Systematics of the avian family Alaudidae using multilocus and genomic data
<p>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).</p> <p>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.</p> <table> <tbody> <tr> <td><strong>VCF_name</strong></td> <td><strong>Taxon</strong></td> <td><strong>ID</strong></td> </tr> <tr> <td>A_hamertoni_hamertoni_1982_3_71</td> <td>Alaemon hamertoni hamertoni</td> <td>NHMUK 1982.3.71</td> </tr> <tr> <td>A_hamertoni_tertia_1982_3_12</td> <td>Alaemon hamertoni tertia</td> <td>NHMUK 1982.3.12</td> </tr> <tr> <td>A_phoenicura_1949_25_4559</td> <td>Ammomanes phoenicura</td> <td>NHMUK 1949.25.4559</td> </tr> <tr> <td>Ala_alaudipes</td> <td>Alaemon alaudipes alaudipes</td> <td>DZUG U5653 </td> </tr> <tr> <td>Alauda_arvensis_KZ</td> <td>Alauda arvensis dulcivox</td> <td>DZUG U0587 </td> </tr> <tr> <td>Alaudala_seebohmi</td> <td>Alaudala cheleensis seebohmi</td> <td>DZUG U5316</td> </tr> <tr> <td>AmmocincU4892_S121</td> <td>Ammomanes cinctura</td> <td>DZUG U4892</td> </tr> <tr> <td>AmmodesU5745_S28</td> <td>Ammomanes deserti</td> <td>DZUG U5745</td> </tr> <tr> <td>AmmodesU5748_S106</td> <td>Galerida cristata magna</td> <td>DZUG U5748</td> </tr> <tr> <td>C_duponti_margaritae_1952_51_107</td> <td>Chersophilus duponti margaritae</td> <td>NHMUK 1952.51.107</td> </tr> <tr> <td>Cal_brachydactyla</td> <td>Calandrella brachydactyla rubiginosa</td> <td>DZUG U5655</td> </tr> <tr> <td>CalbarlU5662_S32</td> <td>Calendulauda erythroclamys patae</td> <td>DZUG U5662</td> </tr> <tr> <td>CalsabotaU2344_S33</td> <td>Calendulauda sabota suffusca</td> <td>DZUG U2344</td> </tr> <tr> <td>CheralboU5652_S52</td> <td>Chersomanes albofasciata</td> <td>DZUG U5652</td> </tr> <tr> <td>E_leucotis_BMNH_1952.25.36</td> <td>Eremopterix leucotis</td> <td>NHMUK 1952.25.36</td> </tr> <tr> <td>ErealpeU4610_S144</td> <td>Eremophila alpestris brandti</td> <td>DZUG U4610</td> </tr> <tr> <td>Eremalauda_dunni</td> <td>Eremalauda eremodites</td> <td>DZUG U4578</td> </tr> <tr> <td>Eremopterix_hova_FMNH449163</td> <td>Eremopterix hova</td> <td>FMNH 449163</td> </tr> <tr> <td>G_deva_1949_whi_1_8153</td> <td>Galerida deva</td> <td>NHMUK 1949.whi.1.8153</td> </tr> <tr> <td>G_malabarica_1949_whi_1_7738</td> <td>Galerida malabarica</td> <td>NHMUK 1949.whi.1.7738</td> </tr> <tr> <td>HetarchU2811_S34</td> <td>Heteromirafra archeri ("sidamoensis")</td> <td>DZUG U2811</td> </tr> <tr> <td>Heteromirafra_ruddi</td> <td>Heteromirafra ruddi</td> <td>DZUG U5661 </td> </tr> <tr> <td>Lullula_arborea_U544</td> <td>Lullula arborea</td> <td>UWBM 64680 </td> </tr> <tr> <td>M_a_africana_BMNH_1927.5.26.5</td> <td>Corypha [Mirafra] africana africana</td> <td>NHMUK 1927.5.26.5</td> </tr> <tr> <td>M_africana_athi_1951_13_2495</td> <td>Corypha [Mirafra] africana athi</td> <td>NHMUK 1951.13.2495</td> </tr> <tr> <td>M_africana_athi_1968_48_2</td> <td>Corypha [Mirafra] africana athi</td> <td>NHMUK 1968.48.2</td> </tr> <tr> <td>M_albicauda_1916_12_1_840</td> <td>Mirafra albicauda </td> <td>NHMUK 1916.12.1.840</td> </tr> <tr> <td>M_ashi_1982_3_4</td> <td>Corypha [Mirafra] ashi</td> <td>NHMUK 1982.3.4</td> </tr> <tr> <td>M_collaris_BMNH_1923.8.7.2633</td> <td>Amirafra [Mirafra] collaris</td> <td>NHMUK 1923.8.7.2633</td> </tr> <tr> <td>M_collaris_BMNH_1923.8.7.2634</td> <td>Amirafra [Mirafra] collaris</td> <td>NHMUK 1923.8.7.2634</td> </tr> <tr> <td>M_cordofanica_1932_8_6_261</td> <td>Mirafra cordofanica</td> <td>NHMUK 1932.8.6.261</td> </tr> <tr> <td>M_cordofanica_1932_8_6_262</td> <td>Mirafra cordofanica</td> <td>NHMUK 1932.8.6.262</td> </tr> <tr> <td>M_gilletti_1982_3_10</td> <td>Calendulauda [Mirafra] gilletti arorihensis</td> <td>NHMUK 1982.3.10</td> </tr> <tr> <td>M_gilletti_1982_3_9</td> <td>Calendulauda [Mirafra] gilletti degodiensis</td> <td>NHMUK 1982.3.9</td> </tr> <tr> <td>M_hypermetra_BMNH_1912.12.23.317</td> <td>Corypha [Mirafra] hypermetra hypermetra</td> <td>NHMUK 1912.12.23.317</td> </tr> <tr> <td>M_rufa_lynesi_1922_12_8_1553</td> <td>Calendulauda [Mirafra] rufa rufa </td> <td>NHMUK 1922.12.8.1553</td> </tr> <tr> <td>M_rufa_nigriticola_1932_8_6_253</td> <td>Calendulauda [Mirafra] rufa nigriticola</td> <td>NHMUK 1932.8.6.253</td> </tr> <tr> <td>M_somalica_somalica_1919_10_6_27</td> <td>Corypha [Mirafra] somalica somalica</td> <td>NHMUK 1919.10.6.27</td> </tr> <tr> <td>MelcalaU0583_S124</td> <td>Melanocorypha calandra psammochroa</td> <td>DZUG U0583</td> </tr> <tr> <td>MelyeltU0580_S35</td> <td>Melanocorypha yeltoniensis</td> <td>DZUG U0580</td> </tr> <tr> <td>Mirafra_alb_ZMB_2000.9488</td> <td>Mirafra albicauda </td> <td>ZMB 2000.9488</td> </tr> <tr> <td>Mirafra_albi_ZMB_49.225</td> <td>Mirafra albicauda </td> <td>ZMB 49.225 (holotype)</td> </tr> <tr> <td>Mirafra_degodiensis</td> <td>Calendulauda [Mirafra] gilletti degodiensis</td> <td>DZUG U2808</td> </tr> <tr> <td>Mirafra_rufocinnamomea_U5657</td> <td>Amirafra [Mirafra] rufocinnamomea fischeri</td> <td>FMNH 484672 (= DZUG U5657)</td> </tr> <tr> <td>MirchenU5660_S37</td> <td>Mirafra cheniana</td> <td>DZUG U5660</td> </tr> <tr> <td>MirchenU5759_S36</td> <td>Mirafra cheniana</td> <td>DZUG U5759</td> </tr> <tr> <td>MirfascU5758_S60</td> <td>Corypha [Mirafra] fasciolata</td> <td>DZUG U5758 </td> </tr> <tr> <td>Panurus</td> <td>Panurus biarmicus</td> <td>1ET92164|SAMN13107499</td> </tr> <tr> <td>Ramphocoris</td> <td>Ramphocoris clotbey</td> <td>CEFE Rhcl1 (= DZUG U5651)</td> </tr> <tr> <td>Spizocorys_fringillaris_U5659</td> <td>Spizocorys fringillaris</td> <td>DZUG U5659</td> </tr> <tr> <td>Spizocorys_obbiensis_1908_5_28_104</td> <td>Spizocorys obbiensis</td> <td>NHMUK 1908.5.28.104</td> </tr> </tbody> </table> <p> </p> <p>For convenience, the same data sorted per