[phylocom-user] low resolution in phylogenetic distances

Megan Bartlett mkbartl at gmail.com
Tue May 14 10:31:30 PDT 2013


Hi all,

I'm using phylocom and phylomatic to construct a tree from a list of 43
taxa, estimate branch lengths with BLADJ, and calculate phylogenetic
distances. The problem I'm having is that I only get a few unique values
for phylogenetic distances, even for species that are not polytomies. I'm
not sure whether this is incorrect, or whether I'm misunderstanding what
BLADJ and phydist do. For example, all species in the node containing
Macropanax- Barringtonia (tree included below) have the same phylogenetic
distances to all of the species in the nodes Aglaia-Syzigium and
Ficus-Antidesma- why are these all the same? If these are the expected
results, is there any way to improve the resolution for branch lengths?

Thanks for your help. Please let me know if I can provide any more info!

Best,

Megan

Tree output from BLADJ:
(((((((((((aglaia_abbreviata:36.363636,aglaia_perviridis:36.363636)aglaia:36.363636,walsura_robusta:72.727272):36.363640,chisocheton_siamensis:109.090912)meliaceae:36.363632,(nephelium_chryseum:72.727272,pometia_tomentosa:72.727272)sapindaceae:72.727272):36.363632,((microcos_chungii:60.606060,pterospermum_menglunense:60.606060)malvaceae:60.606060,parashorea_chinensis:121.212120):60.606056):36.363647,syzygium_latilimbum:218.181824)malvids:36.363632,((((antidesma_montanum:72.727272,baccaurea_ramiflora:72.727272)phyllanthaceae:72.727272,(((cleidion_brevipetiolatum:36.363636,mallotus_garrettii:36.363636):36.363636,sumbaviopsis_albicans:72.727272):36.363640,trigonostemon_thyrsoideum:109.090912)euphorbiaceae:36.363632,dichapetalum_gelonioides:145.454544,drypetes_hoaensis:145.454544,(garcinia_cowa:72.727272,garcinia_lancilimba:72.727272)garcinia:72.727272)malpighiales:36.363632,(elaeocarpus_glabripetalus:90.909088,sloanea_tomentosa:90.909088)elaeocarpaceae:90.909088):36.363647,(cylindrokelupha_yunnanensis:145.454544,(ficus_fistulosa:72.727272,ficus_langkokensis:72.727272)ficus:72.727272):72.727280):36.363632):36.363632,leea_compactiflora:290.909088)rosids:36.363647,((barringtonia_pendula:181.818192,(diospyros_nigrocortex:90.909096,eurya_austroyunnanensis:90.909096):90.909096):90.909103,((((lasianthus_verticillatus:54.545456,saprosma_ternata:54.545456,urophyllum_chinense:54.545456)rubiaceae:54.545456,tabernaemontana_corymbosa:109.090912)gentianales:54.545456,pittosporopsis_kerrii:163.636368)lamiids:54.545456,macropanax_dispermus:218.181824):54.545471)ericales_to_asterales:54.545441):36.363617,((beilschmiedia_robusta:193.939392,(phoebe_lanceolata:96.969696,cinnamomum_bejolghota:96.969696):96.969696)lauraceae:96.969696,(((knema_furfuracea:72.727272,knema_globularia:72.727272)knema:72.727272,myristica_yunnanensis:145.454544)myristicaceae:72.727280,(mezzettiopsis_creaghii:109.090912,pseuduvaria_indochinensis:109.090912)annonaceae:109.090912)magnoliales:72.727264):72.727264)magnoliales_to_asterales:36.363636)euphyllophyte:1.000000;
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