TreeBASE Search-Analyses for study 20436

@ARTICLE{TreeBASE2Ref26756, author = {Dennis Ren? Uit de Weerd and Alejandro Fernandez Velazquez}, title = {Pinning down Tenuistemma (Pulmonata: Urocoptidae): local evolution of an extreme shell type}, year = {2017}, keywords = {Cuba ? conchological ? ecological speciation ? endemic - generic characters ? morphological divergence ? morphospace ? selection - shell }, doi = {10.1093/biolinnean/blx041}, url = {http://}, pmid = {}, journal = {Biological Journal of the Linnean Society}, volume = {}, number = {}, pages = {}, abstract = {We report an extraordinary case of local and extreme shell-morphological differentiation within a group of otherwise relatively uniform eastern Cuban land snails. Analyses of multi-copy nuclear (ITS2) and of mitochondrial (COI) DNA sequences congruently place the ?genus? Tenuistemma, occurring monotypically on the Yunque de Baracoa mountain in eastern Cuba, within the more wide-spread species Pleurostemma perplicata from adjacent lower areas. This result is in sharp contrast with patterns of variation in supposedly diagnostic shell-morphological characters, namely (1) differences in both shell form and shell sculpture between Tenuistemma and Pleurostemma perplicata, (2) the shell-morphological coherence of paraphyletic Pleurostemma perplicata, and (3) the resemblance between Pleurostemma perplicata and phylogenetically and geographically more distant species placed in Pleurostemma. We conclude that Tenuistemma evolved from Pleurostemma perplicata on the Yunque de Baracoa, a process that probably started between 0.01 and 1.42 million years ago. The remarkable set of shell features distinguishing Tenuistemma from Pleurostemma perplicata probably evolved as a result of unique local selection pressures, possibly affecting multiple characters linked in shell development. This study provides a basis for further research into the evolutionary processes behind this remarkable morphological transition. To render the genus Pleurostemma monophyletic, we transfer Pleurostemma perplicata to the genus Tenuistemma. } }

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Analyses for Study 20436

Citation title: "Pinning down Tenuistemma (Pulmonata: Urocoptidae): local evolution of an extreme shell type".

Study name: "Pinning down Tenuistemma (Pulmonata: Urocoptidae): local evolution of an extreme shell type".

This study is part of submission 20436 (Status: Published).

Analyses

Analysis 1

Analysis details

Name
Notes

Input data

1 Input object(s)

Analysis step

MrBayes analysis of the ITS2 dataset --

Step details

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Notes

Software used

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Version
URL
Algorithm
Commands
BEGIN MRBAYES; set autoclose=yes nowarn=yes; Prset statefreqpr=dirichlet(1,1,1,1); Lset nst=6 rates=gamma; log start filename=loganalysis; mcmc nruns = 2 ngen = 100000000 printfreq = 10000 samplefreq = 1000 Diagnfreq = 1000 nchains = 6 savebrlens = yes ; sumt relburnin=no burnin=50000; sump relburnin=no burnin=50000; log stop; END;

Output data

1 Output object(s)

Analysis 2

Analysis details

Name
Notes

Input data

1 Input object(s)

Analysis step

GARLI maximum likelihood bootstrap analysis of the ITS2 dataset --

Step details

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Notes

Software used

Name
Version
URL
Algorithm
Commands
[general] datafname = ITS2unamb.nex constraintfile = none streefname = stepwise attachmentspertaxon = 50 ofprefix = garli randseed = -1 availablememory = 512 logevery = 100000 saveevery = 100000 refinestart = 1 outputeachbettertopology = 0 outputcurrentbesttopology = 0 enforcetermconditions = 1 genthreshfortopoterm = 20000 scorethreshforterm = 0.05 significanttopochange = 0.01 outputphyliptree = 0 outputmostlyuselessfiles = 0 writecheckpoints = 0 restart = 0 outgroup = 1 searchreps = 2 bootstrapreps = 1000 resampleproportion = 1.0 inferinternalstateprobs = 0 outputsitelikelihoods = 0 collapsebranches = 1 datatype = nucleotide ratematrix = 6rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = none [master] nindivs = 4 holdover = 1 selectionintensity = 0.5 holdoverpenalty = 0 stopgen = 5000000 stoptime = 5000000 startoptprec = 0.5 minoptprec = 0.01 numberofprecreductions = 10 treerejectionthreshold = 50.0 topoweight = 1.0 modweight = 0.05 brlenweight = 0.2 randnniweight = 0.1 randsprweight = 0.3 limsprweight = 0.6 intervallength = 100 intervalstostore = 5 limsprrange = 6 meanbrlenmuts = 5 gammashapebrlen = 1000 gammashapemodel = 1000 uniqueswapbias = 0.1 distanceswapbias = 1.0

Output data

1 Output object(s)

Analysis 3

Analysis details

Name

Input data

1 Input object(s)

Analysis step

MrBayes analysis of the COI dataset --

Step details

Name

Software used

Name
Version
URL
Algorithm
Commands
BEGIN MRBAYES; Prset statefreqpr=dirichlet(1,1,1,1); Lset nst=6 rates=invgamma; mcmc nruns = 2 ngen = 100000000 printfreq = 10000 samplefreq = 1000 Diagnfreq = 1000 nchains = 6 savebrlens = yes ; log start filename=loganalysis; sumt relburnin=no burnin=50000; sump relburnin=no burnin=50000; log stop; END;

Output data

1 Output object(s)

Analysis 4

Analysis details

Name

Input data

1 Input object(s)

Analysis step

GARLI maximum likelihood bootstrap analysis of the COI dataset --

Step details

Name

Software used

Name
Version
URL
Algorithm
Commands
[general] datafname = COI.nex constraintfile = none streefname = stepwise attachmentspertaxon = 50 ofprefix = garli randseed = -1 availablememory = 512 logevery = 100000 saveevery = 100000 refinestart = 1 outputeachbettertopology = 0 outputcurrentbesttopology = 0 enforcetermconditions = 1 genthreshfortopoterm = 20000 scorethreshforterm = 0.05 significanttopochange = 0.01 outputphyliptree = 0 outputmostlyuselessfiles = 0 writecheckpoints = 0 restart = 0 outgroup = 1 searchreps = 2 bootstrapreps = 1000 resampleproportion = 1.0 inferinternalstateprobs = 0 outputsitelikelihoods = 0 collapsebranches = 1 datatype = nucleotide ratematrix = 6rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate [master] nindivs = 4 holdover = 1 selectionintensity = 0.5 holdoverpenalty = 0 stopgen = 5000000 stoptime = 5000000 startoptprec = 0.5 minoptprec = 0.01 numberofprecreductions = 10 treerejectionthreshold = 50.0 topoweight = 1.0 modweight = 0.05 brlenweight = 0.2 randnniweight = 0.1 randsprweight = 0.3 limsprweight = 0.6 intervallength = 100 intervalstostore = 5 limsprrange = 6 meanbrlenmuts = 5 gammashapebrlen = 1000 gammashapemodel = 1000 uniqueswapbias = 0.1 distanceswapbias = 1.0

Output data