Published February 15, 2023
| Version v1
Dataset
Open
Systematics of the avian family Alaudidae using multilocus and genomic data
Creators
- 1. Uppsala University
- 2. Golestan University
- 3. University of California Santa Cruz
- 4. Swedish Museum of Natural History
- 5. University of Limpopo
- 6. Centre for Functional and Evolutionary Ecology
- 7. Troy University
- 8. University of Groningen
- 9. University of Gothenburg
- 10. Birdlife International
- 11. Natural History Museum
Description
SNP datasets (gzipped VCF files) and tree output (newick-formatted trees in .trees files) associated with the publication Systematics of the avian family Alaudidae using multilocus and genomic data by Alström et al. (2023).
In the VCF files, samples have intermediary sequence names. Below is a key (sorted per name in VCF file) to taxon and ID. Further information can be found in Dataset SM1 in the original publication.
VCF_name | Taxon | ID |
A_hamertoni_hamertoni_1982_3_71 | Alaemon hamertoni hamertoni | NHMUK 1982.3.71 |
A_hamertoni_tertia_1982_3_12 | Alaemon hamertoni tertia | NHMUK 1982.3.12 |
A_phoenicura_1949_25_4559 | Ammomanes phoenicura | NHMUK 1949.25.4559 |
Ala_alaudipes | Alaemon alaudipes alaudipes | DZUG U5653 |
Alauda_arvensis_KZ | Alauda arvensis dulcivox | DZUG U0587 |
Alaudala_seebohmi | Alaudala cheleensis seebohmi | DZUG U5316 |
AmmocincU4892_S121 | Ammomanes cinctura | DZUG U4892 |
AmmodesU5745_S28 | Ammomanes deserti | DZUG U5745 |
AmmodesU5748_S106 | Galerida cristata magna | DZUG U5748 |
C_duponti_margaritae_1952_51_107 | Chersophilus duponti margaritae | NHMUK 1952.51.107 |
Cal_brachydactyla | Calandrella brachydactyla rubiginosa | DZUG U5655 |
CalbarlU5662_S32 | Calendulauda erythroclamys patae | DZUG U5662 |
CalsabotaU2344_S33 | Calendulauda sabota suffusca | DZUG U2344 |
CheralboU5652_S52 | Chersomanes albofasciata | DZUG U5652 |
E_leucotis_BMNH_1952.25.36 | Eremopterix leucotis | NHMUK 1952.25.36 |
ErealpeU4610_S144 | Eremophila alpestris brandti | DZUG U4610 |
Eremalauda_dunni | Eremalauda eremodites | DZUG U4578 |
Eremopterix_hova_FMNH449163 | Eremopterix hova | FMNH 449163 |
G_deva_1949_whi_1_8153 | Galerida deva | NHMUK 1949.whi.1.8153 |
G_malabarica_1949_whi_1_7738 | Galerida malabarica | NHMUK 1949.whi.1.7738 |
HetarchU2811_S34 | Heteromirafra archeri ("sidamoensis") | DZUG U2811 |
Heteromirafra_ruddi | Heteromirafra ruddi | DZUG U5661 |
Lullula_arborea_U544 | Lullula arborea | UWBM 64680 |
M_a_africana_BMNH_1927.5.26.5 | Corypha [Mirafra] africana africana | NHMUK 1927.5.26.5 |
M_africana_athi_1951_13_2495 | Corypha [Mirafra] africana athi | NHMUK 1951.13.2495 |
M_africana_athi_1968_48_2 | Corypha [Mirafra] africana athi | NHMUK 1968.48.2 |
M_albicauda_1916_12_1_840 | Mirafra albicauda | NHMUK 1916.12.1.840 |
M_ashi_1982_3_4 | Corypha [Mirafra] ashi | NHMUK 1982.3.4 |
