Additional file 1: of Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

Additional file 1 of Phylogenomics of palearctic Formica species suggests a single origin of temporary parasitism and gives insights to the evolutionary pathway toward slave-making behaviour

Jonathan Romiguier (175235)
Jonathan Rolland (515851)
Claire Morandin (3266637)
Laurent Keller (4463)

March 2018

Figure S1 Phylogenetic tree of the CLEAN supermatrix (970,619Â bp) built using RAxML (GTRâ+âGAMM...

Additional file 10: of Deep divergence and rapid evolutionary rates in gut-associated Acetobacteraceae of ants

Bryan Brown (174875)
Jennifer Wernegreen (3484133)

July 2016

Alignment file of 1,333 nucleotides and 36 taxa. This alignment was used for phylogenetic inference ...

Additional file 1: of Phylogenomic analysis of Apoidea sheds new light on the sister group of bees

Manuela Sann (5237537)
Oliver Niehuis (153801)
Ralph Peters (3399620)
Christoph Mayer (57204)
Alexey Kozlov (5237534)
Lars Podsiadlowski (21724)
Sarah Bank (4519429)
Karen Meusemann (216039)
Bernhard Misof (153798)
Christoph Bleidorn (187253)
Michael Ohl (586920)

May 2018

Table S1. Assembly statistics and number of identified single-copy genes in the analyzed enriched da...

Additional file 2: of Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

Bonnie Blaimer (3344411)
SeĂĄn Brady (3517679)
Ted Schultz (611143)
Michael Lloyd (2672767)
Brian Fisher (2460859)
Philip Ward (3517676)

December 2015

Genbank accessions for PCR-amplified sequences included in this study. Table including specimen iden...

Additional file 3: of Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

Bonnie Blaimer (3344411)
SeĂĄn Brady (3517679)
Ted Schultz (611143)
Michael Lloyd (2672767)
Brian Fisher (2460859)
Philip Ward (3517676)

December 2015

Calibration points used to define prior calibration densities for dating analyses with BEAST. (PDF 9...

Additional file 9: of Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

Bonnie Blaimer (3344411)
SeĂĄn Brady (3517679)
Ted Schultz (611143)
Michael Lloyd (2672767)
Brian Fisher (2460859)
Philip Ward (3517676)

December 2015

Phylogenetic trees from analyses not illustrated in the main text, continued. Additional results fro...

Additional file 10: of Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

Bonnie Blaimer (3344411)
SeĂĄn Brady (3517679)
Ted Schultz (611143)
Michael Lloyd (2672767)
Brian Fisher (2460859)
Philip Ward (3517676)

December 2015

Summary of taxon exclusion experiments. Summary sketches of phylogenetic relationships contrasting t...

Additional file 8: of Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

Bonnie Blaimer (3344411)
SeĂĄn Brady (3517679)
Ted Schultz (611143)
Michael Lloyd (2672767)
Brian Fisher (2460859)
Philip Ward (3517676)

December 2015

Phylogenetic trees from analyses not illustrated in the main text. Additional results from Bayesian ...

Additional file 5: of Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

Bonnie Blaimer (3344411)
SeĂĄn Brady (3517679)
Ted Schultz (611143)
Michael Lloyd (2672767)
Brian Fisher (2460859)
Philip Ward (3517676)

December 2015

Dispersal constraint matrices used for DEC and S-DEC analyses in RASP. (PDF 75Â kb

Additional file 1: of Deep divergence and rapid evolutionary rates in gut-associated Acetobacteraceae of ants

Bryan Brown (174875)
Jennifer Wernegreen (3484133)

July 2016

Methods and results of the estimation of empirical error rate for Ion PGM amplicon sequencing, based...

Additional file 1: of Insights into the evolution, biogeography and natural history of the acorn ants, genus Temnothorax Mayr (hymenoptera: Formicidae)

Matthew Prebus (4684447)

December 2017

Extended background on the taxonomic history and fossil record of Temnothorax and relatives. (PDF 88...

Phylogenomics Resolves The Timing And Pattern Of Insect Evolution: Supplementary File Archives.

