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.