M_collaris_BMNH_1923.8.7.2633 | Amirafra [Mirafra] collaris | NHMUK 1923.8.7.2633 |
M_collaris_BMNH_1923.8.7.2634 | Amirafra [Mirafra] collaris | NHMUK 1923.8.7.2634 |
M_cordofanica_1932_8_6_261 | Mirafra cordofanica | NHMUK 1932.8.6.261 |
M_cordofanica_1932_8_6_262 | Mirafra cordofanica | NHMUK 1932.8.6.262 |
M_gilletti_1982_3_10 | Calendulauda [Mirafra] gilletti arorihensis | NHMUK 1982.3.10 |
M_gilletti_1982_3_9 | Calendulauda [Mirafra] gilletti degodiensis | NHMUK 1982.3.9 |
M_hypermetra_BMNH_1912.12.23.317 | Corypha [Mirafra] hypermetra hypermetra | NHMUK 1912.12.23.317 |
M_rufa_lynesi_1922_12_8_1553 | Calendulauda [Mirafra] rufa rufa | NHMUK 1922.12.8.1553 |
M_rufa_nigriticola_1932_8_6_253 | Calendulauda [Mirafra] rufa nigriticola | NHMUK 1932.8.6.253 |
M_somalica_somalica_1919_10_6_27 | Corypha [Mirafra] somalica somalica | NHMUK 1919.10.6.27 |
MelcalaU0583_S124 | Melanocorypha calandra psammochroa | DZUG U0583 |
MelyeltU0580_S35 | Melanocorypha yeltoniensis | DZUG U0580 |
Mirafra_alb_ZMB_2000.9488 | Mirafra albicauda | ZMB 2000.9488 |
Mirafra_albi_ZMB_49.225 | Mirafra albicauda | ZMB 49.225 (holotype) |
Mirafra_degodiensis | Calendulauda [Mirafra] gilletti degodiensis | DZUG U2808 |
Mirafra_rufocinnamomea_U5657 | Amirafra [Mirafra] rufocinnamomea fischeri | FMNH 484672 (= DZUG U5657) |
MirchenU5660_S37 | Mirafra cheniana | DZUG U5660 |
MirchenU5759_S36 | Mirafra cheniana | DZUG U5759 |
MirfascU5758_S60 | Corypha [Mirafra] fasciolata | DZUG U5758 |
Panurus | Panurus biarmicus | 1ET92164|SAMN13107499 |
Ramphocoris | Ramphocoris clotbey | CEFE Rhcl1 (= DZUG U5651) |
Spizocorys_fringillaris_U5659 | Spizocorys fringillaris | DZUG U5659 |
Spizocorys_obbiensis_1908_5_28_104 | Spizocorys obbiensis | NHMUK 1908.5.28.104 |
For convenience, the same data sorted per taxon:
VCF_name | Taxon | ID |
Ala_alaudipes | Alaemon alaudipes alaudipes | DZUG U5653 |
A_hamertoni_hamertoni_1982_3_71 | Alaemon hamertoni hamertoni | NHMUK 1982.3.71 |
A_hamertoni_tertia_1982_3_12 | Alaemon hamertoni tertia | NHMUK 1982.3.12 |
Alauda_arvensis_KZ | Alauda arvensis dulcivox | DZUG U0587 |
Alaudala_seebohmi | Alaudala cheleensis seebohmi | DZUG U5316 |
M_collaris_BMNH_1923.8.7.2633 | Amirafra [Mirafra] collaris | NHMUK 1923.8.7.2633 |
M_collaris_BMNH_1923.8.7.2634 | Amirafra [Mirafra] collaris | NHMUK 1923.8.7.2634 |
Mirafra_rufocinnamomea_U5657 | Amirafra [Mirafra] rufocinnamomea fischeri | FMNH 484672 (= DZUG U5657) |
AmmocincU4892_S121 | Ammomanes cinctura | DZUG U4892 |
AmmodesU5745_S28 | Ammomanes deserti | DZUG U5745 |
A_phoenicura_1949_25_4559 | Ammomanes phoenicura | NHMUK 1949.25.4559 |
Cal_brachydactyla | Calandrella brachydactyla rubiginosa | DZUG U5655 |
M_gilletti_1982_3_10 | Calendulauda [Mirafra] gilletti arorihensis | NHMUK 1982.3.10 |
M_gilletti_1982_3_9 | Calendulauda [Mirafra] gilletti degodiensis | NHMUK 1982.3.9 |
