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Cytochrome B Supplementary Fig. 1. Galerida macrorhyncha randoni PFP CL2a 1.00 Galerida cristata brachyura 1.00 Cytochrome b Galerida malabarica 1.00 Galerida theklae ruficolor PFP TkL Galerida magnirostris 0.85 0.88 Galerida modesta nigrita Alauda arvensis arvensis PFP SkyL1 0.68 1.00 Alauda gulgula inconspicua NRM 20066712 0.71 Alauda razae Melanocorypha leucoptera Lullula arborea pallida 0.96 Spizocorys starki Pseudalaemon freemantlii delamerei 1.00 Spizocorys conirostris conirostris Spizocorys fringillaris Spizocorys personata intensa Spizocorys sclateri 0.82 0.95 Calandrella raytal raytal DZUG 2200 1.00 Calandrella rufescens minor PFP LST1 0.95 Calandrella cheleensis cheleensis U2202 0.97 Calandrella athensis PFP AST1 Eremalauda dunni eremodites Chersophilus duponti duponti 1.00 0.86 Melanocorypha maxima DZUG U588 0.88 1.00 Melanocorypha mongolica 1.00 Melanocorypha yeltoniensis 1.00 Melanocorypha calandra psammochroa Melanocorypha bimaculata DZUG U2283 Calandrella acutirostris tibetana DZUG U577 1.00 Calandrella brachydactyla rubiginosa 1.00 Calandrella cinerea cinerea 1.00 Eremophila alpestris praticola Eremophila bilopha 0.52 Mirafra affinis 0.89 Mirafra erythrocephala 1.00 Mirafra erythroptera sindiana 1.00 Mirafra assamica Mirafra microptera 0.74 1.00 Mirafra cantillans cantillans 0.94 Mirafra javanica williamsoni 0.50 Mirafra cheniana 1.00 0.56 Mirafra williamsi KNM WL1 Mirafra passerina 1.00 Mirafra africana harterti KNM RN1 0.85 Mirafra hypermetra hypermetra 1.00 Mirafra apiata apiata 0.56 Mirafra fasciolata fasciolata Mirafra angolensis antonii Heteromirafra ruddi 0.81 1.00 Heteromirafra archeri sidamoensis Mirafra rufocinnamomea torrida 1.00 Calendulauda barlowi patae 0.96 Calendulauda erythroclamys 1.00 Calendulauda burra 0.87 Calendulauda albescens guttata 1.00 Calendulauda africanoides austinrobertsi 1.00 Calendulauda alopex intercedens 0.51 0.58 Calendulauda sabota bradfieldi Calendulauda poecilosterna 0.89 Certhilauda brevirostris 1.00. Certhilauda semitorquata algida 1.00 Certhilauda curvirostris curvirostris 1.00 0.97 Certhilauda benguelensis benguelensis Certhilauda subcoronata subcoronata 1.00 Certhilauda chuana 1.00 Chersomanes albofasciata boweni 0.93 0.81 Chersomanes beesleyi 1.00 Ammomanopsis grayi hoeschi Alaemon alaudipes desertorum PFP HpB4 0.75 Eremopterix leucopareia Eremopterix verticalis verticalis 0.59 Eremopterix nigriceps affinis 1.00 Eremopterix signatus 0.97 Eremopterix griseus DZUG 2257 1.00 Mirafra hova Eremopterix australis 1.00 1.00 Ammomanes cinctura arenicolor PFP BrTdLk1 0.79 Ammomanes deserti payni PFP DLS6 0.93 Ramphocoris clotbey PFP CLOT1 1.00 Pinarocorys erythropygia DZUG U2818 Pinarocorys nigricans nigricans Panurus biarmicus Prinia bairdii 0.08 Supplementary Fig. 2. 