taxon:</p> <table> <tbody> <tr> <td><strong>VCF_name</strong></td> <td><strong>Taxon</strong></td> <td><strong>ID</strong></td> </tr> <tr> <td>Ala_alaudipes</td> <td>Alaemon alaudipes alaudipes</td> <td>DZUG U5653 </td> </tr> <tr> <td>A_hamertoni_hamertoni_1982_3_71</td> <td>Alaemon hamertoni hamertoni</td> <td>NHMUK 1982.3.71</td> </tr> <tr> <td>A_hamertoni_tertia_1982_3_12</td> <td>Alaemon hamertoni tertia</td> <td>NHMUK 1982.3.12</td> </tr> <tr> <td>Alauda_arvensis_KZ</td> <td>Alauda arvensis dulcivox</td> <td>DZUG U0587 </td> </tr> <tr> <td>Alaudala_seebohmi</td> <td>Alaudala cheleensis seebohmi</td> <td>DZUG U5316</td> </tr> <tr> <td>M_collaris_BMNH_1923.8.7.2633</td> <td>Amirafra [Mirafra] collaris</td> <td>NHMUK 1923.8.7.2633</td> </tr> <tr> <td>M_collaris_BMNH_1923.8.7.2634</td> <td>Amirafra [Mirafra] collaris</td> <td>NHMUK 1923.8.7.2634</td> </tr> <tr> <td>Mirafra_rufocinnamomea_U5657</td> <td>Amirafra [Mirafra] rufocinnamomea fischeri</td> <td>FMNH 484672 (= DZUG U5657)</td> </tr> <tr> <td>AmmocincU4892_S121</td> <td>Ammomanes cinctura</td> <td>DZUG U4892</td> </tr> <tr> <td>AmmodesU5745_S28</td> <td>Ammomanes deserti</td> <td>DZUG U5745</td> </tr> <tr> <td>A_phoenicura_1949_25_4559</td> <td>Ammomanes phoenicura</td> <td>NHMUK 1949.25.4559</td> </tr> <tr> <td>Cal_brachydactyla</td> <td>Calandrella brachydactyla rubiginosa</td> <td>DZUG U5655</td> </tr> <tr> <td>M_gilletti_1982_3_10</td> <td>Calendulauda [Mirafra] gilletti arorihensis</td> <td>NHMUK 1982.3.10</td> </tr> <tr> <td>M_gilletti_1982_3_9</td> <td>Calendulauda [Mirafra] gilletti degodiensis</td> <td>NHMUK 1982.3.9</td> </tr> <tr> <td>Mirafra_degodiensis</td> <td>Calendulauda [Mirafra] gilletti degodiensis</td> <td>DZUG U2808</td> </tr> <tr> <td>M_rufa_nigriticola_1932_8_6_253</td> <td>Calendulauda [Mirafra] rufa nigriticola</td> <td>NHMUK 1932.8.6.253</td> </tr> <tr> <td>M_rufa_lynesi_1922_12_8_1553</td> <td>Calendulauda [Mirafra] rufa rufa </td> <td>NHMUK 1922.12.8.1553</td> </tr> <tr> <td>CalbarlU5662_S32</td> <td>Calendulauda erythroclamys patae</td> <td>DZUG U5662</td> </tr> <tr> <td>CalsabotaU2344_S33</td> <td>Calendulauda sabota suffusca</td> <td>DZUG U2344</td> </tr> <tr> <td>CheralboU5652_S52</td> <td>Chersomanes albofasciata</td> <td>DZUG U5652</td> </tr> <tr> <td>C_duponti_margaritae_1952_51_107</td> <td>Chersophilus duponti margaritae</td> <td>NHMUK 1952.51.107</td> </tr> <tr> <td>M_a_africana_BMNH_1927.5.26.5</td> <td>Corypha [Mirafra] africana africana</td> <td>NHMUK 1927.5.26.5</td> </tr> <tr> <td>M_africana_athi_1951_13_2495</td> <td>Corypha [Mirafra] africana athi</td> <td>NHMUK 1951.13.2495</td> </tr> <tr> <td>M_africana_athi_1968_48_2</td> <td>Corypha [Mirafra] africana athi</td> <td>NHMUK 1968.48.2</td> </tr> <tr> <td>M_ashi_1982_3_4</td> <td>Corypha [Mirafra] ashi</td> <td>NHMUK 1982.3.4</td> </tr> <tr> <td>MirfascU5758_S60</td> <td>Corypha [Mirafra] fasciolata</td> <td>DZUG U5758 </td> </tr> <tr> <td>M_hypermetra_BMNH_1912.12.23.317</td> <td>Corypha [Mirafra] hypermetra hypermetra</td> <td>NHMUK 1912.12.23.317</td> </tr> <tr> <td>M_somalica_somalica_1919_10_6_27</td> <td>Corypha [Mirafra] somalica somalica</td> <td>NHMUK 1919.10.6.27</td> </tr> <tr> <td>Eremalauda_dunni</td> <td>Eremalauda eremodites</td> <td>DZUG U4578</td> </tr> <tr> <td>ErealpeU4610_S144</td> <td>Eremophila alpestris brandti</td> <td>DZUG U4610</td> </tr> <tr> <td>Eremopterix_hova_FMNH449163</td> <td>Eremopterix hova</td> <td>FMNH 449163</td> </tr> <tr> <td>E_leucotis_BMNH_1952.25.36</td> <td>Eremopterix leucotis</td> <td>NHMUK 1952.25.36</td> </tr> <tr> <td>AmmodesU5748_S106</td> <td>Galerida cristata magna</td> <td>DZUG U5748</td> </tr> <tr> <td>G_deva_1949_whi_1_8153</td> <td>Galerida deva</td> <td>NHMUK 1949.whi.1.8153</td> </tr> <tr> <td>G_malabarica_1949_whi_1_7738</td> <td>Galerida malabarica</td> <td>NHMUK 1949.whi.1.7738</td> </tr> <tr> <td>HetarchU2811_S34</td> <td>Heteromirafra archeri ("sidamoensis")</td> <td>DZUG U2811</td> </tr> <tr> <td>Heteromirafra_ruddi</td> <td>Heteromirafra ruddi</td> <td>DZUG U5661 </td> </tr> <tr> <td>Lullula_arborea_U544</td> <td>Lullula arborea</td> <td>UWBM 64680 </td> </tr> <tr> <td>MelcalaU0583_S124</td> <td>Melanocorypha calandra psammochroa</td> <td>DZUG U0583</td> </tr> <tr> <td>MelyeltU0580_S35</td> <td>Melanocorypha yeltoniensis</td> <td>DZUG U0580</td> </tr> <tr> <td>M_albicauda_1916_12_1_840</td> <td>Mirafra albicauda </td> <td>NHMUK 1916.12.1.840</td> </tr> <tr> <td>Mirafra_alb_ZMB_2000.9488</td> <td>Mirafra albicauda </td> <td>ZMB 2000.9488</td> </tr> <tr> <td>Mirafra_albi_ZMB_49.225</td> <td>Mirafra albicauda </td> <td>ZMB 49.225 (holotype)</td> </tr> <tr> <td>MirchenU5660_S37</td> <td>Mirafra cheniana</td> <td>DZUG U5660</td> </tr> <tr> <td>MirchenU5759_S36</td> <td>Mirafra cheniana</td> <td>DZUG U5759</td> </tr> <tr> <td>M_cordofanica_1932_8_6_261</td> <td>Mirafra cordofanica</td> <td>NHMUK 1932.8.6.261</td> </tr> <tr> <td>M_cordofanica_1932_8_6_262</td> <td>Mirafra cordofanica</td> <td>NHMUK 1932.8.6.262</td> </tr> <tr> <td>Panurus</td> <td>Panurus biarmicus</td> <td>1ET92164|SAMN13107499</td> </tr> <tr> <td>Ramphocoris</td> <td>Ramphocoris clotbey</td> <td>CEFE Rhcl1 (= DZUG U5651)</td> </tr> <tr> <td>Spizocorys_fringillaris_U5659</td> <td>Spizocorys fringillaris</td> <td>DZUG U5659</td> </tr> <tr> <td>Spizocorys_obbiensis_1908_5_28_104</td> <td>Spizocorys obbiensis</td> <td>NHMUK 1908.5.28.104</td> </tr> </tbody> </table> <p>Questions can be directed to the corresponding authors.</p>
ShareScore
44/100
Overall dataset sharing score
Score breakdown
These five areas show where the dataset supports — or may limit — practical reuse.
- Stewardship
- 8
- Harmonization
- 4
- Access
- 20
- Reuse readiness
- 8
- Engagement
- 4