An Introduction To MEDUSA

Joseph W. Brown, Richard G. FitzJohn, Graham J. Slater, Luke J. Harmon, and Michael E. Alfaro [email protected] Wednesday, 13 June, 12

Talk Outline I. The tempo of macroevolution II. Clade size disparity across the ToL III. The problem of extinction IV. Cetaceans & Carnivores V. Conclusions/Future directions

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An Introduction To MEDUSA - MacroInR 2012

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http://www.webpages.uidaho.edu/~lukeh/software/index.html An Introduction To MEDUSA - MacroInR 2012

Measuring the Tree of Life •

Estimates of the tempo of evolution can guide us towards an understanding of the mode of evolution



Allow contemplation of a number of questions 1.

Why is the ToL shaped the way it is?

2.

Why are some lineages more diverse than others?

3.

How are rates of lineage diversification and trait evolution related?

4.

Do changes in lineage diversification rates follow mass extinctions?

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An Introduction To MEDUSA - MacroInR 2012

speciation (λ)

Neontology-based Methods

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extinction (μ)

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An Introduction To MEDUSA - MacroInR 2012

High turnover

speciation (λ)

Neontology-based Methods

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extinction (μ)

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Wednesday, 13 June, 12

An Introduction To MEDUSA - MacroInR 2012

Modelling Lineage Diversification Birth-death Models •

Assume a time-homogeneous constant rate of speciation (λ) and extinction (μ)



units of lineage/lineage-unit-time Goal: to find the parameter values which best explain the observed edge lengths and speciation times.

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Nee et al. 1994. Phil. Trans. Roy. Soc. Y

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An Introduction To MEDUSA - MacroInR 2012

Fitting BD Models to Phylogenies Richness

The complete extant tree

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An Introduction To MEDUSA - MacroInR 2012

Merging Phylogenetic and Taxonomic Information Richness

Unsampled taxa

The complete extant tree

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Wednesday, 13 June, 12

An Introduction To MEDUSA - MacroInR 2012

Merging Phylogenetic and Taxonomic Information Richness

Unsampled taxa

The complete extant tree Collapse nodes, update richnesses X

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An Introduction To MEDUSA - MacroInR 2012

Merging Phylogenetic and Taxonomic Information Richness

Uncertain position

The complete extant tree It is often the case that we do not know exactly where an unsampled taxa lies in the tree i.e. crown vs. stem X

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Wednesday, 13 June, 12

An Introduction To MEDUSA - MacroInR 2012

Merging Phylogenetic and Taxonomic Information Richness

Uncertain position

The complete extant tree It is often the case that we do not know exactly where an unsampled taxa lies in the tree X

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An Introduction To MEDUSA - MacroInR 2012

Fitting a Birth-Death Process to a Tree

Construct our likelihood model by considering both phylogenetic (internal) and taxonomic (pendant) information

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An Introduction To MEDUSA - MacroInR 2012

Fitting a Birth-Death Process to a Tree

Internal Edges = Phylogenetic likelihood log LP = N•log(r) - r∑ELi - ∑log[1 - ε • exp(-r • xi)] N = # internal edges ε = extinction fraction (μ/λ) r = net diversification (λ-μ) xi = birth time of edge i X

ELi = length of edge i

Rabosky et al. 2007. Proc. Roy. Soc.

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An Introduction To MEDUSA - MacroInR 2012

Fitting a Birth-Death Process to a Tree

Pendant Edges = Taxonomic Likelihood log LT = ∑log(1-βi) + ∑(ni - 1) • βi ni = # extant species at tip i exp(r • ti) - 1 βi = exp(r • ti) - epsilon * These calculations are conditioned on survival (i.e. the phylogeny is observed) X

Raup. 1985. Paleobiology; Foote et al. 1999. Science Y

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An Introduction To MEDUSA - MacroInR 2012

Fitting a Birth-Death Process to a Tree

Likelihood Of Entire Tree log L(tree+diversity) = log LP + log LT

Goal: Identify values of r and ε that maximize the likelihood X

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An Introduction To MEDUSA - MacroInR 2012

