@ARTICLE{TreeBASE2Ref20828,
author = {Eva Verena Bärmann and Gertrud Elisabeth R??ner and Gert W?rheide},
title = {A revised phylogeny of Antilopini (Bovidae, Artiodactyla) using combined mitochondrial and nuclear genes},
year = {2013},
keywords = {supermatrix; partitioned analysis; Bayesian inference; maximum likelihood; maximum parsimony; random-outgroup rooting},
doi = {},
url = {http://dx.doi.org/10.1016/j.ympev.2013.02.015},
pmid = {},
journal = {Molecular Phylogenetics and Evolution},
volume = {},
number = {},
pages = {},
abstract = {Antilopini (gazelles and their allies) are one of the most diverse but phylogenetically controversial groups of bovids. Here we provide a molecular phylogeny of this poorly understood taxon using combined analyses of mitochondrial (CYTB, COII, 12S, 16S) and nuclear (KCAS, SPTBN1, PRKCI, MC1R, THYR) genes. We explore the influence of data partitioning and different analytical methods, including Bayesian inference, maximum likelihood and maximum parsimony, on the inferred relationships within Antilopini. We achieve increased resolution and support compared to previous analyses especially in the two most problematic parts of their tree. First, taxa commonly referred to as ?gazelles? are recovered as paraphyletic, as the genus Gazella appears more closely related to the Indian blackbuck (Antilope cervicapra) than to the other two gazelle genera (Nanger and Eudorcas). Second, we recovered a strongly supported sister relationship between one of the dwarf antelopes (Ourebia) and the Antilopini subgroup Antilopina (Saiga, Gerenuk, Springbok, Blackbuck and gazelles). The assessment of the influence of taxon sampling, outgroup rooting, and data partitioning in Bayesian analyses helps explain the contradictory results of previous studies.}
}
Analyses for Study 12859
Citation title:
"A revised phylogeny of Antilopini (Bovidae, Artiodactyla) using combined mitochondrial and nuclear genes" .
Study name:
"A revised phylogeny of Antilopini (Bovidae, Artiodactyla) using combined mitochondrial and nuclear genes" .
This study is part of submission 12859
(Status: Published).
Analyses
Analysis 1
Analysis details
Input data
1 Input object(s)
Output data
1 Output object(s)
MrBayes
Analysis 2
Analysis details
Input data
1 Input object(s)
Analysis step
MP full-taxon set
--
Step details
Software used
Output data
3 Output object(s)
PAUP MP1
PAUP MP2
PAUP MP3
Analysis 3
Analysis details
Input data
1 Input object(s)
Analysis step
ML full-taxon set
--
Step details
Software used
Output data
1 Output object(s)
RAxML
Analysis 4
Analysis details
Input data
1 Input object(s)
Analysis step
Bayesian Inference reduced-taxon set
--
Step details
Software used
Name
Algorithm
Commands
begin mrbayes;
set autoclose=yes nowarn=yes;
exclude 2011- 2017 2042- 2043 2048- 2053 2234- 2242 2282- 2293 2393- 2397 2565- 2571 2588- 2595 2657- 2677 2792- 2837 2906- 2942 2958- 2964 2989- 2998 3038- 3045 3105- 3110 3169- 3176 3299- 3308 3316- 3322 3456- 3490 3502- 3507 3524- 3532 4008- 4020 4135- 4141 4158- 4163 4414- 4418 4453- 4475 6057- 6092 6559- 6560 6770- 6786;
delete Eudorcas_rufifrons Gazella_bennettii Gazella_cuvieri Gazella_gazella Gazella_leptoceros Gazella_marica Gazella_spekei Gazella_subgutturosa Nanger_granti Nanger_soemmerringi Procapra_picticaudata Procapra_przewalskii Madoqua_guentheri Madoqua_saltiana Raphicerus_melanotis Raphicerus_sharpei Neotragus_batesi;
outgroup Tragelaphus_sp.;
charset cytb = 1 - 1140;
charset coxiii = 1141 - 1923;
charset 12S = 1924 - 2891;
charset 16S = 2892 - 4494;
charset MC1R = 4495 - 5430;
charset KCAS = 5431 - 6197;
