PowerPoint Presentation

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)

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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