Clade Disparity Across the ToL Problem



The ToL is decidedly unbalanced

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vertebrates, arthropods, plants, etc. Birth-death models predict trees more balanced than observed Suggests a single diversification model may be inadequate

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the is a general problem of any model-based inference: as data grow larger, it becomes increasingly less likely that the data conform to (or are best explained by) a single generating model

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Alfaro et al. 2009 PNAS

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An Introduction To MEDUSA - MacroInR 2012

Stepwise AIC Approach (MEDUSA) Algorithm For (x in 1:(num.nodes)): 1. Split move: Fit individual (piecewise) BD models to: 1. The clade defined by x, plus the edge leading to x 2. The remaining edges 2. Merge move (if num(models) > 2) 3. Find piecewise model with optimal AICc score



Is this a significant improvement over base model?

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Yes: Test subsequent splits.

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No:You’re done.

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AICc(break) - AICc(base)

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A drawback of fitting so many models is that spurious ‘significant’ results can arise

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Data Dredging •

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An Introduction To MEDUSA - MacroInR 2012

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Birth-Death AIC

We can use a threshold value of AICc to determine significant improvements to the model

• NOTE: this renders AIC-weights as

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meaningless (being an artefact of the size of the tree).

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However, the relationship between tree size and Type I error is straightforward

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AIC(no break) - AIC(break)

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An Introduction To MEDUSA - MacroInR 2012

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MEDUSA •

Learn about diversification dynamics through fitting piecewise models of birth (λ) and death (μ) -

Where have rates changed?

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By what magnitude?

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Why do clades differ in size? r = net diversification rate =λ-μ ε = extinction fraction =μ/λ X

Alfaro et al. 2009 PNAS

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Mammals

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Best described by a 26-piece diversification model

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An Introduction To MEDUSA - MacroInR 2012

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Angiosperms

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Best described by a 42-piece diversification model

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An Introduction To MEDUSA - MacroInR 2012

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Pereskia aculeata Maihuenia patagonica Pereskia lychnidiflora Quiabentia verticillata Pereskiopsis sp Opuntia leptocaulis Grusonia bradtiana Tephrocactus alexanderi Maihueniopsis atacamensis Pterocactus gonjianii Tunilla corrugata Miqueliopuntia miquelii Tacinga funalis Opuntia megasperma Nopalea cochenillifera Blossfeldia liliputana Echinocactus horizonthalonius Astrophytum capricorne Geohintonia mexicana Aztekium ritteri Ferocactus latispinus Stenocactus coptogonus Thelocactus hastifer Leuchtenbergia principis Strombocactus disciformis Ariocarpus fissuratus Turbinicarpus shcmedickeanus Acharagma aguirreana Obregonia denegrii Lophophora williamsii Coryphantha erecta Mammillaria magnimmama Cochemiea poselgeri Neolloydia conoidea Ortegocactus macdougalii Copiapoa humilis Frailea pumila Calymmanthium substerile Lepismium cruciforme Rhipsalis baccifera Schlumbergera truncata Hatiora salicornoides Neowerdermannia vorwerkii Eriosyce taltalensis Parodia erinaceae Uebelmania pectinifera Browningia hertlingiana Rebutia arenacea Cereus aethiops Micranthocereus albicephalus Coleocephalocereus fluminensis Stetsonia coryne Pilosocereus chrysacanthus Arrojadoa rhodantha Melocactus curvispinus Discocactus boomianus Gymnocalycium guanchinense Espostoa nana Matucana madisoniorum Espostoopsis dybowskii Rauhocereus sp Oreocereus celsianus Mila caespitosa Pygmaeocereus bylesianus Haagocereus limensis Acanthocalycium spiniflorum Denmoza rhodacantha Echinopsis pasacana Harrisia pomanensis Cleistocactus parviflorus Samaipaticereus corroanus Weberbauerocereus johnsonii Pfeiffera ianthothele Eulychnia castanea Austrocactus bertinii Corryocactus aureus Neoraimondia herzogiana Pseudoacanthocereus sicariguensis Armatocereus godingianus Castellanosia caineana Dendrocereus nudiflorus Leptocereus leonii Acanthocereus tetragonus Peniocereus chiapensis Epiphyllum phyllanthus Disocactus flageliformis Hylocereus undatus Weberocereus glaber Selenicereus donkelaarii Echinocereus cinerasens Pachycereus dumortierii Myrtillocactus geometrisans Escontria chiotilla Stenocereus pruinosus Polaskia chichipe Bergerocactus emoryi Neobuxbaumia polylopha Cephalocereus senilis Mytrocereus fulviceps Peniocereus greggii Lophocereus schottii Pachycereus pecten aboriginum Carnegiea gigantea

