Description
These 2 phylogenies are with and without Wollemia nobilis. We ran phylonext for both of these phylogenies. All parameters were default except for type of phylogenetic tree labels (Latin) family (Araucariaceae), min year (1980) and country (Australia), number of randomisation (20).
The problem is that some cells where Wollemia nobilis is not present have different amounts of PD between the 2 runs. We would expect if Wollemia nobilis is not present, they would have exactly the same amount of PD.
These are the two phylogenies we ran:
(((Agathis_australis,Agathis_palmerstonii,((((Agathis_atropurpurea,Agathis_microstachya),Agathis_robusta),((Agathis_dammara,Agathis_borneensis),(Agathis_silbae,Agathis_macrophylla))),((Agathis_moorei,(Agathis_ovata,Agathis_corbassonii)),Agathis_lanceolata)),Agathis_montana,Agathis_obtusa,Agathis_vitiensis,Agathis_brownii,Agathis_alba,Agathis_philippinensis,Agathis_flavescens,Agathis_orbicula,Agathis_kinabaluensis,Agathis_labillardierei,Agathis_lenticula,Agathis_endertii,Agathis_silbaii)Agathis,(Wollemia_nobilis)Wollemia),(((Araucaria_heterophylla,((((Araucaria_columnaris,(Araucaria_luxurians,Araucaria_nemorosa)),((Araucaria_humboldtensis,Araucaria_laubenfelsii),Araucaria_rulei)),((Araucaria_bernieri,(Araucaria_schmidii,Araucaria_subulata)),Araucaria_scopulorum)),(Araucaria_biramulata,Araucaria_montana))),(Araucaria_cunninghamii_var._cunninghamii)Araucaria_cunninghamii),((Araucaria_araucana,Araucaria_angustifolia),(Araucaria_bidwillii,Araucaria_hunsteinii)),Araucaria_excelsa,Araucaria_muelleri,Araucaria_braziliana,Araucaria_lignitici,Araucaria_bernieri,Araucaria_annulata,Araucaria_balcombensis,Araucaria_fimbriatus,Araucaria_grandifolia,Araucaria_hastiensis,Araucaria_longifolia,Araucaria_marensii,Araucaria_nathorsti,Araucaria_planus,Araucaria_prominens,Araucaria_readiae,Araucaria_taeriensis,Araucaria_uncinatus,Araucaria_araucoensis,Araucaria_brownii,Araucaria_jeffreyi,Araucaria_marylandica,Araucaria_neocookii,Araucaria_pichileufensis,Araucaria_prodromus)Araucaria,(Agathoxylon_pseudoparenchymatosum)Agathoxylon,(Balmeisporites_minutus)Balmeisporites)Araucariaceae;
((Agathis_australis,Agathis_palmerstonii,((((Agathis_atropurpurea,Agathis_microstachya),Agathis_robusta),((Agathis_dammara,Agathis_borneensis),(Agathis_silbae,Agathis_macrophylla))),((Agathis_moorei,(Agathis_ovata,Agathis_corbassonii)),Agathis_lanceolata)),Agathis_montana,Agathis_obtusa,Agathis_vitiensis,Agathis_brownii,Agathis_alba,Agathis_philippinensis,Agathis_flavescens,Agathis_orbicula,Agathis_kinabaluensis,Agathis_labillardierei,Agathis_lenticula,Agathis_endertii,Agathis_silbaii)Agathis,(((Araucaria_heterophylla,((((Araucaria_columnaris,(Araucaria_luxurians,Araucaria_nemorosa)),((Araucaria_humboldtensis,Araucaria_laubenfelsii),Araucaria_rulei)),((Araucaria_bernieri,(Araucaria_schmidii,Araucaria_subulata)),Araucaria_scopulorum)),(Araucaria_biramulata,Araucaria_montana))),(Araucaria_cunninghamii_var._cunninghamii)Araucaria_cunninghamii),((Araucaria_araucana,Araucaria_angustifolia),(Araucaria_bidwillii,Araucaria_hunsteinii)),Araucaria_excelsa,Araucaria_muelleri,Araucaria_braziliana,Araucaria_lignitici,Araucaria_bernieri,Araucaria_annulata,Araucaria_balcombensis,Araucaria_fimbriatus,Araucaria_grandifolia,Araucaria_hastiensis,Araucaria_longifolia,Araucaria_marensii,Araucaria_nathorsti,Araucaria_planus,Araucaria_prominens,Araucaria_readiae,Araucaria_taeriensis,Araucaria_uncinatus,Araucaria_araucoensis,Araucaria_brownii,Araucaria_jeffreyi,Araucaria_marylandica,Araucaria_neocookii,Araucaria_pichileufensis,Araucaria_prodromus)Araucaria,(Agathoxylon_pseudoparenchymatosum)Agathoxylon,(Balmeisporites_minutus)Balmeisporites)Araucariaceae;