Saga of the Extinct Giant Kangaroos: Ancient DNA and Fossils Combined to Reveal the Evolutionary History of Macropods

Saga of the extinct giant kangaroos: ancient DNA and fossils combined to reveal the evolutionary history of macropods.

EVOLUTION 2018 – 19/08/2018 Montpellier

Manuela Cascini Matthew J. Phillips ([email protected])

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. 2018 © 48th European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . What can DNA and fossils tell us about macropods evolution and how do we make the most of these data? DNA + Morphology from extant and fossils macropods to investigate:

1)Phylogeny

2)Divergence times

Sequenced at the Australian Centre of Ancient DNA (ACAD), Adelaide

Sthenurinae (short faced Giant wallaby: kangaroos):

Simosthenurus occidentalis Protemnodon anak *98.5% complete *100% complete

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . No agreement on their phylogenetic relationships Hypsiprymnodon moschatus Potoroidae

Lagostrophus fasciatus 3 1 Dorcopsini 2 4 Thylogale billardierii Simosthenurus occidentalis

Dendrolagus Macropodinae

Petrogale

Setonix brachyurus

2018 © II Joint Congress on EvolutionaryOnychogalea Biology 2018. All rightsunguifera reserved - Any reproduction even in part is prohibited. 5 Protemnodon anak Lagorchestes

Wallabia bicolor

Macropus 6 1. Prideaux 2004, 2. Prideaux and Warburton 2010; Llamas et al. 2015, 3. Flannery 1983, 1989, Murray 1995) and Protemnodon (filled arrows: 4. Flannery 1989, 5. Prideaux and2018 Warburton © II Joint Congress 2010, on Evolutionary 6. Raven Biology 2018. and All rights Gregory, reserved - Any 1946). reproduction even in part is prohibited. 2018 © 48th European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

Phalanger interpositus Trichosurus vulpecula Pseudocheirus peregrinus 100/87 Lagostrophus fasciatus Simosthenurus occidentalis† Protemnodonanak † Macropus Wallabia bicolor Onychogalea unguifera Lagorchestes Setonix brachyurus Dendrolagus Petrogale xanthopus Macropodinae Petrogale brachyotis Thylogale billardierii Dorcopsulus vanheurni 2018 © II Joint Congress on Evolutionary Biology 2018.Dorcopsulus All rights reservedhageni - Any reproduction even in part is prohibited. Aepyprymnus rufescens Bettongia lesueur Potoroidae Bettongia penicillata Potorous longipes Potorous tridactylus Hypsyprimnodon moschatus

Node values are Bayesian posterior probabilities/IQ-TREE bootstrap values. 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. 2018 © 48th European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . Molecular Total Evidence (15,253 bp, ancient + modern mtDNA) (molecular + 119 morphological characters *)

Phalanger interpositus Phalanger interpositus Trichosurus vulpecula Trichosurus vulpecula Pseudocheirus peregrinus Pseudocheirus peregrinus 100/87 Lagostrophus fasciatus 96/X Lagostrophus fasciatus Simosthenurus occidentalis† Simosthenurus occidentalis† Protemnodonanak † Protemnodon anak † Macropus Macropus Wallabia bicolor Wallabia bicolor Lagorchestes Lagorchestes Onychogalea unguifera Onychogalea unguifera Setonix brachyurus Setonix brachyurus Petrogale xanthopus Dendrolagus Dendrolagus Petrogale xanthopus Macropodinae Macropodinae Petrogale brachyotis Petrogale brachyotis Thylogale billardierii Thylogale billardierii Dorcopsulus vanheurni Dorcopsulus vanheurni 2018 © II Joint Congress on Evolutionary Biology 2018.Dorcopsulus All rights reservedhageni - Any reproduction even in part is prohibited. Dorcopsulus hageni Aepyprymnus rufescens Aepyprymnus rufescens Bettongia lesueur Potoroidae Potoroidae Bettongia lesueur Bettongia penicillata Bettongia penicillata Potorous longipes Potorous longipes Potorous tridactylus Potorous tridactylus Hypsyprimnodon moschatus Hypsyprimnodon moschatus Node values are Bayesian posterior probabilities/IQ-TREE bootstrap values. *Butler et al.2016, Kear and Pledge 2008, 2018 © II Joint Congress on Evolutionary Biology 2018. AllPrideaux rights reservedand Warburton- Any reproduction 2010. even in part is prohibited. 2018 © 48th European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

Morphology rejects “true” topology (Meredith et al. 2008) with high significance

Morphology = less reliable topology

1) Node-dating (DNA data only) 7 calibration priors assigned to specific NODES

Hadronomaspuckridgi †

2) Tip-dating (DNA and morpho data) 6 fossils TIPS for temporal calibration

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. Ganguroo bilamina † Ganguroo robustiter † Balbaroonalima † Nambaroo gillespiae †

Hadronomaspuckridgi †

Simosthenurus occidentalis† Sthenurinae Procoptodon goliah † 41-46 divergence Sthenurus andersoni † from arboreal Hadronomas puckridgi † possums Lagostrophus fasciatus Protemnodonanak † Macropus eugenii Macropus rufogriseus Macropus fuliginosus Macropus robustus Macropodidae Wallabia bicolor

Macropodini Lagorchestes hirsutus Lagorchestes conspicillatus Onychogalea unguifera Dendrolagus dorianus Setonix brachyurus Dendrolagus lumholtzi Bohra illuminata

