Systematics of the avian family Alaudidae using multilocus and genomic data

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.