Published February 15, 2023 | Version v1
Dataset Open

Systematics of the avian family Alaudidae using multilocus and genomic data

  • 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