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Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics. New Guinea forest wallaby. matt.phillips@anu.edu.au Centre for Macroevolution & Macroecology, Research School of Biology, Australian National University.

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Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

New Guinea forest wallaby

matt.phillips@anu.edu.au

Centre for Macroevolution & Macroecology, Research School of Biology, Australian National University


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

“Phylogenetics is concerned with the problem of reconstructing the past evolutionary history of extant organisms from present day molecular data”

– Phylomania 2010 website

Horse evolution & Macroevolutionary theory, e.g. Cope’s rule

Darwin’s (the 1st ?) phylogenetic tree


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Molecular data reconstructing the past evolutionary history of extant organisms from present day molecular data”:

Invaluable for phylogenetic inference

Morphological studies had left us with 1.99  1021 possible relationships among the 29 orders

Molecular studies now leave us with ≈405 possible relationships

Phillips & Penny (2010)


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Molecular data reconstructing the past evolutionary history of extant organisms from present day molecular data”:

Is molecular phylogeny above the species level a pursuit of diminishing returns (for theoreticians)?

Remaining uncertainty involves lineage sorting: genomic retroposons better than species-tree methods for assigning ancestry

In either case, the interesting question of individual gene ancestry is defeated by stochastic error


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

21kb of nuclear genes for 57 marsupial&placental mammals reconstructing the past evolutionary history of extant organisms from present day molecular data”

BEAST relaxed clock (lognormal dist. branch rates), 13 FR calibration priors – unconstrained, 20 lineages originate in the Cretaceous

99 mya

(83-116HPD)

Cretaceous Period

Work with Kate Loynes


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Rates of DNA substitution (subs/site/Ma) on individual branches

Dark blue: unconstrained

Light blue: 4 placental lineages in Cretaceous

Red: no placentals cross into Cretaceous

Cretaceous Tertiary

Loynes & Phillips (in prep)


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

21kb nuclear genes for 57 marsupial & placentals mammals branches

BEAST relaxed clock (as previous) – now constraining ≤4 placental lineages to originate in the Cretaceous

82 mya

(73-93HPD)

Cretaceous Period


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Cut-out section of the placental mammal tree, with putative relationships of fossils from close to or before the K/T boundary

More fossils confidently assigned to branches on the modern tree could immediately solve the K/T boundary problem

67

86

All these fossils may be stem placentals

Kulbeckia

86

92

And for the overall evolutionary timescale , reduces reliance on assumptions for how rates vary among branches

65


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Ancestral state reconstruction relationships of fossils from close to or before the K/T boundary

Meredith et al (MPE, 2009)

Foraging height

Arboreality inferred at all deep nodes

But megafaunal extinction was biased towards large/terrestrial

Palorchestes

Include 5 extinct sub-families


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

“Pull of the recent” peaks relationships of fossils from close to or before the K/T boundary

Lineage through time analysis

Null hypothesis of constant net diversification (speciation-extinction) is linear

Marsupial divergence times

Ln (accumulated branching events)

Penny & Phillips (Nature, 2006)

Million years ago

Turnover associated with recent biotic/aboitic events overwrites more ancient signals


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Hurdles for morphological phylogenetics relationships of fossils from close to or before the K/T boundary: progress is being made in some areas

  • Long branch attraction – A serious problem when MP is standard

ML models (e.g. Mk or Mkv of Lewis (Syst Biol, 2001) outperform MP


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

State 1 State 2 relationships of fossils from close to or before the K/T boundary

frequency

Trait score

Other problems include:

  • Developmental correlations (e.g. upper/lower molars)

  • Outgroup attraction of ecological long branches (e.g. turtles)

  • Objectivity in character state discrimination

If no clear pattern or unimodal, exclude or score as constant


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Functional/ecological correlations relationships of fossils from close to or before the K/T boundary

  • Babies cute/ugly

  • Wing development slow/rapid

  • Leg development rapid/slow

Pigeon

Emu

Chicken

Ducks

Galah

Not really three characters providing a strong phylogenetic signal Evolutionarily non-independent, associated with parenting strategy


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Marsupials arrived in Australasia 55-70 mya from S.America, via Antarctica

Microbiotheria

Diprotodontia

“Polyprotodontia”


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Thylacoleo carnifex via Antarctica110kg