Multiple Trees Rate

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A distribution of trees can be passed to MEDUSA Each tree is individually fit

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Shifts

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1.0 0.5 0.1

1.044 0.899 0.755 0.610 0.466 0.321 0.177

The results are plotted on some consensus or optimal tree

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Wednesday, 13 June, 12

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Divergence Time (MYA)

An Introduction To MEDUSA - MacroInR 2012

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Hypothesis Testing With MEDUSA



Sometimes we may not be interested in dredging for the best model, but instead some specific hypothesis

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this may involve fixing specific parameter values (say, with extinction results from the fossil record)

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comparison of a focal clade against the larger tree comparisons across sister clades

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Wednesday, 13 June, 12

An Introduction To MEDUSA - MacroInR 2012

Large Problems



For large and/or multiple trees, it is efficient to utilize multiple computing cores



MEDUSA can make use of multiple cores, but: 1. only non-Windows 2. only non-GUI

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An Introduction To MEDUSA - MacroInR 2012

The Problem of Extinction

1. Extinction rates are poorly estimated if birth-death model assumptions are violated



E.g. rates are not time-homogeneous

2. We know that some lineages were more speciose in the past!

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Rabosky. 2010. Evolution

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An Introduction To MEDUSA - MacroInR 2012

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Fitting birth-death models to molecular phylogenies

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An Introduction To MEDUSA - MacroInR 2012

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Fitting birth-death models to molecular phylogenies

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An Introduction To MEDUSA - MacroInR 2012

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Fitting birth-death models to molecular phylogenies

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An Introduction To MEDUSA - MacroInR 2012

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Fitting birth-death models to molecular phylogenies

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An Introduction To MEDUSA - MacroInR 2012

Existing Maths •

The paleontological literature is replete with maths describing changes in diversity (both increases and decreases)



These paleontological likelihoods can be spliced with phylogenetic likelihoods to more fully explain macroevolutionary dynamics

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Raup. 1985. Paleobiology; Foote et al. 1999. Science Y

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Wednesday, 13 June, 12

An Introduction To MEDUSA - MacroInR 2012

Fit Birth-Death Process to Tree, With Fossils n fossils

Divide edge into 2 (or more) sub-edges For interval t1, calculate like pendant edge For interval t2, assuming fossils are exact:

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t2

Entire Tree log LT = log LI + log LP + log LF X

Raup. 1985. Paleobiology; Foote et al. 1999. Science Y

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Wednesday, 13 June, 12

An Introduction To MEDUSA - MacroInR 2012

Fit Birth-Death Process to Tree, With Fossils Treating a fossil as a minimum count:

t1

t2

Entire Tree log LT = log LI + log LP + log LF X

Raup. 1985. Paleobiology; Foote et al. 1999. Science Y

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An Introduction To MEDUSA - MacroInR 2012



Fossil richness information can come from: 1.

Time-slice(s) through the tree



May be appropriate when considering periods of following mass extinction

2. Unique time periods for each taxon



Appropriate when temporal quality of the fossil record differs across taxa, or if trying to incorporate the maximum amount of information from the fossil record

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An Introduction To MEDUSA - MacroInR 2012

