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A novel metatree approach to generating large phylogenetic hypotheses of extinct taxa
Graeme T. Lloyd @GraemeTLloyd
AcknowledgementsKatie Davis
Where evolution happens
Where evolution happens
Phylogeny and macroevolution
1. Diversification models.(why are some clades more diverse than others?2. Trait models (tempo and mode)3. Biogeography4. Phylogenetic selectivity of mass extinction (Prune whole clade versus set of tips)
5
Phylogeny and macroevolution
1. Diversification models.(why are some clades more diverse than others?2. Trait models (tempo and mode)3. Biogeography4. Phylogenetic selectivity of mass extinction (Prune whole clade versus set of tips)
6
Phylogeny and macroevolution
1. Diversification models.(why are some clades more diverse than others?2. Trait models (tempo and mode)3. Biogeography4. Phylogenetic selectivity of mass extinction (Prune whole clade versus set of tips)
7
Phylogeny and macroevolution
1. Diversification models.(why are some clades more diverse than others?2. Trait models (tempo and mode)3. Biogeography4. Phylogenetic selectivity of mass extinction (Prune whole clade versus set of tips)
8
Phylogeny and macroevolutionvs
1. Diversification models.(why are some clades more diverse than others?2. Trait models (tempo and mode)3. Biogeography4. Phylogenetic selectivity of mass extinction (Prune whole clade versus set of tips)
9
Go big or go home
1200 spp
Go big or go home
1200 spp
Go big or go home2000 spp
1200 spp
Go big or go home2000 spp
5000 spp
1200 spp
Go big or go home20000 spp2000 spp
5000 spp
Largest morphological matrices
Largest morphological matrices
86 | 4541
188 | 2954
192 | 610Gauthier et al 2012; Livezey and Zusi 2007; OLeary et al 2013
A practical alternative
A practical alternative
Pipelines
Pipelines
Informal supertree:
Pipelines
Formal supertree:
Informal supertree:
Pipelines
Informal supertree:Formal supertree:Metatree:
Problems with entering trees
Problems with entering trees
SupertreePublished figure:MetatreeTree from reanalysed matrix:Xu et al 2013
Problems with entering treesBell and Lloyd 2015
Informal supertrees dont adequately deal with phylogenetic uncertianty (maybe not best plot to show this!!!!!!!!!)25
Problems with entering trees
Bell and Lloyd 2015
Informal supertrees dont adequately deal with phylogenetic uncertianty (maybe not best plot to show this!!!!!!!!!)26
Metatree pipeline
Metatree pipeline
Datacollection
Taxonomicreconciliation
Filterdata
Addtaxonotree
Inference
Safe TaxonReduction
Weightingscheme
Metatree pipeline
Datacollection
Taxonomicreconciliation
Filterdata
Addtaxonotree
Inference
Safe TaxonReduction
Weightingscheme
Metatree pipeline
Datacollection
Metatree pipelinegraemetlloyd.com
Datacollection
Metatree pipelinegraemetlloyd.com
Datacollection2359 datasets
Metatree pipelinegraemetlloyd.com
Datacollection
2359 datasets
Metatree pipelinegraemetlloyd.com
Datacollection
2359 datasets
Metatree pipeline
Datacollection
ABCDEBaum 1992; Ragan 1992ABCDE
MatrixRepresentation
Metatree pipeline
Datacollection
MatrixRepresentation
ABCDE
ABCDE
01100Baum 1992; Ragan 1992
Metatree pipeline
Datacollection
MatrixRepresentation
ABCDE
ABCDE
0110000011Baum 1992; Ragan 1992
Metatree pipeline
Datacollection
MatrixRepresentation
ABCDE
ABCDE
011000001101111Baum 1992; Ragan 1992
Metatree pipeline
Datacollection
ABCDE
ABCDE
011000001101111Baum 1992; Ragan 1992
Metatree pipeline
Datacollection
MatrixRepresentation?
Metatree pipeline
Taxonomicreconciliation
Metatree pipeline
TaxonomicreconciliationOutgroupShortened nameJunior synonymValid taxonInvalid taxonHigher taxonPruneFull nameSenior synonymNothingPruneConstituent species
Metatree pipeline
Taxonomicreconciliation
Metatree pipeline
Taxonomicreconciliation
Metatree pipeline
Taxonomicreconciliation13285 962
Metatree pipeline
Filterdata
Metatree pipeline
Filterdata
Metatree pipeline
1998
Filterdata
Metatree pipeline
Addtaxonotree
Metatree pipelineABCDEFGHIJKL
ClassOrderFamilyGenus
Addtaxonotree
Metatree pipeline
Weightingscheme
Metatree pipeline
Weightingscheme
Metatree pipeline
Safe TaxonReduction
Metatree pipelinegithub.com/graemetlloyd/Claddis
Safe TaxonReduction
Metatree pipelinegithub.com/graemetlloyd/Claddis
Safe TaxonReduction-50 OTUs
Metatree pipeline
Inference
Metatree pipeline
Inference
Other metatrees
Other metatrees
Lloyd et al 2008; Lloyd 2014; Clarke et al in revision
Conclusions
Conclusions
Conclusions
Conclusions
Conclusions