Diprotodon opatum ~2500kg

Diprotodontia: The most ecologically diverse mammal order

Terrestrial herbivores, arboreal insectivores and a multitude of niches in between


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Diprotodontia: 10 extant families via Antarctica(≈ 120 species)

Vombatidae = wombats (Burrowing grazers)

Phascolarctidae = koala (Arboreal folivores)

Burramyidae = pygmy possums (Mostly-terrestrial to mostly arboreal gramnivores and generalized omnivores)


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Macropodidae = kangaroos and potoroos via Antarctica (Bipedal hopping browsers/grazers and semi-fossorial root/fungi feeders)

Tarsipedidae = honey possum (Arboreal nectivore)

Hypsiprymnodontidae = musky rat-kangaroo (Terrestrial, bounding frugivore-omnivore)


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Acrobatidae = feathertail possums via Antarctica (Gliding/arboreal omnivores)

Pseudocheiridae = Ringtail possums (Arboreal folivores)

Petauridae = gliders and trioks (Gliding gumnivores and arboreal insectivores)

Phalangeridae = Brushtail possums and cuscuces (Scansorial to arboreal frugivores-folivores)


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Diprotodontian consensus phylogeny via Antarctica: Cardillo et al. (J. Zool, 2004)

Vombatidae (wombats)

Vombatiformes

Phascolarctidae (koala)

Burramyidae (pygmy possums)

Tarsipedidae (honey possum)

Petauridae (gliders, stripped possums)

“Core” Petauroidea

Pseudocheiridae (ringtail possums)

Acrobatidae (feathertail possums)

Phalangeridae (cuscuses and brushtail possums)

Macropodidae (kangaroos and potoroos)

Macropodoidea

Hypsiprymnodontidae (musky rat-kangaroo)


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Phillips and Pratt ( via AntarcticaMPE, 2008): mitochondrial (mt) genomes

Beck (J. Mammalogy, 2008): several mt & nuclear genes

Meredith et al. (MPE, 2009): 5-nuclear genes

Vombatidae

Phascolarctidae

Acrobatidae

Tarsipedidae

Petauridae

Pseudocheiridae

Macropodidae

Hypsiprymnodontidae

Phalangeridae

Burramyidae


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Molecular “supermatrix” via Antarctica: 26 marsupials  20,654 nucleotides

Complete mt genome protein/RNA coding sequences & 5 nuclear genes (RAG1, BRCA1, IRBP, vWF, APOB)

  • Analysed as 13 separately modelled process partitions

  • Mitochondrial protein 3rd codons RY-coded to reduce saturation and compositional non-stationarity


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

All nodes MrBayes BPP = 1.00 and RAxML BP >95%, via Antarctica(except where noted)

wombats

koala

musky rat-kangaroo

kangaroos

Diprotodontia

pygmy possums

cuscuses

feathertail possums

honey possum

gliders

ringtail possums

bandicoots

“Polyprotodontia”

marsupial mole

0.97 / 72

dasyurids


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Mt sequence analyses MRP supertree summary via Antarctica

Single nuclear genes MRP supertree summary

Albumin M’CF Baverstock et al. 1990 (review)

DNA hybridization Kirsch et al. 1997 (review)

Algorithmic morphology morphol352 (MP)

Algorithmic morphology morphol352 (ML, Bayesian)

Previous work on the family-level phylogeny of Diprotodontia

Informal-comparative morphology MRP supertree

Algorithmic morphology (MP) MRP supertree summary


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Differences between informal-comparative and algorithmic morphology

Algorithmic

MP, ML etc.

Homology, otherwise biology-free

Many and varied (inc. bootstrap)

Informal-comparative

vague

Homology, untangling funct/dev correlation form phylogenetic signal

Non-statistical

Selection criterion

Character analysis

Hypothesis testing


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

How do these data / methods perform? morphology

One test would be whether or not they reject the molecular consensus - not helpful … Hypothesis testing is difficult with distance methods like DNA hybridization and impossible with informal-comparative morphology

Alternative: Likelihood disadvantage on the 20,654 nucleotide molecular matrix for a fairer comparison of data / methods

Example:

–lnL(consensus) = 121,316.3

–lnL(DNA hybridization tree) = 121,438.2

lnL disadvantage = 121.9


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Mt sequence analyses 84.4 morphology