Balaenopteroidea Eubalaena Pontoporiidae Iniidae Lipotes vexillifer AF304071 Delphinapterus leucas DLU72037 Monodon monoceros MMU72038 Phocoenidae Orcinus orca AF084061 Orcaella brevirostris AF084063 Pseudorca crassidens AF084057 Grampus griseus AF084059 Globicephala macrorhynchus AF084055 Feresa attenuata AF084052 Lagenorhynchus acutus AF084075 Lagenorhynchus albirostris Lagenorhynchus cruciger AF084068 Lagenorhynchus australis AF084069 Cephalorhynchus hectori AF084071 Cephalorhynchus commersonii AF084073 Cephalorhynchus eutropia AF084072 Cephalorhynchus heavisidii AF084070 Lagenorhynchus obscurus AY257161 Lagenorhynchus obliquidens AF084067 Lissodelphis borealis AF084064 Steno bredanensis AF084077 Sotalia guianensis DQ086827 Sotalia fluviatilis AF304067 Tursiops truncatus AF084095 Tursiops aduncus AF084091 Stenella frontalis AF084090 Stenella coeruleoalba AF084082 Stenella clymene AF084083 Delphinus tropicalis AF084088 Delphinus delphis AF084085 Delphinus capensis AF084087 Lagenodelphis hosei AF084099 Stenella attenuata AF084096 Sousa chinensis AF084080 Stenella longirostris AF084103 Ziphiidae Platinistoidea Physeteroidea

Cetaceans •

Cetaceans are of particular interest, as several lineages have previously enjoyed higher diversity in the past

Slater et al. 2010. Proc. Roy. Soc. X

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An Introduction To MEDUSA - MacroInR 2012

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Fossil richness at 10 MY 42

Balaenopteroidea Eubalaena Pontoporiidae Iniidae Lipotes vexillifer AF304071 Delphinapterus leucas DLU72037 Monodon monoceros MMU72038 Phocoenidae Orcinus orca AF084061 Orcaella brevirostris AF084063 Pseudorca crassidens AF084057 Grampus griseus AF084059 Globicephala macrorhynchus AF084055 Feresa attenuata AF084052 Lagenorhynchus acutus AF084075 Lagenorhynchus albirostris Lagenorhynchus cruciger AF084068 Lagenorhynchus australis AF084069 Cephalorhynchus hectori AF084071 Cephalorhynchus commersonii AF084073 Cephalorhynchus eutropia AF084072 Cephalorhynchus heavisidii AF084070 Lagenorhynchus obscurus AY257161 Lagenorhynchus obliquidens AF084067 Lissodelphis borealis AF084064 Steno bredanensis AF084077 Sotalia guianensis DQ086827 Sotalia fluviatilis AF304067 Tursiops truncatus AF084095 Tursiops aduncus AF084091 Stenella frontalis AF084090 Stenella coeruleoalba AF084082 Stenella clymene AF084083 Delphinus tropicalis AF084088 Delphinus delphis AF084085 Delphinus capensis AF084087 Lagenodelphis hosei AF084099 Stenella attenuata AF084096 Sousa chinensis AF084080 Stenella longirostris AF084103 Ziphiidae Platinistoidea Physeteroidea

2 4

Cetaceans

2



Cetaceans are of particular interest, as several lineages have previously enjoyed higher diversity in the past Data from G Slater via the Paleobiology Database (http://paleodb.org)

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Slater et al. 2010. Proc. Roy. Soc. X

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An Introduction To MEDUSA - MacroInR 2012

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Balaenoptera acutorostrata Eubalaena japonica Pontoporia blainvillei AF334488 Inia geoffrensis geoffrensis AF334485 Lipotes vexillifer AF304071 Delphinapterus leucas DLU72037 Monodon monoceros MMU72038 Neophocaena phocaenoides AF334489 Orcinus orca AF084061 Orcaella brevirostris AF084063 Pseudorca crassidens AF084057 Grampus griseus AF084059 Globicephala macrorhynchus AF084055 Feresa attenuata AF084052 Lagenorhynchus acutus AF084075 Lagenorhynchus albirostris Lagenorhynchus cruciger AF084068 Lagenorhynchus australis AF084069 Cephalorhynchus hectori AF084071 Cephalorhynchus commersonii AF084073 Cephalorhynchus eutropia AF084072 Cephalorhynchus heavisidii AF084070 Lagenorhynchus obscurus AY257161 Lagenorhynchus obliquidens AF084067 Lissodelphis borealis AF084064 Steno bredanensis AF084077 Sotalia guianensis DQ086827 Sotalia fluviatilis AF304067 Tursiops truncatus AF084095 Tursiops aduncus AF084091 Stenella frontalis AF084090 Stenella coeruleoalba AF084082 Stenella clymene AF084083 Delphinus tropicalis AF084088 Delphinus delphis AF084085 Delphinus capensis AF084087 Lagenodelphis hosei AF084099 Stenella attenuata AF084096 Sousa chinensis AF084080 Stenella longirostris AF084103 Tasmacetus shepherdi AF334484 Platanista gangetica AF304070 Physeter catodon X75589

