phasidus niger

• Andropadus_tephrolaemus == Andropadus tephrolaemus / Arizelocichla tephrolaema

• Aphelocoma_californica == Aphelocoma californica / Aphelocoma woodhouseii

• Arremon_torquatus == Buarremon torquatus / Buarremon basilicus

• Automolus_infuscatus == Automolus infuscatus / Automolus paraensis

• Basileuterus_coronatus == Myiothlypis coronatus / Basileuterus coronatus / Myiothlypis coronata

• Camaroptera_brachyura == Camaroptera brachyura / Camaroptera brevicaudata

• Cyanopica_cyanus == Cyanopica cooki / Cyanopica cyanus

• Ficedula_hypoleuca == Ficedula hypoleuca / Ficedula speculigera

• Hippolais_pallida == Hippolais pallida / Iduna pallida

• Icterus_cayanensis == Icterus cayanensis / Icterus chrysocephalus

• Larus_argentatus == Larus argentatus / Larus mongolicus

• Nectarinia_chloropygia == Cinnyris chloropygius / Nectarinia chloropygia

• Nectarinia_olivacea == Cyanomitra olivacea / Nectarinia olivacea / Cyanomitra obscura

• Nectarinia_oritis == Cyanomitra oritis / Nectarinia oritis

• Nectarinia_senegalensis == Nectarinia senegalensis / Chalcomitra senegalensis

• Nectarinia_venusta == Nectarinia venusta / Cinnyris venustus

• Petroica_australis == Petroica australis / Petroica longipes

• Phaeothlypis_fulvicauda == Basileuterus fulvicauda / Phaeothlypis fulvicauda

• Saxicola_torquatus == Saxicola torquata / Saxicola maura

• Serinus_mozambicus == Serinus mozambicus / Crithagra mozambica

• Sylvia_hortensis == Sylvia hortensis / Sylvia crassirostris

• Thraupis_sayaca == Thraupis sayaca / Tangara sayaca

• Thryothorus_genibarbis == Pheugopedius genibarbis / Thryothorus genibarbis

• Troglodytes_aedon == Troglodytes musculus / Troglodytes aedon

• Zosterops_borbonicus == Zosterops borbonicus / Zosterops mauritianus

• Zosterops_ficedulinus == Zosterops ficedulinus / Zosterops feae

• Zosterops_pallidus == Zosterops capensis / Zosterops virens

References

Bensch S, Hellgren O, and Perez-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. http://mbio-serv2.mbioekol.lu.se/Malavi/

Jetz W, Thomas GH, Joy JB, Hartmann K, and Mooers AO. 2012. The global diversity of birds in space and time. Nature 491: 444-448. http://birdtree.org/

Examples

data(taxonomy)

vincenzoaellis/malaviR documentation built on Oct. 10, 2019, 10:55 p.m.