0.67 Spizocorys personata intensa 16S 0.52 Spizocorys conirostris conirostris Pseudalaemon freemantlii delamerei 0.66 Spizocorys sclateri 0.92 Spizocorys starki Spizocorys fringillaris Lullula arborea pallida 1.00 Alauda razae 0.78 Alauda arvensis arvensis/cantarella Galerida theklae ruficolor 0.88 Galerida macrorhyncha randoni 0.56 0.81 Galerida cristata brachyura Galerida magnirostris 1.00 Calandrella cinerea williamsi 0.60 Calandrella cinerea cinerea 1.00 Eremophila alpestris praticola Eremophila bilopha 1.00 Calandrella rufescens minor PFP LST ad 1.00 Calandrella rufescens minor PFP LST1 0.98 Calandrella athensis 1.00 Mirafra cantillans simplex 0.91 Mirafra cantillans marginata 0.84 0.97 Mirafra cheniana 0.98 Mirafra passerina Mirafra williamsi 0.76 Mirafra rufocinnamomea torrida 0.60 Mirafra apiata apiata 0.81 0.91 Mirafra africana harterti Mirafra hypermetra hypermetra Eremalauda dunni eremodites 0.54 0.99 Calendulauda erythroclamys 0.99 Calendulauda barlowi patae 1.00 Calendulauda albescens guttata Calendulauda burra 0.98 1.00 Calendulauda alopex intercedens 0.59 Calendulauda africanoides austinrobertsi Calendulauda poecilosterna Calendulauda sabota bradfieldi Heteromirafra ruddi 0.75 Eremopterix leucopariea 0.96 Eremopterix signatus 0.99 1.00 1.00 Eremopterix verticalis verticalis 1.00 Eremopterix nigriceps affinis Eremopterix australis Mirafra hova 1.00 1.00 Ammomanes cinctura arenicolor PFP BrTdLk1 1.00 Ammomanes cintura arenicolor PFP BTL 1.00 Ammomanes deserti payni Ramphocoris clotbey 0.99 Certhilauda benguelensis benguelensis 0.82 Certhilauda subcoronata subcoronata 0.94 0.88 0.66 Certhilauda semitorquata algida 1.00 Certhilauda curvirostris curvirostris Certhilauda brevirostris 0.60 Certhilauda chuana 1.00 1.00 1.00 Chersomanes beesleyi 0.88 Chersomanes albofasciata boweni Ammomanopsis grayi hoeschi Alaemon alaudipes desertorum 1.00 Cisticola brachyptera Prinia bairdii Aegithalos concinnus Acrocephalus arundinaceus 0.03 Supplementary Fig. 3. ODC introns 6–7 Alauda arvensis arvensis EF625336 1.00 Alauda gulgula inconspicua 1.00 Melanocorypha leucoptera 0.94 Galerida macrorhyncha randoni 1.00 Galerida modesta nigrita 0.82 Pseudalaemon freemantlii delamerei 0.84 Spizocorys conirostris conirostris Spizocorys personata intensa 0.97 0.59 Lullula arborea pallida 0.53 Eremophila alpestris elwesi 0.99 Eremophila alpestris praticola 0.99 Eremophila bilopha 0.95 Calandrella brachydactyla rubiginosa 0.88 0.98 Calandrella cinerea williamsi Calandrella acutirostris tibetana Melanocorypha yeltoniensis 0.94 Melanocorypha mongolica 0.99 Melanocorypha maxima DZUG U578 Melanocorypha maxima DZUG U588 1.00 1.00 Melanocorypha calandra calandra Melanocorypha bimaculata 1.00 Calandrella cheleensis cheleensis 0.96 Calandrella raytal raytal 1.00 Calandrella rufescens minor 0.58 1.00 Calandrella athensis 0.99 Eremalauda dunni eremodites Chersophilus duponti duponti 1.00 Calendulauda sabota bradfieldi Calendulauda sabota suffusca 1.00 Calendulauda burra Calendulauda poecilosterna 0.51 Ammomanes deserti payni 0.75 Ammomanes deserti annae 0.99 Ammomanes deserti phoenicuroides Ammomanes cinctura arenicolor 1.00 Ramphocoris clotbey Pinarochorys erythropygia 0.80 Pinarochorys nigricans nigricans 0.53 Mirafra hova 0.94 Eremopterix australis 1.00 Eremopterix leucopareia 1.00 Eremopterix griseus Eremopterix nigriceps melanauchen 0.99 0.94 Mirafra cantillans marginata 0.55 Mirafra javanica javanica 0.97 Mirafra javanica williamsoni 0.65 Mirafra cantillans cantillans Mirafra rufocinnamomea torrida 0.89 Mirafra angolensis antonii 0.98 Mirafra passerina Mirafra williamsi 0.97 Mirafra assamica Mirafra affinis 0.86 0.74 