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Very low extinction rates inferred

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An Introduction To MEDUSA - MacroInR 2012

Incorporating Fossils

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3Balaenopteroidea Eubalaena Pontoporiidae Iniidae Lipotes vexillifer AF304071 Delphinapterus leucas DLU72037 Monodon monoceros MMU72038 Phocoenidae Orcinus orca AF084061 Orcaella brevirostris AF084063 Pseudorca crassidens AF084057 Grampus griseus AF084059 Globicephala macrorhynchus AF084055 Feresa attenuata AF084052 Lagenorhynchus acutus AF084075 Lagenorhynchus albirostris Lagenorhynchus cruciger AF084068 Lagenorhynchus australis AF084069 Cephalorhynchus hectori AF084071 Cephalorhynchus commersonii AF084073 Cephalorhynchus eutropia AF084072 Cephalorhynchus heavisidii AF084070 Lagenorhynchus obscurus AY257161 Lagenorhynchus obliquidens AF084067 Lissodelphis borealis AF084064 Steno bredanensis AF084077 Sotalia guianensis DQ086827 Sotalia fluviatilis AF304067 Tursiops truncatus AF084095 Tursiops aduncus AF084091 Stenella frontalis AF084090 Stenella coeruleoalba AF084082 Stenella clymene AF084083 Delphinus tropicalis AF084088 Delphinus delphis AF084085 Delphinus capensis AF084087 Lagenodelphis hosei AF084099 Stenella attenuata AF084096 Sousa chinensis AF084080 Stenella longirostris AF084103 Ziphiidae Platinistoidea Physeteroidea

0

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An Introduction To MEDUSA - MacroInR 2012

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Base model

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3Balaenopteroidea Eubalaena Pontoporiidae Iniidae Lipotes vexillifer AF304071 Delphinapterus leucas DLU72037 Monodon monoceros MMU72038 Phocoenidae Orcinus orca AF084061 Orcaella brevirostris AF084063 Pseudorca crassidens AF084057 Grampus griseus AF084059 Globicephala macrorhynchus AF084055 Feresa attenuata AF084052 Lagenorhynchus acutus AF084075 Lagenorhynchus albirostris Lagenorhynchus cruciger AF084068 Lagenorhynchus australis AF084069 Cephalorhynchus hectori AF084071 Cephalorhynchus commersonii AF084073 Cephalorhynchus eutropia AF084072 Cephalorhynchus heavisidii AF084070 Lagenorhynchus obscurus AY257161 Lagenorhynchus obliquidens AF084067 Lissodelphis borealis AF084064 Steno bredanensis AF084077 Sotalia guianensis DQ086827 Sotalia fluviatilis AF304067 Tursiops truncatus AF084095 Tursiops aduncus AF084091 Stenella frontalis AF084090 Stenella coeruleoalba AF084082 Stenella clymene AF084083 Delphinus tropicalis AF084088 Delphinus delphis AF084085 Delphinus capensis AF084087 Lagenodelphis hosei AF084099 Stenella attenuata AF084096 Sousa chinensis AF084080 Stenella longirostris AF084103 Ziphiidae Platinistoidea Physeteroidea

0

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Incorporating Fossils

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0.498 r (b-d)