Mirafra_degodiensis | Calendulauda [Mirafra] gilletti degodiensis | DZUG U2808 |
M_rufa_nigriticola_1932_8_6_253 | Calendulauda [Mirafra] rufa nigriticola | NHMUK 1932.8.6.253 |
M_rufa_lynesi_1922_12_8_1553 | Calendulauda [Mirafra] rufa rufa | NHMUK 1922.12.8.1553 |
CalbarlU5662_S32 | Calendulauda erythroclamys patae | DZUG U5662 |
CalsabotaU2344_S33 | Calendulauda sabota suffusca | DZUG U2344 |
CheralboU5652_S52 | Chersomanes albofasciata | DZUG U5652 |
C_duponti_margaritae_1952_51_107 | Chersophilus duponti margaritae | NHMUK 1952.51.107 |
M_a_africana_BMNH_1927.5.26.5 | Corypha [Mirafra] africana africana | NHMUK 1927.5.26.5 |
M_africana_athi_1951_13_2495 | Corypha [Mirafra] africana athi | NHMUK 1951.13.2495 |
M_africana_athi_1968_48_2 | Corypha [Mirafra] africana athi | NHMUK 1968.48.2 |
M_ashi_1982_3_4 | Corypha [Mirafra] ashi | NHMUK 1982.3.4 |
MirfascU5758_S60 | Corypha [Mirafra] fasciolata | DZUG U5758 |
M_hypermetra_BMNH_1912.12.23.317 | Corypha [Mirafra] hypermetra hypermetra | NHMUK 1912.12.23.317 |
M_somalica_somalica_1919_10_6_27 | Corypha [Mirafra] somalica somalica | NHMUK 1919.10.6.27 |
Eremalauda_dunni | Eremalauda eremodites | DZUG U4578 |
ErealpeU4610_S144 | Eremophila alpestris brandti | DZUG U4610 |
Eremopterix_hova_FMNH449163 | Eremopterix hova | FMNH 449163 |
E_leucotis_BMNH_1952.25.36 | Eremopterix leucotis | NHMUK 1952.25.36 |
AmmodesU5748_S106 | Galerida cristata magna | DZUG U5748 |
G_deva_1949_whi_1_8153 | Galerida deva | NHMUK 1949.whi.1.8153 |
G_malabarica_1949_whi_1_7738 | Galerida malabarica | NHMUK 1949.whi.1.7738 |
HetarchU2811_S34 | Heteromirafra archeri ("sidamoensis") | DZUG U2811 |
Heteromirafra_ruddi | Heteromirafra ruddi | DZUG U5661 |
Lullula_arborea_U544 | Lullula arborea | UWBM 64680 |
MelcalaU0583_S124 | Melanocorypha calandra psammochroa | DZUG U0583 |
MelyeltU0580_S35 | Melanocorypha yeltoniensis | DZUG U0580 |
M_albicauda_1916_12_1_840 | Mirafra albicauda | NHMUK 1916.12.1.840 |
Mirafra_alb_ZMB_2000.9488 | Mirafra albicauda | ZMB 2000.9488 |
Mirafra_albi_ZMB_49.225 | Mirafra albicauda | ZMB 49.225 (holotype) |
MirchenU5660_S37 | Mirafra cheniana | DZUG U5660 |
MirchenU5759_S36 | Mirafra cheniana | DZUG U5759 |
M_cordofanica_1932_8_6_261 | Mirafra cordofanica | NHMUK 1932.8.6.261 |
M_cordofanica_1932_8_6_262 | Mirafra cordofanica | NHMUK 1932.8.6.262 |
Panurus | Panurus biarmicus | 1ET92164|SAMN13107499 |
Ramphocoris | Ramphocoris clotbey | CEFE Rhcl1 (= DZUG U5651) |
Spizocorys_fringillaris_U5659 | Spizocorys fringillaris | DZUG U5659 |
Spizocorys_obbiensis_1908_5_28_104 | Spizocorys obbiensis | NHMUK 1908.5.28.104 |
Questions can be directed to the corresponding authors.
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Additional details
Funding
- UK Research and Innovation
- UK Crop Diversity Bioinformatics Resource BB/S019669/1