Bernhard Misof (153798)
Shanlin Liu (2851853)
Karen Meusemann (216039)
Ralph S. Peters (153790)
Alexander Donath (3318930)
Christoph Mayer (57204)
Paul B. Frandsen (3318969)
Jessica Ware (818040)
Tomas Flouri (3201012)
Rolf G. Beutel (3318954)
Oliver Niehuis (153801)
Malte Petersen (3183417)
Fernando Izquierdo-Carrasco (3318951)
Torsten Wappler (150884)
Jes Rust (150893)
Andre J. Aberer (3266361)
Ulrike Aspöck (162539)
Horst Aspöck (162532)
Daniela Bartel (532190)
Alexander Blanke (3137607)
Simon Berger (1321149)
Alexander Böhm (3318927)
Thomas Buckley (344503)
Brett Calcott (376631)
Junqing Chen (84035)
Frank Friedrich (98771)
Makiko Fukui (3318909)
Mari Fujita (397912)
Carola Greve (172813)
Peter Grobe (377392)
Shengchang Gu (3318933)
Ying Huang (53474)
Lars S. Jermiin (153781)
Akito Y. Kawahara (263501)
Lars Krogmann (3277686)
Martin Kubiak (3318957)
Robert Lanfear (395145)
Harald Letsch (3296787)
Yiyuan Li (3245487)
Zhenyu Li (295387)
Jiguang Li (3318924)
Haorong Lu (3318900)
Ryuichiro Machida (524093)
Yuta Mashimo (3318939)
Pashalia Kapli (3313107)
Duane D. McKenna (244919)
Guanliang Meng (3252522)
Yasutaka Nakagaki (3318963)
José Luis Navarrete-Heredia (3318897)
Michael Ott (191936)
Yanxiang Ou (3318912)
Günther Pass (532195)
Lars Podsiadlowski (21724)
Hans Pohl (292246)
Björn M von Reumont (3318915)
Kai Schütte (3318972)
Kaoru Sekiya (3318903)
Shota Shimizu (821464)
Adam Slipinski (3318945)
Alexandros Stamatakis (84055)
Wenhui Song (3318960)
Xu Su (688635)
Nikolaus U. Szucsich (532191)
Meihua Tan (296737)
Xuemei Tan (723836)
Min Tang (142347)
Jingbo Tang (3318921)
Gerald Timelthaler (532192)
Shigekazu Tomizuka (524092)
Michelle Trautwein (622371)
Xiaoli Tong (3318906)
Toshiki Uchifune (3318981)
Manfred G. Walzl (3318966)
Brian M. Wiegmann (3265674)
Jeanne Wilbrandt (3318942)
Benjamin Wipfler (98770)
Thomas KF Wong (3318918)
Qiong Wu (84327)
Gengxiong Wu (3318948)
Yinlong Xie (3318975)
Shenzhou Yang (3252513)
Qing Yang (67856)
David K. Yeates (3265707)
Kazunori Yoshizawa (161242)
Qing Zhang (1802)
Rui Zhang (13940)
Wenwei Zhang (165134)
Yunhui Zhang (65111)
Jing Zhao (21160)
Chengran Zhou (442123)
Lili Zhou (265076)
Tanja Ziesmann (3318936)
Shijie Zou (3318978)
Yingrui Li (149030)
Xun Xu (276108)
Yong Zhang (5893)
Huanming Yang (5905)
Jian Wang (5901)
Jun Wang (5906)
Karl M. Kjer (3276648)
Xin Zhou (54275)

November 2016

Phylogenomics Resolves The Timing And Pattern Of Insect Evolution: Supplementary File Archives. This...

Additional file 22: of Insights into the evolution, biogeography and natural history of the acorn ants, genus Temnothorax Mayr (hymenoptera: Formicidae)

Matthew Prebus (4684447)

December 2017

Biogeographic reconstructions inferred from BioGeoBEARS anaylsis of empirical data and sensitivity a...

Additional file 3: of Phylogenomic analysis of Apoidea sheds new light on the sister group of bees

Manuela Sann (5237537)
Oliver Niehuis (153801)
Ralph Peters (3399620)
Christoph Mayer (57204)
Alexey Kozlov (5237534)
Lars Podsiadlowski (21724)
Sarah Bank (4519429)
Karen Meusemann (216039)
Bernhard Misof (153798)
Christoph Bleidorn (187253)
Michael Ohl (586920)

May 2018

Table 1. Information on grouping of species in a given quartet when assessing the phylogenetic posit...

Phylogeography in Response to Reproductive Strategies and Ecogeographic Isolation in Ant Species on Madagascar: Genus Mystrium (Formicidae: Amblyoponinae)

Natalie r. Graham (697792)

December 2015

<p>Nexus file from four gene nuclear phylogeny (long-wavelength rhodopsin, 28s, wingless and abdomin...

Additional file 1 of Phylogenomics of palearctic Formica species suggests a single origin of temporary parasitism and gives insights to the evolutionary pathway toward slave-making behaviour

Jonathan Romiguier (175235)
Jonathan Rolland (515851)
Claire Morandin (3266637)
Laurent Keller (4463)

March 2018

Figure S1 Phylogenetic tree of the CLEAN supermatrix (970,619Â bp) built using RAxML (GTRâ+âGAMM...

Additional file 10: of Deep divergence and rapid evolutionary rates in gut-associated Acetobacteraceae of ants

Bryan Brown (174875)
Jennifer Wernegreen (3484133)

July 2016

Alignment file of 1,333 nucleotides and 36 taxa. This alignment was used for phylogenetic inference ...