charset SPTBN1 = 6198 - 7053;
charset THYR = 7054 - 7652;
charset PRKCI = 7653 - 8168;
charset mitPos1 = 1 - 1921\3;
charset mitPos2 = 2 - 1922\3;
charset mitPos3 = 3 - 1923\3;
charset nuclPos1 = 4495-5428\3 5655-6309\3 7012-7120\3 7545-7704\3 8151-8166\3;
charset nuclPos2 = 4496-5429\3 5656-6310\3 7013-7121\3 7546-7705\3 8152-8167\3;
charset nuclPos3 = 4497-5430\3 5657-6311\3 7014-7122\3 7547-7706\3 8153-8168\3;
charset nuclnoncoding = 5431-5654 6312-7011 7123-7544 7707- 8150;
partition allgenes6_6 = 9: mitPos1, mitPos2, mitPos3, 12S, 16S, nuclPos1, nuclPos2, nuclPos3, nuclnoncoding;
set partition = allgenes6_6;
lset applyto=(1,3,4,5,9) nst=6 rates=gamma;
lset applyto=(2,6,7,8) nst=2 rates=gamma;
unlink statefreq=(all) revmat=(all) shape=(all) tratio=(all);
prset applyto=(all) ratepr=variable;
mcmcp ngen= 40000000 relburnin=yes burninfrac=0.5 printfreq=5000 samplefreq=5000 diagnfreq=50000 temp=0.05 nchains=4 nswaps=6 savebrlens=yes;
mcmc;
sump burnin=4000;
sumt burnin=4000;
end;
Output data
1 Output object(s)
MrBayes
Analysis 5
Analysis details
Input data
1 Input object(s)
Analysis step
MP reduced-taxon set
--
Step details
Software used
Output data
2 Output object(s)
PAUP
PAUP
Analysis 6
Analysis details
Input data
1 Input object(s)
Analysis step
ML reduced-taxon set
--
Step details
Software used
Output data
1 Output object(s)
RAxML
Analysis 7
Analysis details
Input data
1 Input object(s)
Analysis step
Bayesian Inference ingroup
--
Step details
Software used
Name
Algorithm
Commands
begin mrbayes;
set autoclose=yes nowarn=yes;
exclude 2011- 2017 2042- 2043 2048- 2053 2234- 2242 2282- 2293 2393- 2397 2565- 2571 2588- 2595 2657- 2677 2792- 2837 2906- 2942 2958- 2964 2989- 2998 3038- 3045 3105- 3110 3169- 3176 3299- 3308 3316- 3322 3456- 3490 3502- 3507 3524- 3532 4008- 4020 4135- 4141 4158- 4163 4414- 4418 4453- 4475 6057- 6092 6559- 6560 6770- 6786;
delete Aepyceros_melampus Capra_sp. Damaliscus_sp. Hippotragus_niger Kobus_ellipsiprymnus Neotragus_batesi Neotragus_moschatus Oreotragus_oreotragus Pantholops_hodgsoni Redunca_fulvorufula Cephalophini_sp. Tragelaphus_sp.;
charset cytb = 1 - 1140;
charset coxiii = 1141 - 1923;
charset 12S = 1924 - 2891;
charset 16S = 2892 - 4494;
charset MC1R = 4495 - 5430;
charset KCAS = 5431 - 6197;
charset SPTBN1 = 6198 - 7053;
charset THYR = 7054 - 7652;
charset PRKCI = 7653 - 8168;
charset mitPos1 = 1 - 1921\3;
charset mitPos2 = 2 - 1922\3;
charset mitPos3 = 3 - 1923\3;
charset nuclPos1 = 4495-5428\3 5655-6309\3 7012-7120\3 7545-7704\3 8151-8166\3;
charset nuclPos2 = 4496-5429\3 5656-6310\3 7013-7121\3 7546-7705\3 8152-8167\3;
charset nuclPos3 = 4497-5430\3 5657-6311\3 7014-7122\3 7547-7706\3 8153-8168\3;
charset nuclnoncoding = 5431-5654 6312-7011 7123-7544 7707- 8150;
partition allgenes6_6 = 9: mitPos1, mitPos2, mitPos3, 12S, 16S, nuclPos1, nuclPos2, nuclPos3, nuclnoncoding;
set partition = allgenes6_6;
lset applyto=(1,3,4,5,9) nst=6 rates=gamma;
lset applyto=(2,6,7,8) nst=2 rates=gamma;
unlink statefreq=(all) revmat=(all) shape=(all) tratio=(all);
prset applyto=(all) ratepr=variable;
mcmcp ngen= 40000000 relburnin=yes burninfrac=0.5 printfreq=5000 samplefreq=5000 diagnfreq=50000 temp=0.05 nchains=4 nswaps=6 savebrlens=yes;
mcmc;
sump burnin=4000;
sumt burnin=4000;
end;
Output data
1 Output object(s)
MrBayes
Analysis 8
Analysis details
Input data
1 Input object(s)
Analysis step
MP ingroup
--
Step details
Software used
Output data
2 Output object(s)
PAUP
PAUP
Analysis 9
Analysis details
Input data
1 Input object(s)
Analysis step
ML ingroup
--
Step details
Software used
Output data
1 Output object(s)
RAxML