An Introduction To MEDUSA - MacroInR 2012

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3Balaenopteroidea Eubalaena Pontoporiidae Iniidae Lipotes vexillifer AF304071 Delphinapterus leucas DLU72037 Monodon monoceros MMU72038 Phocoenidae Orcinus orca AF084061 Orcaella brevirostris AF084063 Pseudorca crassidens AF084057 Grampus griseus AF084059 Globicephala macrorhynchus AF084055 Feresa attenuata AF084052 Lagenorhynchus acutus AF084075 Lagenorhynchus albirostris Lagenorhynchus cruciger AF084068 Lagenorhynchus australis AF084069 Cephalorhynchus hectori AF084071 Cephalorhynchus commersonii AF084073 Cephalorhynchus eutropia AF084072 Cephalorhynchus heavisidii AF084070 Lagenorhynchus obscurus AY257161 Lagenorhynchus obliquidens AF084067 Lissodelphis borealis AF084064 Steno bredanensis AF084077 Sotalia guianensis DQ086827 Sotalia fluviatilis AF304067 Tursiops truncatus AF084095 Tursiops aduncus AF084091 Stenella frontalis AF084090 Stenella coeruleoalba AF084082 Stenella clymene AF084083 Delphinus tropicalis AF084088 Delphinus delphis AF084085 Delphinus capensis AF084087 Lagenodelphis hosei AF084099 Stenella attenuata AF084096 Sousa chinensis AF084080 Stenella longirostris AF084103 Ziphiidae Platinistoidea Physeteroidea

epsilon (d/b)

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High baseline extinction inferred

0.747

Incorporating Fossils

An Introduction To MEDUSA - MacroInR 2012

0.747

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epsilon (d/b)

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New shift in diversification rate identified

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X

30

1

0

40

0.747

r (b-d)

epsilon (d/b)

2

3Balaenopteroidea Eubalaena Pontoporiidae Iniidae Lipotes vexillifer AF304071 Delphinapterus leucas DLU72037 Monodon monoceros MMU72038 Phocoenidae Orcinus orca AF084061 Orcaella brevirostris AF084063 Pseudorca crassidens AF084057 Grampus griseus AF084059 Globicephala macrorhynchus AF084055 Feresa attenuata AF084052 Lagenorhynchus acutus AF084075 Lagenorhynchus albirostris Lagenorhynchus cruciger AF084068 Lagenorhynchus australis AF084069 Cephalorhynchus hectori AF084071 Cephalorhynchus commersonii AF084073 Cephalorhynchus eutropia AF084072 Cephalorhynchus heavisidii AF084070 Lagenorhynchus obscurus AY257161 Lagenorhynchus obliquidens AF084067 Lissodelphis borealis AF084064 Steno bredanensis AF084077 Sotalia guianensis DQ086827 Sotalia fluviatilis AF304067 Tursiops truncatus AF084095 Tursiops aduncus AF084091 Stenella frontalis AF084090 Stenella coeruleoalba AF084082 Stenella clymene AF084083 Delphinus tropicalis AF084088 Delphinus delphis AF084085 Delphinus capensis AF084087 Lagenodelphis hosei AF084099 Stenella attenuata AF084096 Sousa chinensis AF084080 Stenella longirostris AF084103 Ziphiidae Platinistoidea Physeteroidea

epsilon (d/b)

1

High baseline extinction inferred

0.747

Incorporating Fossils

An Introduction To MEDUSA - MacroInR 2012

0.747

1

0

0

0.245

0.498

epsilon (d/b)

0.498 0.245

epsilon (d/b)

0.747

0.747

1

1

Cetaceans

0

0.245

0.498

0.747

r (b-d)

0

0.245

0.498

time

Wednesday, 13 June, 12

1

With fossils

The incorporation of fossil richness information dramatically changes our inference from little extinction to very high extinction

Y

Z

0.747

r (b-d)

No fossils

X

1

An Introduction To MEDUSA - MacroInR 2012

Carnivore Fossil Richness

15 10

richness

5

10

richness

10

5 0

0 -15

-10

-5

-15

-10

-5

-40 -30 -20 -10

0

-35

-25

-15

-5

-15

-10

-5

age (mya)

age (mya)

age (mya)

age (mya)

Otariidae

Odobenidae

Mephitidae

Mustelidae

Procyonidae

-12

-8 -6 -4 -2 age (mya)

8 6 2

4

richness

40 30 10

2 -15

-10

age (mya)

-5

-12

-8 -6 -4 -2 age (mya)

0

0

0

1

2

2

20

richness

6 4

richness

4 3

6

richness

8

5

50

8

10

6

60

age (mya)

