TreeBASE Search-Analyses for study 695

@ARTICLE{TreeBASE2Ref17566, author = {Vincent S. Smith}, title = {Avian Louse Phylogeny (Phthiraptera: Ischnocera): A cladistic study based on morphology.}, year = {2001}, keywords = {lice; Phthiraptera; Ischnocera; ontogeny; bird phylogeny; coevolution; congruence}, doi = {10.1111/j.1096-3642.2001.tb02272.x}, url = {}, pmid = {}, journal = {Zoological Journal of the Linnean Society}, volume = {132}, number = {1}, pages = {81--144}, abstract = {The louse suborder Ischnocera (Phthiraptera) contains 3,060 currently described species from over 150 genera. These lice are permanent obligatory ectoparasites of a diverse selection of birds and mammals with a worldwide distribution. Historically, they have played a major role in the development of our ideas on coevolution, and species hosted by mammals have been used extensively as model organisms for the study of cospeciation. In contrast, avian taxa comprising 90% of ischnoceran species have been neglected due to a lack of data on their wider systematics. A comparative study based on the adult and nymphal instar morphology of avian lice yielded 138 characters from 56 species (51 genera), all of which are illustrated or discussed here for the first time. A further five outgroup taxa were examined from the mammalian ischnoceran family Trichodectidae. Phylogenetic analyses of these data produced three most parsimonious cladograms, the strict consensus of which is highly resolved and broadly consistent with previous classifications. Morphological character variation is extensive, and nymphal character traits are useful in identifying instances of convergent evolution in adult morphology. The role of ontogeny in the development of the major character complexes of the head and abdomen is discussed, and its implications for further work on the phylogeny of avian Ischnocera is considered. Comparison with host taxonomy reveals a series of complex host-parasite associations that do not support a hypothesis of strict one to one cospeciation. However, extrapolation of these associations is compromised by the low sample size. The role of niche specialisation to explain the presence of multiple unrelated lineages on the same host taxon is considered.} }

Delicious

Connotea

Analyses for Study 695

Citation title: "Avian Louse Phylogeny (Phthiraptera: Ischnocera): A cladistic study based on morphology.".

This study was previously identified under the legacy study ID S535 (Status: Published).

Analyses

Analysis 1

Analysis details

Name

Input data

4 Input object(s)

Analysis step

COMBI_ML Analysis --

Output data

1 Output object(s)

Analysis 2

Analysis details

Name

Input data

2 Input object(s)

Analysis step

CPall_MB Analysis --

Step details

Name
Notes

Software used

Name
Algorithm
Commands
begin mrbayes; nowarn=yes autoreplace=no; set autoclose=yes; charset CP=1-1445; charset rpoB=1446-1902; charset indels= 1903-1912; partition names=3: CP, rpoB, indels; set partition=names; lset applyto=(1) nst=2 rates=gamma; lset applyto=(2) nst=2 rates=propinv; lset applyto=(3) coding=variable; unlink shape= (all); Prset applyto=(1,2) statefreqpr=dirichlet(1,1,1,1); end; BEGIN MRBAYES; nowarn=yes autoreplace=no; set autoclose=yes; outgroup Hcrispulum_PA29; outgroup Harboreum_PA17a; outgroup Harboreum_PA17b; outgroup Harboreum_PA18; end; begin mrbayes; nowarn=yes autoreplace=no; set autoclose=yes; mcmcp ngen=30000000 samplefreq=1000 printfreq=1000 nchains=4 nruns=2 temp=0.05 savebrlens=yes diagnfreq=30000;

Output data

1 Output object(s)

Analysis 3

Analysis details

Name

Input data

2 Input object(s)

Analysis step

ITS_ML analysis --

Output data

1 Output object(s)

Analysis 4

Analysis details

Name

Input data

2 Input object(s)

Analysis step

CPall_ML analysis --

Output data

1 Output object(s)

Analysis 5

Analysis details

Name

Input data

2 Input object(s)

Analysis step

Dic_ITS_MB analysis --

Step details

Name

Software used

Name
Algorithm
Commands
begin mrbayes; set autoclose=yes nowarn=yes autoreplace=no; charset ITS=1-941; charset indels= 942-1072; partition names=2: ITS, indels; set partition=names; lset applyto=(1) nst=2 rates=propinv; lset applyto=(2) coding=variable; unlink shape= (all); Prset applyto=(1) statefreqpr=dirichlet(1,1,1,1); end; BEGIN MRBAYES; set autoclose=yes nowarn=yes autoreplace=no; outgroup Hcrispulum_PA29; outgroup Harboreum_PA17a; outgroup Harboreum_PA17b; outgroup Harboreum_PA18; end; begin mrbayes; set autoclose=yes nowarn=yes autoreplace=no; mcmcp ngen=11000000 samplefreq=1000 printfreq=1000 nchains=4 nruns=2 temp=0.05 savebrlens=yes diagnfreq=30000;

Output data

2 Output object(s)

Analysis 6

Analysis details

Name

Input data

4 Input object(s)

Analysis step

COMBI_MB_analysis --

Step details

Name

Software used

Name
Algorithm
Commands
begin mrbayes; set autoclose=yes nowarn=yes autoreplace=no; charset CP=1-1445; charset rpoB=1446-1902; charset ITS=1903-2843; charset indels= 2844-2984; partition names=4: CP, rpoB, ITS, indels; set partition=names; lset applyto=(1) nst=2 rates=gamma; lset applyto=(2,3) nst=2 rates=propinv; lset applyto=(4) coding=variable; unlink shape= (all); Prset applyto=(1,2,3) statefreqpr=dirichlet(1,1,1,1); end; BEGIN MRBAYES; set autoclose=yes nowarn=yes autoreplace=no; outgroup Hcrispulum_PA29; outgroup Harboreum_PA17a; outgroup Harboreum_PA17b; outgroup Harboreum_PA18; end; begin mrbayes; set autoclose=yes nowarn=yes autoreplace=no; mcmcp ngen=30000000 samplefreq=1000 printfreq=1000 nchains=4 nruns=2 temp=0.05 savebrlens=yes diagnfreq=30000;

Output data