TreeBASE Search-Analyses for study 18808

@ARTICLE{TreeBASE2Ref25507, author = {Yaoyao Cui and Chaochao Yan and Jing LI and Tianlin Sun and Bisong Yue and Xiuyue Zhang and Jing Li}, title = {Identification of CR1 Retroposons in Arborophila rufipectus and their application to Phasianidae Phylogeny}, year = {2016}, keywords = {CR1 retroposons, repetitive elements, Arborophila rufipectus, Phasianidae, phylogeny}, doi = {10.1111/1755-0998.12514}, url = {http://}, pmid = {}, journal = {Molecular Ecology Resources}, volume = {}, number = {}, pages = {}, abstract = {Chicken repeat 1 (CR1), a member of non-LTR retroposon, is an important phylogenetic marker in avian systematics. In the present study, we reported several characteristics of CR1 elements in a draft genome of Arborophila rufipectus (Sichuan partridge). According to the analyses of RepeatMasker, approximately 254,966 CR1 elements were identified in A. rufipectus, covering 6.7% of the genome. Subsequently, we selected eighteen novel CR1 elements by comparing the chicken genome, turkey genome and assembled A. rufipectus scaffolds. Here, a combined dataset comprising of twenty two CR1 loci, mitochondrial genomes and eight unlinked introns was analyzed to infer the evolutionary relationships of twelve Phasianidae species. The applicability of CR1 sequences for inferring avian phylogeny relative to mtDNA and intron sequences was investigated as well. Our results elucidated the position of A. rufipectus in Phasianidae with robust supports that it presented a sister clade to Arborophila ardens/Arborophila brunneopectus, and implied that genus Arborophila was in a basal phylogenetic position within Phasianidae and a phylogenetic affinity between Meleagris gallopavo and Pucrasia macrolopha. Therefore, this work not only resolved some of the confounding relationships among Phasianidae, but also suggested CR1 sequences could provide powerful complementary data for phylogeny reconstruction.} }

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Analyses for Study 18808

Citation title: "Identification of CR1 Retroposons in Arborophila rufipectus and their application to Phasianidae Phylogeny".

Study name: "Identification of CR1 Retroposons in Arborophila rufipectus and their application to Phasianidae Phylogeny".

This study is part of submission 18808 (Status: Published).

Analyses

Analysis 1

Analysis details

Name

Input data

1 Input object(s)

Phasianidae combined 12 mitochondrial protein coding genes

Analysis step

ML analysis --

Step details

Name

Software used

Name
Algorithm
Commands
BEGIN PAUP; Lset Base=(0.2971 0.3679 0.1249) Nst=6 Rmat=(1.0050 7.5802 1.2262 0.0872 12.9324) Rates=gamma Shape=1.2998 Pinvar=0.4999; END;

Output data

1 Output object(s)

Fig 2

Analysis 2

Analysis details

Name

Input data

1 Input object(s)

Phasianidae intron sequences

Analysis step

BI analysis --

Step details

Name

Software used

Name
Algorithm
Commands
begin mrbayes; log filename=8NTS.txt; outgroup ALDB_AP; lset nst=6 rates=gamma; Prset Statefreqpr=fixed(0.2540,0.2216,0.2350,0.2894) Revmatpr=fixed(0.9691,4.7084,1.0557,1.3674,4.0372,1.0000) shapepr=fixed(1.0389) pinvarpr=fixed(0); set autoclose=yes; mcmcp ngen=1000000 printfreq=100 samplefreq=100 nchains=4 savebrlens=yes filename=8NTS ; mcmc; sumt burnin=2500 filename=8NTS contype=allcompat; end;

Output data

1 Output object(s)

Fig 3

Analysis 3

Analysis details

Name

Input data

1 Input object(s)

Phasianidae twenty two CR1 sequences under default parameters in Gblocks (allowed gap positions = all)

Analysis step

BI analysis --

Step details

Name

Software used

Name
Algorithm
Commands
begin mrbayes; log filename=FULLCR1ALL.txt; outgroup 7675_AP; lset nst=6 rates=gamma; Prset Statefreqpr=fixed( 0.2611,0.2527,0.2215,0.2647) Revmatpr=fixed(0.9430,4.3769,0.7954,1.2293,3.7669,1.0000) shapepr=fixed(0.7415) pinvarpr=fixed(0); set autoclose=yes; mcmcp ngen=3000000 printfreq=100 samplefreq=100 nchains=4 savebrlens=yes filename=FULLCR1ALL ; mcmc; sumt burnin=7500 filename=FULLCR1ALL contype=allcompat; end;

Output data

1 Output object(s)

Fig 4

Input data

1 Input object(s)

Phasianidae twenty two CR1 sequences under default parameters in Gblocks (allowed gap positions = withhalf)

Analysis step

BI analysis --

Step details

Name

Software used

Name
Algorithm
Commands
begin mrbayes; log filename=FULLCR1WITHHALF.txt; outgroup 7675_AP; lset nst=6 rates=gamma; Prset Statefreqpr=fixed(0.2614,0.2531,0.2207,0.2648) Revmatpr=fixed(0.9410,4.3816,0.7988,1.2320,3.7661,1.0000) shapepr=fixed(0.7418) pinvarpr=fixed(0); set autoclose=yes; mcmcp ngen=3000000 printfreq=100 samplefreq=100 nchains=4 savebrlens=yes filename=FULLCR1WITHHALF ; mcmc; sumt burnin=7500 filename=FULLCR1WITHHALF contype=allcompat; end;