1.00 Mirafra erythrocephala Mirafra microptera 1.00 Mirafra erythroptera sindiana 1.00 Mirafra apiata apiata 1.00 Mirafra fasciolata fasciolata Mirafra africana harterti Heteromirafra ruddi Chersomanes albofasciata ssp. 0.58 Ammomanopsis grayi hoeschi 1.00 Certhilauda semitorquata algida Alaemon alaudipes alaudipes Prinia bairdii Panurus biarmicus 0.01 Supplementary Fig. 4. Myoglobin intron 2 Melanocorypha yeltoniensis 0.96 Melanocorypha calandra calandra 1.00 Melanocorypha mongolica Melanocorypha maxima Melanocorypha bimaculata 1.00 Calandrella raytal raytal 1.00 1.00 Calandrella rufescens minor 1.00 Calandrella cheleensis cheleensis Calandrella athensis Chersophilus duponti duponti 1.00 Alauda arvensis arvensis Alauda gulgula inconspicua 0.98 1.00 Galerida macrorhyncha randoni 0.63 Galerida modesta nigrita Melanocorypha leucoptera 0.89 1.00 Lullula arborea pallida 1.00 Pseudalaemon freemantlii delamerei Spizocorys personata intensa 1.00 Calandrella acutirostris tibetana Calandrella cinerea williamsi 1.00 Eremophila bilopha Eremophila alpestris elwesi Mirafra affinis Mirafra assamica 1.00 Mirafra erythroptera sindiana 0.93 Mirafra erythrocephala 0.99 Mirafra microptera Mirafra passerina 0.91 1.00 Mirafra cantillans cantillans Mirafra javanica williamsoni 1.00 0.95 Mirafra angolensis antonii Mirafra rufocinnamomea torrida 0.90 Mirafra apiata apiata 1.00 Mirafra fasciolata fasciolata Mirafra africana harterti 1.00 Calendulauda sabota bradfieldi 0.77 0.96 Calendulauda sabota suffusca 1.00 Calendulauda poecilosterna Calendulauda burra 0.92 1.00 Heteromirafra archeri archeri 1.00 Heteromirafra archeri sidamoensis Heteromirafra ruddi Ammomanes deserti payni 1.00 Ammomanes deserti annae Ammomanes deserti phoenicuroides 0.54 Pinarochorys nigricans nigricans 1.00 1.00 Pinarochorys nigricans occidentis Pinarocorys erythropygia Ammomanes cinctura arenicolor 1.00 0.68 Ramphocoris clotbey 1.00 Eremopterix leucopareia Eremopterix nigriceps melanauchen 1.00 0.92 Mirafra hova Eremopterix australis 0.63 Ammomanopsis grayi hoeschi 1.00 Certhilauda semitorquata algida 0.85 Chersomanes albofasciata ssp. Alaemon alaudipes alaudipes Prinia bairdii Panurus biarmicus 0.0050 Supplementary Fig. 5. 1.00 Melanocorypha calandra calandra RAG 1+2 0.88 Melanocorypha yeltoniensis 0.76 Calandrella cinerea williamsi 0.87 0.97 Calandrella athensis 0.78 Calandrella rufescens minor Eremophila alpestris praticola 1.00 Melanocorypha mongolica 0.92 Chersophilus duponti duponti Eremalauda dunni eremodites 0.97 1.00 Alauda arvensis arvensis 0.93 Alauda gulgula inconspicua 1.00 Galerida modesta nigrita Galerida macrorhyncha randoni 0.77 Melanocorypha leucoptera 0.98 0.68 Lullula arborea pallida Spizocorys conirostris conirostris 1.00 0.98 Pseudalaemon freemantlii delamerei 1.00 Mirafra erythroptera sindiana 1.00 Mirafra microptera Mirafra javanica williamsoni 1.00 0.54 Mirafra passerina 1.00 Mirafra angolensis antoni 0.96 1.00 Mirafra rufocinnamomea torrida Mirafra apiata apiata 1.00 Heteromirafra ruddi Calendulauda burra 1.00 Calendulauda poecilosterna 1.00 Calendulauda sabota bradfieldi 0.92 Ammomanes deserti payni 1.00 Ammomanes deserti annae 1.00 0.87 Ammomanes deserti
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