Phylogenomics resolves the timing and pattern of insect evolution.
Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.
Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB), Bonn, Germany. xinzhou@genomics.cn b.misof.zfmk@uni-bonn.de kjer@aesop.rutgers.edu wangj@genomics.cn.
Bernhard
B
Misof
China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China.
Shanlin
S
Liu
Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB), Bonn, Germany. Australian National Insect Collection, Commonwealth Scientific and Industrial Research Organization (Australia) (CSIRO), National Research Collections Australia, Canberra, ACT, Australia.
Karen
K
Meusemann
Abteilung Arthropoda, Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany.
Ralph S
RS
Peters
Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB), Bonn, Germany.
Alexander
A
Donath
Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB), Bonn, Germany.
Christoph
C
Mayer
Department of Entomology, Rutgers University, New Brunswick, NJ 08854, USA.
Paul B
PB
Frandsen
Department of Biological Sciences, Rutgers University, Newark, NJ 08854, USA.
Jessica
J
Ware
Scientific Computing, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.
Tomáš
T
Flouri
Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum Jena, FSU Jena, Germany.
Rolf G
RG
Beutel
Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB), Bonn, Germany.
Oliver
O
Niehuis
Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB), Bonn, Germany.
Malte
M
Petersen
Scientific Computing, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.
Fernando
F
Izquierdo-Carrasco
Steinmann-Institut, Bereich Paläontologie, Universität Bonn, Germany.
Torsten
T
Wappler
Steinmann-Institut, Bereich Paläontologie, Universität Bonn, Germany.
Jes
J
Rust
Scientific Computing, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.
Andre J
AJ
Aberer
2. Zoologische Abteilung (Insekten), Naturhistorisches Museum Wien, Vienna, Austria. Department of Integrative Zoology, Universität Wien, Vienna, Austria.
Ulrike
U
Aspöck
Institut für Spezifische Prophylaxe und Tropenmedizin, Medizinische Parasitologie, Medizinische Universität Wien (MUW), Vienna, Austria.
Horst
H
Aspöck
Department of Integrative Zoology, Universität Wien, Vienna, Austria.
Daniela
D
Bartel
Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB), Bonn, Germany. Sugadaira Montane Research Center/Hexapod Comparative Embryology Laboratory, University of Tsukuba, Japan.
Alexander
A
Blanke
Scientific Computing, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.
Simon
S
Berger
Department of Integrative Zoology, Universität Wien, Vienna, Austria.
Alexander
A
Böhm
Manaaki Whenua Landcare Research, Auckland, New Zealand.
Thomas R
TR
Buckley
Center for Advanced Modeling, Emergency Medicine Department, Johns Hopkins University, Baltimore, MD 21209, USA.
Brett
B
Calcott
BGI-Shenzhen, China.
Junqing
J
Chen
Biozentrum Grindel und Zoologisches Museum, Universität Hamburg, Hamburg, Germany.
Frank
F
Friedrich
Evolutionary Morphology Laboratory, Graduate School of Science and Engineering, Ehime University, Japan.
Makiko
M
Fukui
Sugadaira Montane Research Center/Hexapod Comparative Embryology Laboratory, University of Tsukuba, Japan.
Mari
M
Fujita
Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB), Bonn, Germany.
Carola
C
Greve
Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB), Bonn, Germany.
Peter
P
Grobe
BGI-Shenzhen, China.
Shengchang
S
Gu
China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China.
Ying
Y
Huang
Land and Water Flagship, CSIRO, Canberra, ACT, Australia.
Lars S
LS
Jermiin
Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
Akito Y
AY
Kawahara
Entomology, Staatliches Museum für Naturkunde Stuttgart (SMNS), Germany.
Lars
L
Krogmann
Biozentrum Grindel und Zoologisches Museum, Universität Hamburg, Hamburg, Germany.
Martin
M
Kubiak
Ecology Evolution and Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia. National Evolutionary Synthesis Center, Durham, NC 27705, USA. Department of Biological Sciences, Macquarie University, Sydney, Australia.
Robert
R
Lanfear
Department für Botanik und Biodiversitätsforschung, Universität Wien, Vienna, Austria.
Harald
H
Letsch
China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China.
Yiyuan
Y
Li
BGI-Shenzhen, China.
Zhenyu
Z
Li
BGI-Shenzhen, China.
Jiguang
J
Li
BGI-Shenzhen, China.
Haorong
H
Lu
Sugadaira Montane Research Center/Hexapod Comparative Embryology Laboratory, University of Tsukuba, Japan.
Ryuichiro
R
Machida
Sugadaira Montane Research Center/Hexapod Comparative Embryology Laboratory, University of Tsukuba, Japan.
Yuta
Y
Mashimo
Scientific Computing, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany. Natural History Museum of Crete, University of Crete, Post Office Box 2208, Gr-71409, Iraklio, and Biology Department, University of Crete, Iraklio, Crete, Greece.
Pashalia
P
Kapli
Department of Biological Sciences and Feinstone Center for Genomic Research, University of Memphis, Memphis, TN 38152, USA.
Duane D
DD
McKenna
China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China.
Guanliang
G
Meng
Sugadaira Montane Research Center/Hexapod Comparative Embryology Laboratory, University of Tsukuba, Japan.
Yasutaka
Y
Nakagaki
Centro Universitario de Ciencias Biólogicas y Agropecuarias, Centro de Estudios en Zoología, Universidad de Guadalajara, Zapopan, Jalisco, México.