Output data

1 Output object(s)

Fig 4

Input data

1 Input object(s)

Phasianidae twenty two CR1 sequences under default parameters in Gblocks (allowed gap positions = none)

Analysis step

BI analysis --

Step details

Name

Software used

Name
Commands
begin mrbayes; log filename=FULLCR1NONE.txt; outgroup 7675_AP; lset nst=6 rates=gamma; Prset Statefreqpr=fixed(0.2643,0.2421,0.2183,0.2753) Revmatpr=fixed(0.9092,4.0141,0.7464,1.2544,3.5042,1.0000) shapepr=fixed(0.7085) pinvarpr=fixed(0); set autoclose=yes; mcmcp ngen=3000000 printfreq=100 samplefreq=100 nchains=4 savebrlens=yes filename=FULLCR1NONE ; mcmc; sumt burnin=7500 filename=FULLCR1NONE contype=allcompat; end;

Output data

1 Output object(s)

Fig 4

Analysis 4

Analysis details

Input data

1 Input object(s)

Phasianidae twenty two CR1 sequences under default parameters in Gblocks (allowed gap positions = all)

Analysis step

MP analysis --

Step details

Name

Software used

Name
Algorithm
Commands
Begin paup; log file=FULLCR1ALL.log; Outgroup 7675_AP; Cstatus; Set criterion=parsimony; Hsearch addseq=random nreps=1000; Describetrees 1/plot=phylogram brlens=yes; Savetrees file=FULLCR1ALL.tre root=yes brlens=yes savebootp=brlens from=1 to=1623; Pscores all/khtest=yes single=all scorefile=pscorefile ci=yes ri=yes re=yes hi=yes; Savetrees file=stem_Allmarkers.tre root=yes brlens=yes savebootp=brlens from=1 to=1; Log stop; End;

Output data

1 Output object(s)

Fig S2a

Input data

1 Input object(s)

Phasianidae twenty two CR1 sequences under default parameters in Gblocks (allowed gap positions = all)

Analysis step

ML analysis --

Step details

Name

Software used

Name
Algorithm

Output data

1 Output object(s)

Fig S2b

Analysis 5

Analysis details

Name

Input data

1 Input object(s)

Phasianidae twenty two CR1 sequences under default parameters in Gblocks (allowed gap positions = all)

Analysis step

Species trees analysis --

Step details

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Software used

Name
Algorithm

Output data

1 Output object(s)

Fig S3a

Input data

1 Input object(s)

Phasianidae intron sequences

Analysis step

Species trees analysis --

Step details

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Software used

Name
Algorithm

Output data

1 Output object(s)

Fig S3b

Analysis 6

Analysis details

Name

Input data

1 Input object(s)

Phasianidae seven CR1 sequences

Analysis step

BI analysis --

Step details

Name

Software used

Name
Algorithm
Commands
begin mrbayes; log filename=7CR1TA.txt; outgroup 272_AP; lset nst=6 rates=gamma; Prset Statefreqpr=fixed(0.2634,0.2517,0.2175,0.2674) Revmatpr=fixed(0.9659,4.8012,0.7579,1.2418,3.9961,1.0000) shapepr=fixed(0.6994) pinvarpr=fixed(0); set autoclose=yes; mcmcp ngen=1000000 printfreq=100 samplefreq=100 nchains=4 savebrlens=yes filename=7CR1TS ; mcmc; sumt burnin=2500 filename=7CR1TS contype=allcompat; end;

Output data

1 Output object(s)

Fig S4

Analysis 7

Analysis details

Name

Input data

1 Input object(s)

Phasianidae twenty two CR1 elements under default parameters in Gblocks (allowed gap positions = with half)

Analysis step

BI analysis --

Step details

Name

Software used

Name
Algorithm
Commands
begin mrbayes; log filename=WITHHALFALLCR1.txt; outgroup 58AP ; lset nst=6 rates=gamma; Prset Statefreqpr=fixed(0.2532,0.2898,0.2220,0.2350) Revmatpr=fixed(1.0000,4.6900,1.0000,1.0000,3.7687,1.0000) shapepr=fixed(0.9033) pinvarpr=fixed(0); set autoclose=yes; mcmcp ngen=1000000 printfreq=100 samplefreq=100 nchains=4 savebrlens=yes filename=WITHHALFALLCR1 ; mcmc; sumt burnin=2500 filename=WITHHALFALLCR1 contype=allcompat; end;

Output data

1 Output object(s)

Fig S5a

Input data

1 Input object(s)

Phasianidae flanking sequences

Analysis step

BI analysis --

Step details

Name

Software used

Name
Algorithm
Commands
begin mrbayes; log filename=WITHHALFALLF.txt; outgroup 58AP ; lset nst=6 rates=gamma; Prset Statefreqpr=fixed(0.2665,0.2385,0.2183,0.2767) Revmatpr=fixed(0.8985,4.1284,0.7421,1.4185,3.5724,1.0000) shapepr=fixed(0.7121) pinvarpr=fixed(0); set autoclose=yes; mcmcp ngen=1000000 printfreq=100 samplefreq=100 nchains=4 savebrlens=yes filename=WITHHALFALLF ; mcmc; sumt burnin=2500 filename=WITHHALFALLF contype=allcompat; end;

Output data

1 Output object(s)

Fig S5b