Macropodinae Petrogale xanthopus Petrogale brachyotis Thylogale billardierii Dorcopsulusvanheurni Dorcopsishageni Dorcopsoides fossilis † Ganguroo bilamina † Bulungamayinae 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited.Ganguroo robustiter† Balbaroo nalima † Macropodoidea Balbaridae Nambaroo gillespieae † Aepyprymnus rufescens Bettongia penicillata Macropodiformes Potoroidae Bettongia lesueur Potorous longipes Potorous tridactylus Hypsiprymnodon moschatus Pseudocheirus peregrinus Phalanger interpositus Trichosurus vulpecula Eocene Oligocene Early Mio Mid Mio Late Mio Pli Pt

40 30 20 2018 © II Joint Congress10 on Evolutionary Biology 2018. All0 rights reservedMa - Any reproduction even in part is prohibited. 2018 © 48th European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

Simosthenurus occidentalis† Sthenurinae Procoptodon goliah † 41-46 divergence Sthenurus andersoni † from arboreal Hadronomas puckridgi † possums Lagostrophus fasciatus 21-28 Ma Protemnodonanak † Macropodoidea Macropus eugenii Macropus rufogriseus Macropus fuliginosus Macropus robustus Macropodidae Wallabia bicolor

Macropodini Lagorchestes hirsutus Lagorchestes conspicillatus Onychogalea unguifera Dendrolagus dorianus Setonix brachyurus Dendrolagus lumholtzi Bohra illuminata

15-21 Ma split giant kangaroos/ smallest Simosthenurus occidentalis† Sthenurinae Procoptodon goliah † 41-46 divergence wallabies Sthenurus andersoni † from arboreal Hadronomas puckridgi † possums Lagostrophus fasciatus 21-28 Ma Protemnodonanak † Macropodoidea Macropus eugenii Macropus rufogriseus Macropus fuliginosus Macropus robustus Macropodidae Wallabia bicolor

Macropodini Lagorchestes hirsutus Lagorchestes conspicillatus Onychogalea unguifera Dendrolagus dorianus Setonix brachyurus Dendrolagus lumholtzi Bohra illuminata

DNA Time Morphology

Current methods

0,7

0,6

0,5

0,4 R² = 0,0429

0,3

(changes site) per (changes 0,2

0 0 0,05 0,1 0,15 0,2 0,25 Molecular branch length (changes per site)

As a morphological character itself, body size evolution might be expected to correlate better with morphological branch-lengths (allometry and covariation with functional and developmental variation)

Molecular Temporal Morphological

Two different models ➢ Brownian motion

Open bars=brownian motion 25 Molecular Temporal Closed bars=stable model 20 Morphological

5 Estimated body mass (Kg) body Estimated 0

STABLE model works better than the BM 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. 2018 © 48th European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . DNA and morphology have complementary roles • Molecular data, including ancient DNA, has primacy for inferring phylogeny

• Inference of evolutionary timescales can benefit from considering total evidence (node and tip) dating

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. • Morphological data beneficial for inferring branch lengths along which to reconstruct character ancestry

Joseph Burgess 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. 2018 © 48th European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

* Including short fragments of ancient mitochondrial DNA

2018 © II Joint Congress on Evolutionary Biology 2018. All rights Llamasreserved - Any reproduction et evenal.2015 in part is prohibited. 2018 © 48th European Contact Lens Society Of Ophthalmologists. All rights reserved - Any reproduction even in part is prohibited] .

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . Our molecular phylogeny Molecular Simosthenurus occidentalis† Lagostrophus fasciatus (15,253 bp, ancient + modern Protemnodon anak † Macropus eugenii mtDNA) Macropus rufogriseus Macropus fuliginosus Macropus robusuts Wallabia bicolor Lagorchestes conspicillatus Lagorchestes hirsutus Onychogalea unguifera Setonix brachyurus Dendrolagus lumholtzi Dendrolagus dorianus Petrogale xanthopus Petrogale brachyotis Thylogale billardierii Dorcopsulus vanheurni Dorcopsis hageni 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. Aepyprymnus rufescens Bettongia lesueur

Simosthenurus occidentalis Bettongia penicillata Lagostrophus fasciatus macropodines Potorous longipes Potorous tridactylus Hypsiprymnodon moschatus

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . 2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited] . (119 (119 craniodental

2018 © II Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. 2018 © II Joint Congress on Evolutionarymacropodines BiologyMorphology 2018. All rights reserved - Any reproduction even in part is prohibited] .

occidentalis phylogeny morphological Our

Lagostrophus fasciatus Hypsiprymnodon Potorous Bettongia Aepyprymnus

2018 © IImoschatus Joint Congress on Evolutionary Biology 2018. All rights reserved - Any reproduction even in part is prohibited. tridactylus penicillata rufescens Lagostrophus Thylogale fasciatus 2008, *Butler et al.2016, Wallabia Petrogale Setonix Protemnodon Lagorchestes Lagorchestes Dorcopsulus Dorcopsis Prideaux&Warburton billardierii brachyurus bicolor Onychogalea Macropus Macropus brachyotis Macropus hageni Dendrolagus Dendrolagus anak Dendrolagus Dendrolagus vanheurni conspicillatus hirsutus eugenii fuliginosus robustus Simosthenurus unguifera † Kear dorianus andPledge lumholtzi 2010 occidentalis † Morphology (119 craniodental & postcranial characters*)

Trichosurus vulpecula

Pseudocheirus peregrinus Lagostrophus fasciatus Simosthenurus occidentalis† Protemnodonanak † Macropus Lagorchestes

Onychogalea unguifera Wallabia bicolor Dendrolagus Petrogale brachyotis Thylogale billarderii

Dorcopsulusvanheurni Dorcopsishageni

Aepyprymnus rufescens Bettongia penicillata Potorous tridactylus Hypsyprimnodon moschatus