José Luis
JL
Navarrete-Heredia
Leibniz Supercomputing Centre of the Bavarian Academy of Sciences and Humanities, Garching, Germany.
Michael
M
Ott
BGI-Shenzhen, China.
Yanxiang
Y
Ou
Department of Integrative Zoology, Universität Wien, Vienna, Austria.
Günther
G
Pass
Institute of Evolutionary Biology and Ecology, Zoology and Evolutionary Biology, University of Bonn, Bonn, Germany.
Lars
L
Podsiadlowski
Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum Jena, FSU Jena, Germany.
Hans
H
Pohl
Department of Life Sciences, The Natural History Museum London, London, UK.
Björn M
BM
von Reumont
Abteilung Entomologie, Biozentrum Grindel und Zoologisches Museum, Universität Hamburg, Hamburg, Germany.
Kai
K
Schütte
Sugadaira Montane Research Center/Hexapod Comparative Embryology Laboratory, University of Tsukuba, Japan.
Kaoru
K
Sekiya
Sugadaira Montane Research Center/Hexapod Comparative Embryology Laboratory, University of Tsukuba, Japan.
Shota
S
Shimizu
Australian National Insect Collection, Commonwealth Scientific and Industrial Research Organization (Australia) (CSIRO), National Research Collections Australia, Canberra, ACT, Australia.
Adam
A
Slipinski
Scientific Computing, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany. Fakultät für Informatik, Karlsruher Institut für Technologie, Karlsruhe, Germany.
Alexandros
A
Stamatakis
China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China.
Wenhui
W
Song
China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China.
Xu
X
Su
Department of Integrative Zoology, Universität Wien, Vienna, Austria.
Nikolaus U
NU
Szucsich
China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China.
Meihua
M
Tan
BGI-Shenzhen, China.
Xuemei
X
Tan
China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China.
Min
M
Tang
BGI-Shenzhen, China.
Jingbo
J
Tang
Department of Integrative Zoology, Universität Wien, Vienna, Austria.
Gerald
G
Timelthaler
Sugadaira Montane Research Center/Hexapod Comparative Embryology Laboratory, University of Tsukuba, Japan.
Shigekazu
S
Tomizuka
California Academy of Sciences, San Francisco, CA 94118, USA.
Michelle
M
Trautwein
Department of Entomology, College of Natural Resources and Environment, South China Agricultural University, China.
Xiaoli
X
Tong
Sugadaira Montane Research Center/Hexapod Comparative Embryology Laboratory, University of Tsukuba, Japan. Yokosuka City Museum, Yokosuka, Kanagawa, Japan.
Toshiki
T
Uchifune
Department of Integrative Zoology, Universität Wien, Vienna, Austria.
Manfred G
MG
Walzl
Department of Entomology, North Carolina State University, Raleigh, NC 27695, USA.
Brian M
BM
Wiegmann
Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB), Bonn, Germany.
Jeanne
J
Wilbrandt
Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum Jena, FSU Jena, Germany.
Benjamin
B
Wipfler
Land and Water Flagship, CSIRO, Canberra, ACT, Australia.
Thomas K F
TK
Wong
China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China.
Qiong
Q
Wu
BGI-Shenzhen, China.
Gengxiong
G
Wu
BGI-Shenzhen, China.
Yinlong
Y
Xie
China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China.
Shenzhou
S
Yang
China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China.
Qing
Q
Yang
Australian National Insect Collection, Commonwealth Scientific and Industrial Research Organization (Australia) (CSIRO), National Research Collections Australia, Canberra, ACT, Australia.
David K
DK
Yeates
Systematic Entomology, Hokkaido University, Sapporo, Japan.
Kazunori
K
Yoshizawa
China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China.
Qing
Q
Zhang
China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China.
Rui
R
Zhang
BGI-Shenzhen, China.
Wenwei
W
Zhang
BGI-Shenzhen, China.
Yunhui
Y
Zhang
China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China.
Jing
J
Zhao
China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China.
Chengran
C
Zhou
China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China.
Lili
L
Zhou
Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB), Bonn, Germany.
Tanja
T
Ziesmann
BGI-Shenzhen, China.
Shijie
S
Zou
BGI-Shenzhen, China.
Yingrui
Y
Li
BGI-Shenzhen, China.
Xun
X
Xu
China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China.
Yong
Y
Zhang
BGI-Shenzhen, China.
Huanming
H
Yang
BGI-Shenzhen, China.
Jian
J
Wang
BGI-Shenzhen, China. Department of Biology, University of Copenhagen, Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia. Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau, China. Department of Medicine, University of Hong Kong, Hong Kong. xinzhou@genomics.cn b.misof.zfmk@uni-bonn.de kjer@aesop.rutgers.edu wangj@genomics.cn.
Jun
J
Wang
Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08854, USA. xinzhou@genomics.cn b.misof.zfmk@uni-bonn.de kjer@aesop.rutgers.edu wangj@genomics.cn.
Karl M
KM
Kjer
China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China. xinzhou@genomics.cn b.misof.zfmk@uni-bonn.de kjer@aesop.rutgers.edu wangj@genomics.cn.
Xin
X
Zhou
D000818:Animals; D005815:Genetic Code; D049750:Genome, Insect; D023281:Genomics; D019476:Insect Proteins / Q000145:classification* / Q000235:genetics; D007313:Insecta / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D013997:Time Factors
D019476:Insect Proteins