Mind the outgroup: influence of taxon sampling on total-evidence dating of pimpliform parasitoid wasps (Hymenoptera, Ichneumonidae)
TAMARA SPASOJEVIC, GAVIN R. BROAD, ILARI E. SÄÄKSJÄRVI, MARTIN SCHWARZ, MASATO ITO, RIKIO MATSUMOTO, STANISLAV KORENKO AND SERAINA KLOPFSTEIN
Basel, 25 June 2018
220 200 180 160 140 120 100 80 60 40 20 0 Pimpliformes morphology (Wahl and Gauld 1998) + 28S (Quicke et al. 2009, 2015) Coleoptera Diptera
? Symphyta Aculeata
Ichneumonidae
Araneae
Lepidoptera
Siricidae
Endoparasitoids Ectoparasitoids
Idiobionts Koinobionts Pimpliformes morphology (Wahl and Gauld 1998) + 28S (Quicke et al. 2009, 2015) Coleoptera Diptera
? Symphyta Aculeata
Ichneumonidae
Araneae
Lepidoptera
Siricidae
Endoparasitoids Ectoparasitoids ? Idiobionts 60 40 20 0 Koinobionts 120 100 80 60 40 20 0 Establishing evolutionary timescale
taxon 1
taxon 2
taxon 3 Establishing evolutionary timescale
taxon 1
taxon 2
taxon 3
≥ 50 Ma
50 Ma Node dating taxon 1 - only the oldest reliable fossil taxon 2
taxon 3 - how to model node age probability? (Warnock et al. 2011, 2015)
0 Million years ago Establishing evolutionary timescale
taxon 1
taxon 2
taxon 3
50 Ma ≥ 50 Ma ?
50 Ma Node dating taxon 1 - only the oldest reliable fossil taxon 2
taxon 3 - how to model node age probability? (Warnock et al. 2011, 2015)
0 Million years ago Establishing evolutionary timescale
taxon 1
taxon 2
taxon 3
50 Ma Total evidence dating taxon 1 (Ronquist, Klopfstein et al. 2012)
taxon 2 - all available fossils
taxon 3 - no need for prior taxonomic placement
million years ago 0 Total evidence dating - TED
Bayesian analysis 0
1 Total evidence dating - TED
Bayesian analysis 0
1
Can we reconstruct a stable phylogeny of Pimpliformes?
How accurately and precisely can fossils be placed? TED dataset Sanger sequencing: 11 genes
28S, CAD, COI 8 genes TED dataset Sanger sequencing: 11 genes
10 genes 4011 base pairs 28S, CAD, COI 8 genes 1st and 2nd codon positions only TED dataset 222 adult morphological characters (Gauld et. al 2002, Bennett in prep.)
> 56 000 cells binary: 34% multistate: 66% continuous: 13 characters new or modified: 43%
completness of coding ntaxa min. max. mean extant 151 31% 99% 80% fossil 79 5% 54% 22% TED dataset TED dataset Sanger sequencing: 11 genes
10 genes 4011 base pairs 28S, CAD, COI 8 genes 1st and 2nd codon 211 extant taxa positions only 79 fossils
222 adult morphological characters (Gauld71% et. aloverlap 2002, Bennett in prep.)
> 56 000 cells binary: 34% multistate: 66% continuous: 13 characters new or modified: 43%
completness of coding ntaxa min. max. mean extant 151 31% 99% 80% fossil 79 5% 54% 22% Morphology only Bayesian non-clock analysis
Ephialtini
Theroniini
Delomeristini
Pimpliformes Ichneumonidae
Pimplini
Majority-rule consensus tree without fossils Spasojevic et al. (in prep.) Bayesian non-clock analysis
Good resolution at the backbone Ephialtini of Pimpliformes (pp > 0.95)
Theroniini Delomeristini
Five of the nine subfamilies Pimpliformes
Ichneumonidae monophyletic
Acaenitinae and Orthocentrinae supported
Pimplini
Long outgroup branches
Majority-rule consensus tree without fossils Spasojevic et al. (in prep.) Pimplinae
Option 1: Pimplinae and Ephialtinae ? Option 2: Xanthopimplinae and Pimplinae Option 3: Pimplinae Pseudopimpla (Hebermehl, 1917)
? Pimplinae Acaenitinae
Choi et al. 2018 Diptera parasitoids
Orthocentrinae + Diacritinae ? + = Orthocentrinae Cylloceriinae TED analysis
Bayesian inference, MrBayes (Ronquist et al. 2012)
Molecular data: IGR clock model PartitionFinder2, <30 parsimony informative sites Linked clocks GTR+G+I Uniform tree prior Topological constraints Morphological data: for rooting Mkv model (Levis 2001; Puttick et al. 2017) TED analysis
Bayesian inference, MrBayes (Ronquist et al. 2012)
Molecular data: IGR clock model PartitionFinder2, <30 parsimony informative sites Linked clocks GTR+G+I Uniform tree prior Topological constraints Morphological data: for rooting Mkv model (Levis 2001; Puttick et al. 2017)
Klopfstein and Spasojevic (2019) PLOS ONE TED analysis
Bayesian inference, MrBayes (Ronquist et al. 2012)
Molecular data: IGR clock model PartitionFinder2, <30 parsimony informative sites Linked clocks GTR+G+I Uniform tree prior Topological constraints Morphological data: for rooting Mkv model (Levis 2001; Puttick et al. 2017)
Klopfstein and Spasojevic (2019) PLOS ONE TED analysis
Bayesian inference, MrBayes (Ronquist et al. 2012)
Molecular data: IGR clock model PartitionFinder2, <30 parsimony informative sites Linked clocks GTR+G+I Uniform tree prior Topological constraints Morphological data: for rooting Mkv model (Levis 2001; Puttick et al. 2017)
Klopfstein and Spasojevic (2019) PLOS ONE TED analysis
Evanioidea
Ichneumonidae Pimpliformes
225 200 175 150 125 100 75 50 25 0 Ma Posterior probability 0.6 1 TED analysis
Evanioidea
Ichneumonidae Pimpliformes
225 200 175 150 125 100 75 50 25 0 Ma Posterior probability The oldest Hymenoptera fossil 0.6 1 TED analysis
Evanioidea
Did the fossil placement influence the age estimates?