Additional file 1: of Phylogenomic analysis of Apoidea sheds new light on the sister group of bees

Manuela Sann (5237537)
Oliver Niehuis (153801)
Ralph Peters (3399620)
Christoph Mayer (57204)
Alexey Kozlov (5237534)
Lars Podsiadlowski (21724)
Sarah Bank (4519429)
Karen Meusemann (216039)
Bernhard Misof (153798)
Christoph Bleidorn (187253)
Michael Ohl (586920)

May 2018

Table S1. Assembly statistics and number of identified single-copy genes in the analyzed enriched da...

Additional file 2: of Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

Bonnie Blaimer (3344411)
SeĂĄn Brady (3517679)
Ted Schultz (611143)
Michael Lloyd (2672767)
Brian Fisher (2460859)
Philip Ward (3517676)

December 2015

Genbank accessions for PCR-amplified sequences included in this study. Table including specimen iden...

Additional file 3: of Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

Bonnie Blaimer (3344411)
SeĂĄn Brady (3517679)
Ted Schultz (611143)
Michael Lloyd (2672767)
Brian Fisher (2460859)
Philip Ward (3517676)

December 2015

Calibration points used to define prior calibration densities for dating analyses with BEAST. (PDF 9...

Additional file 9: of Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

Bonnie Blaimer (3344411)
SeĂĄn Brady (3517679)
Ted Schultz (611143)
Michael Lloyd (2672767)
Brian Fisher (2460859)
Philip Ward (3517676)

December 2015

Phylogenetic trees from analyses not illustrated in the main text, continued. Additional results fro...

Additional file 10: of Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

Bonnie Blaimer (3344411)
SeĂĄn Brady (3517679)
Ted Schultz (611143)
Michael Lloyd (2672767)
Brian Fisher (2460859)
Philip Ward (3517676)

December 2015

Summary of taxon exclusion experiments. Summary sketches of phylogenetic relationships contrasting t...

Additional file 8: of Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

Bonnie Blaimer (3344411)
SeĂĄn Brady (3517679)
Ted Schultz (611143)
Michael Lloyd (2672767)
Brian Fisher (2460859)
Philip Ward (3517676)

December 2015

Phylogenetic trees from analyses not illustrated in the main text. Additional results from Bayesian ...

Additional file 5: of Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

Bonnie Blaimer (3344411)
SeĂĄn Brady (3517679)
Ted Schultz (611143)
Michael Lloyd (2672767)
Brian Fisher (2460859)
Philip Ward (3517676)

December 2015

Dispersal constraint matrices used for DEC and S-DEC analyses in RASP. (PDF 75Â kb

Additional file 1: of Deep divergence and rapid evolutionary rates in gut-associated Acetobacteraceae of ants

Bryan Brown (174875)
Jennifer Wernegreen (3484133)

July 2016

Methods and results of the estimation of empirical error rate for Ion PGM amplicon sequencing, based...

Additional file 1: of Insights into the evolution, biogeography and natural history of the acorn ants, genus Temnothorax Mayr (hymenoptera: Formicidae)

Matthew Prebus (4684447)

December 2017

Extended background on the taxonomic history and fossil record of Temnothorax and relatives. (PDF 88...

Phylogenomics Resolves The Timing And Pattern Of Insect Evolution: Supplementary File Archives.

