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 <em>Systematics of the avian family Alaudidae using multilocus and genomic data</em> 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. <strong>VCF_name</strong> <strong>Taxon</strong> <strong>ID</strong> 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: <strong>VCF_name</strong> <strong>Taxon</strong> <strong>ID</strong> 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.