4

richness

Phocidae

15

40 30 20

richness

20 15 10 5

richness

Ursidae

20

Canidae

25

Hyaenidae

10 20 30 40 50 60

richness

Felidae

-35

-25

-15

-5

age (mya)

-20 -15 -10

-5

age (mya)

X

G Slater via the Paleobiology Database (http://paleodb.org) Y

Z

time

Wednesday, 13 June, 12

An Introduction To MEDUSA - MacroInR 2012

Without Fossil Information

0.495 0.242

epsilon (d/b)

0.747

1

Piecewise Birth-Death Model #1

0

1

2 0.009

0.05

0.092

0.134

0.177

r (b-d)

0.495 0

0.242

epsilon (d/b)

0.747

1

Piecewise Birth-Death Model #2

Cryptoprocta ferox Fossa fossana Eupleres goudotii Cynogale bennettii Chrotogale owstoni Hemigalushosei derbyanus Diplogale Nandinia binotata Arctogalidia trivirgata Macrogalidia musschenbroekii Paguma larvata Arctictis binturong Paradoxurus hermaphroditus Paradoxurus zeylonensis Paradoxurus jerdoni Civettictis civetta Viverricula indica Viverra zibetha Viverra tangalunga Viverra megaspila Viverra civettina Genettaleightoni piscivora Poiana Poiana richardsonii Prionodon pardicolor Prionodon linsang Genetta victoriae Genetta Genetta cristata servalina Genetta tigrina Genetta genetta Genetta maculata Genetta poensis pardina Genetta Genetta angolensis Genetta johnstoni Genetta Genetta thierryi abyssinica Mungotictis decemlineata Galidia elegans Galidictis grandidieri Galidictis concolor fasciata Salanoia Atilax paludinosus Rhynchogale melleri Dologale dybowskii Herpestes vitticollis Herpestes naso Herpestes Herpestes smithii semitorquatus Herpestes ichneumon Herpestes urva Herpestes fuscus Herpestes javanicus brachyurus Herpestes Herpestes edwardsi Galerella flavescens pulverulenta Galerella Galerella ochracea Galerella sanguinea Paracynictis selousi Cynictis penicillata Bdeogale nigripes Bdeogale jacksoni Bdeogale crassicauda Liberiictissuricatta kuhni Suricata Ichneumia albicauda Crossarchus alexandri Crossarchus ansorgei Crossarchus platycephalus Crossarchus obscurus Mungos gambianus mungo Mungos Helogale parvula Helogale hirtula Proteles crocuta cristata Crocuta Hyaena brunnea Hyaena hyaena Acinonyx jubatus Puma yagouaroundi concolor Puma Prionailurus Prionailurus planiceps rubiginosus Prionailurus viverrinus Prionailurus iriomotensis Prionailurus bengalensis Leptailurus serval Caracal caracal Felis manul Felis chaus Felis bieti Felis silvestris catus Felis Felis Felis nigripes margarita Leopardus wiedii Leopardus pardalis Leopardus Leopardus jacobitus colocolo Leopardus pajeros Leopardus braccatus Leopardus guigna Leopardus geoffroyi Leopardus tigrinus Profelis aurata Catopuma temminckii Catopuma badia Lynx pardinus rufus Lynx Lynx lynx Lynx canadensis Pardofelis marmorata Neofelis nebulosa Uncia uncia Panthera tigris Panthera onca Panthera pardus Panthera leo Otocyon megalotis Urocyon littoralis Urocyon cinereoargenteus Vulpes chama pallida Vulpes Vulpes bengalensis Vulpes zerda Vulpes cana Vulpes velox macrotis Vulpes Vulpes lagopus Vulpes Vulpes vulpes rueppellii Vulpes ferrilata Vulpes corsac Nyctereutes procyonoides Lycalopex vetulus Lycalopex griseus Lycalopex Lycalopex fulvipes culpaeus Lycalopex sechurae Lycalopex gymnocercus Atelocynus microtis Chrysocyon brachyurus Speothos venaticus Lycaon pictus Canis mesomelas Canis Canis aureus adustus Canis latrans Canis Canis lupus simensis Cerdocyon thous Cuon alpinus Ailuropoda melanoleuca Tremarctos ornatus Ursus americanus Ursus thibetanus Ursus maritimus Ursus arctos Melursus ursinus Helarctos malayanus Monachus monachus Monachusleonina schauinslandi Mirounga Mirounga angustirostris Ommatophoca rossii Leptonychotes weddellii Lobodon carcinophaga Hydrurga leptonyx Erignathus barbatus Cystophora cristata Pagophilus groenlandicus Histriophoca fasciata Halichoerus grypus Phoca largha vitulina Phoca Pusa caspica Pusa Pusa sibirica hispidaursinus Callorhinus Arctocephalus pusillus Arctocephalus tropicalis gazella Arctocephalus Arctocephalus townsendi Arctocephalus Arctocephalus australis galapagoensis Arctocephalus forsteri Arctocephalus philippii Zalophus japonicus Zalophus wollebaeki Zalophus californianus Eumetopias jubatus Otaria flavescens Phocarctos hookeri Neophoca cinerea Odobenus rosmarus Ailurusflavus fulgens Potos Bassaricyon Bassaricyon lasius alleni Bassaricyon pauli Bassaricyon gabbii Bassaricyon beddardi Bassariscus astutus sumichrasti Bassariscus Nasuella olivacea Nasua nasua Nasua narica Procyon cancrivorus pygmaeus Procyon Procyon lotor Mellivora Neovison capensis vison Neovison macrodon Mustela Mustela kathiah felipei Mustela africana Mustela erminea Mustela altaica Mustela subpalmata Mustela frenata nivalis Mustela Mustela putorius Mustela Mustela nigripes eversmanii Mustela nudipes Mustela itatsi Mustela strigidorsa sibirica Mustela Mustela lutreola Mustela lutreolina Poecilogale albinucha Vormela peregusna Ictonyx striatus Ictonyx libyca Lyncodon patagonicus Galictis cuja vittata Galictis Eira Gulobarbara gulo Martes pennanti Martes gwatkinsii Martes Martes flavigula foina Martes martes Martes zibellina Martes Martes melampus americana Spilogale pygmaea Spilogale putorius Spilogale angustifrons Spilogale gracilis Mephitis macroura mephitis Mephitis Conepatus Conepatus semistriatus humboldtii Conepatus leuconotus Conepatus chinga Enhydra lutris Pteronura perspicillata brasiliensis Lutrogale Hydrictis maculicollis Aonyx cinerea Aonyx capensis Lutra nippon sumatrana Lutra Lutra Lontralutra canadensis Lontra longicaudis Lontra provocax Lontra Mydausfelina marchei Mydaus javanensis Meles leucurus Meles meles Meles anakuma Arctonyx collaris Taxidea taxus Melogale personata Melogale Melogale everetti moschata Melogale orientalis