Bernhard Misof (153798)
Shanlin Liu (2851853)
Karen Meusemann (216039)
Ralph S. Peters (153790)
Alexander Donath (3318930)
Christoph Mayer (57204)
Paul B. Frandsen (3318969)
Jessica Ware (818040)
Tomas Flouri (3201012)
Rolf G. Beutel (3318954)
Oliver Niehuis (153801)
Malte Petersen (3183417)
Fernando Izquierdo-Carrasco (3318951)
Torsten Wappler (150884)
Jes Rust (150893)
Andre J. Aberer (3266361)
Ulrike Aspöck (162539)
Horst Aspöck (162532)
Daniela Bartel (532190)
Alexander Blanke (3137607)
Simon Berger (1321149)
Alexander Böhm (3318927)
Thomas Buckley (344503)
Brett Calcott (376631)
Junqing Chen (84035)
Frank Friedrich (98771)
Makiko Fukui (3318909)
Mari Fujita (397912)
Carola Greve (172813)
Peter Grobe (377392)
Shengchang Gu (3318933)
Ying Huang (53474)
Lars S. Jermiin (153781)
Akito Y. Kawahara (263501)
Lars Krogmann (3277686)
Martin Kubiak (3318957)
Robert Lanfear (395145)
Harald Letsch (3296787)
Yiyuan Li (3245487)
Zhenyu Li (295387)
Jiguang Li (3318924)
Haorong Lu (3318900)
Ryuichiro Machida (524093)
Yuta Mashimo (3318939)
Pashalia Kapli (3313107)
Duane D. McKenna (244919)
Guanliang Meng (3252522)
Yasutaka Nakagaki (3318963)
José Luis Navarrete-Heredia (3318897)
Michael Ott (191936)
Yanxiang Ou (3318912)
Günther Pass (532195)
Lars Podsiadlowski (21724)
Hans Pohl (292246)
Björn M von Reumont (3318915)
Kai Schütte (3318972)
Kaoru Sekiya (3318903)
Shota Shimizu (821464)
Adam Slipinski (3318945)
Alexandros Stamatakis (84055)
Wenhui Song (3318960)
Xu Su (688635)
Nikolaus U. Szucsich (532191)
Meihua Tan (296737)
Xuemei Tan (723836)
Min Tang (142347)
Jingbo Tang (3318921)
Gerald Timelthaler (532192)
Shigekazu Tomizuka (524092)
Michelle Trautwein (622371)
Xiaoli Tong (3318906)
Toshiki Uchifune (3318981)
Manfred G. Walzl (3318966)
Brian M. Wiegmann (3265674)
Jeanne Wilbrandt (3318942)
Benjamin Wipfler (98770)
Thomas KF Wong (3318918)
Qiong Wu (84327)
Gengxiong Wu (3318948)
Yinlong Xie (3318975)
Shenzhou Yang (3252513)
Qing Yang (67856)
David K. Yeates (3265707)
Kazunori Yoshizawa (161242)
Qing Zhang (1802)
Rui Zhang (13940)
Wenwei Zhang (165134)
Yunhui Zhang (65111)
Jing Zhao (21160)
Chengran Zhou (442123)
Lili Zhou (265076)
Tanja Ziesmann (3318936)
Shijie Zou (3318978)
Yingrui Li (149030)
Xun Xu (276108)
Yong Zhang (5893)
Huanming Yang (5905)
Jian Wang (5901)
Jun Wang (5906)
Karl M. Kjer (3276648)
Xin Zhou (54275)

November 2016

Phylogenomics Resolves The Timing And Pattern Of Insect Evolution: Supplementary File Archives. This...

Additional file 22: of Insights into the evolution, biogeography and natural history of the acorn ants, genus Temnothorax Mayr (hymenoptera: Formicidae)

Matthew Prebus (4684447)

December 2017

Biogeographic reconstructions inferred from BioGeoBEARS anaylsis of empirical data and sensitivity a...

Additional file 3: of Phylogenomic analysis of Apoidea sheds new light on the sister group of bees

Manuela Sann (5237537)
Oliver Niehuis (153801)
Ralph Peters (3399620)
Christoph Mayer (57204)
Alexey Kozlov (5237534)
Lars Podsiadlowski (21724)
Sarah Bank (4519429)
Karen Meusemann (216039)
Bernhard Misof (153798)
Christoph Bleidorn (187253)
Michael Ohl (586920)

May 2018

Table 1. Information on grouping of species in a given quartet when assessing the phylogenetic posit...

Phylogeography in Response to Reproductive Strategies and Ecogeographic Isolation in Ant Species on Madagascar: Genus Mystrium (Formicidae: Amblyoponinae)

Natalie r. Graham (697792)

December 2015

<p>Nexus file from four gene nuclear phylogeny (long-wavelength rhodopsin, 28s, wingless and abdomin...

Additional file 1 of Phylogenomics of palearctic Formica species suggests a single origin of temporary parasitism and gives insights to the evolutionary pathway toward slave-making behaviour

Jonathan Romiguier (175235)
Jonathan Rolland (515851)
Claire Morandin (3266637)
Laurent Keller (4463)

March 2018

Figure S1 Phylogenetic tree of the CLEAN supermatrix (970,619Â bp) built using RAxML (GTRâ+âGAMM...

Additional file 10: of Deep divergence and rapid evolutionary rates in gut-associated Acetobacteraceae of ants

Bryan Brown (174875)
Jennifer Wernegreen (3484133)

July 2016

Alignment file of 1,333 nucleotides and 36 taxa. This alignment was used for phylogenetic inference ...

Additional file 1: of Phylogenomic analysis of Apoidea sheds new light on the sister group of bees

Manuela Sann (5237537)
Oliver Niehuis (153801)
Ralph Peters (3399620)
Christoph Mayer (57204)
Alexey Kozlov (5237534)
Lars Podsiadlowski (21724)
Sarah Bank (4519429)
Karen Meusemann (216039)
Bernhard Misof (153798)
Christoph Bleidorn (187253)
Michael Ohl (586920)

May 2018

Table S1. Assembly statistics and number of identified single-copy genes in the analyzed enriched da...

Additional file 1: of Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

Abstract

Extracted data

Additional file 1: of Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

Abstract

Extracted data

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