Did the outgroup choice influence the age estimates?
Ichneumonidae Pimpliformes
225 200 175 150 125 100 75 50 25 0 Ma Posterior probability The oldest Hymenoptera fossil 0.6 1 Where were the fossils placed? Where were the fossils placed?
Most of the Cretaceous fossils had similar placement
Highest probabilty of placement on branches to extant genera (Banchinae)
… and on morphologically empty branches Outgroup setting
Evanioidea full outgroup
Ichneumonidae Pimpliformes Outgroup setting
Evanioidea full outgroup
Braconidae (7)
Ichneumonidae Pimpliformes Outgroup setting
Evanioidea full outgroup
Braconidae (7)
one braconid
Ichneumonidae Pimpliformes Outgroup setting
Evanioidea full outgroup Tanychorinae Braconidae (7)
one braconid
Tanychorinae
Ichneumonidae Pimpliformes Outgroup setting
Evanioidea full outgroup
Braconidae (7)
one braconid
Tanychorinae
Xoridinae
Ichneumonidae Pimpliformes TED analysis – age estimates
Median age estimates in million years
300 Permian
250 Triassic
(7)
Jurassic s 200 Cretaceou (1)
100 Full outgroup Braconidae Tanychorinae Xoridinae TED analysis – age estimates
Median age estimates in million years
300 Permian
250 Triassic
(7)
Jurassic s 200 Cretaceou (1)
100 Full outgroup Braconidae Tanychorinae Xoridinae TED analysis – age estimates
Median age estimates in million years
300 Permian
250 Triassic
(7)
Jurassic s 200 Cretaceou (1)
100 Full outgroup Braconidae Tanychorinae Xoridinae
Placement of the Cretaceous fossils is an artefact
Distant outgroups: long branches, no fossils and almost no morphological data When did the Pimpliformes originate and diversify?
̴ 23 Ma
̴ 66 Ma
̴ 100 Ma
̴ 145 Ma
̴ 201 Ma When did the Pimpliformes originate and diversify?
̴ 23 Ma
The oldest fossil of Pimpliformes
̴ 66 Ma The oldest fossil of an extant subfamily?
̴ 100 Ma
The oldest fossil of Ichneumonidae ̴ 145 Ma
̴ 201 Ma When did the Pimpliformes originate and diversify?
Ichneumonidae
̴ 23 Ma
The oldest fossil of Pimpliformes
̴ 66 Ma The oldest fossil of an extant subfamily?
̴ 100 Ma Peters et al. 2017
The oldest fossil of Ichneumonidae ̴ 145 Ma
Our estimate
̴ 201 Ma When did the Pimpliformes originate and diversify?
Pimpliformes
̴ 23 Ma
The oldest fossil of Pimpliformes
̴ 66 Ma Peters et al. 2017 The oldest fossil of an extant subfamily?
̴ 100 Ma
The oldest fossil of Ichneumonidae ̴ 145 Ma
Our estimate
̴ 201 Ma When did the Pimpliformes originate and diversify?
Pimpliformes
̴ 23 Ma
The oldest fossil of Pimpliformes
̴ 66 Ma Peters et al. 2017 The oldest fossil of an extant subfamily?
̴ 100 Ma
The oldest fossil of Ichneumonidae ̴ 145 Ma (Misof et al. 2014)
Our estimate
̴ 201 Ma (Tong et al. 2015) What do we need to date Pimpliformes and Ichneumonidae?
Thorough examination and even sampling of fossils
Thorough sampling of extant taxa - especially outgroup - eliminate morphology empty branches
New molecular datasets ??? Acknowledgments
Andrew Bennett Sonja Wedmann Dmitry Kopylov Thalia Karim David Zelagin Marsh Finnegan Alan M. Rulis Richardo Pérez-de la Fuente Bernhard Hostettler Ursula Menkveld-Gfeller Achim Reisdorf Christian Kropf