X

0.03

0.167

0.311 r (b-d)

Y

Z

time

Wednesday, 13 June, 12

0.454

0.597

60

Fritz et al. 2009. Ecol. Lett

50

40

30

20

Divergence Time (MYA)

An Introduction To MEDUSA - MacroInR 2012

10

0

Incorporating Fossils

Current Richness 8 1 34 2 33

split

r

epsilon

1

0.039537

0.98054

4 40 35

2

0.081911

0.42352

3

4.79E-11

0.51603

4

0.075288

0.72951

16

5

0.085828

0.60761

1

8 19

1 14 12 59

X

Y

Z

time

Wednesday, 13 June, 12

An Introduction To MEDUSA - MacroInR 2012

Conclusions/Implications 1. Incorporating fossil richness information:



gives reasonable estimates of extinction rate



refines/overturns our understanding of patterns of macroevolutionary diversification

2. However, methods are only applicable to lineages with a decent fossil record



Can we accurately reconstruct past diversification dynamics from taxa lacking a fossil record?

X

Y

Z

time

Wednesday, 13 June, 12

An Introduction To MEDUSA - MacroInR 2012

An Introduction To MEDUSA

Jun 13, 2012 - http://www.webpages.uidaho.edu/~lukeh/software/index.html. Wednesday, 13 June, 12 ..... Time-slice(s) through the tree. • May be appropriate ...

12MB Sizes 1 Downloads 54 Views

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