Single nuclear genes 96.0

Albumin M’CF 182.4

DNA hybridization 121.9

Algorithmic morphology morphol352 (MP/ML) 594.6

Algorithmic morphology morphol352 (Bayes) 617.5

Likelihood disadvantages

Informal-comparative morphology 71.7

Algorithmic morphology (MP) 690.1


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

5 outgroup taxa morphology

Vombatidae

100

Phascolarctidae

Acrobatidae

100

95

Tarsipedidae

53

Petauridae

74

87

Pseudocheiridae

Macropodidae

*

Hypsiprymnodontidae

73

Phalangeridae

61

Burramyidae

Do the algorithmic analyses just suffer from stochastic blindness?

  • Scaled the molecular-dated marsupial tree to the treelength of the morphol352 ML tree

  • Simulated 60,000 character “pseudomorphological” dataset, Sim352 in Seq-gen (JC, equivalent to Mk4). 1000 boots, 352 chs


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Vombatidae morphology

Phascolarctidae

Macropodidae

Phalangeridae

Pseudoch’idae

Petauridae

Acrobatidae

Burramyidae

Tarsipedidae

Algorithmic morphology

Molecular consensus

Vombatidae

Phascolarctidae

Acrobatidae

Tarsipedidae

Petauridae

Pseudocheiridae

Macropodidae

Phalangeridae

Burramyidae


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Can we mimic the real morphological data by combining molecular phylogenetic and ecological signals ?

60,000 characters

5 outgroup taxa

Vombatidae

Size

Diet

Phascolarctidae

Sim352

phylogenetic signal as per the molecular dated tree, scaled to morphol352 treelength

Acrobatidae

0 = <50g

0 = herb

Tarsipedidae

1 = 50-200g

1 = sub-herb

2 = 200-800g

2 = omniv

Petauridae

3 = 800g-3kg

3 = sub-carn

Pseudocheiridae

4 = 3-12kg

4 = carn

Macropodidae

5 = >12kg

Phalangeridae

Burramyidae

ordered states


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Optimum fit to the molecular consensus tree (0% ecological contribution)

Optimum fit to the algorithmic morphology tree (9% ecol. cont.)

0

2

4

% MP tree length disadvantage

6

8

10

0

8

16

24

32

% ecological contribution to MP tree length


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Phylo-ecol sim contribution)

Vombatidae

Phascolarctidae

Macropodidae

Phalangeridae

Pseudoch’idae

Petauridae

Acrobatidae

Burramyidae

Tarsipedidae

Algorithmic morphology

Molecular consensus

Vombatidae

Phascolarctidae

Acrobatidae

Tarsipedidae

Petauridae

Pseudocheiridae

Macropodidae

Phalangeridae

Burramyidae

Phylogenetic randomization test P-value = 0.00016


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Alg. Morphol. tree “True” tree contribution)

a. MP on morphol352741 steps 782 steps

Tempting next move: Reverse engineered phylogeny

If the algorithmic morphology (morphol352) data is effectively 91% phylogenetic signal, 9% ecological signal … what if we subtract the 9% ecological signal from the observed signal?

b. MP on diet+size: 14 steps 26 steps

c. Ave. over 9% “true” TL 61.8 steps 114.7 steps

c. Rev Eng Phylogeny (a-c) 679.2 steps 667.3 steps


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Improvements contribution)

Co-inferring the relative weightings of the ecological correlates simultaneously with the relative apparent contributions of phylogenetic and ecological signal

Searching tree space for the reverse engineered phylogeny - current phylogenetic programs are well set up for addition of log-likelihoods (e.g. for partitioned data), but not for subtraction


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

Microraptor contribution)

Eomaia

Molecular tree is employed in the discrimination of apparent phylogenetic and ecological signals - so has some influence on the reverse engineered phylogeny.

However, the ultimate aim here is the placement of fossils. The correction for ecological signal (inferred with extant taxa) can be employed for fossil taxa, independent of their DNA


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

>99% of all species are extinct contribution)

Their fossils provide the only direct evidence for answering many key questions in macroecology and macroevolution and for calibrating molecular timescales


Marsupial herbivore evolution and the failure of morphological algorithmic phylogenetics

  • Acknowledgements contribution)

  • Kate Loynes (ANU, PhD student)

  • Emily Lake (ANU, Honours student)

  • Australian Research Council