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TDikow Hennig 2011

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A presentation on morphological and molecular phylogenetic studies on insects and flies given at the 30th Willi Hennig Society Meeting in July-August 2011.

A presentation on morphological and molecular phylogenetic studies on insects and flies given at the 30th Willi Hennig Society Meeting in July-August 2011.

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  • 1. 1Molecules and morphology: insights from phylogeneticanalyses of insect taxa Torsten Dikow Biodiversity Synthesis Center Field Museum of Natural History Chicago, IL, USA
  • 2. 2Overview ◊ Morphological and Molecular Data ◊ Simultaneous Analyses of Insect Taxa ◊ Methodological Considerations Efferia sp. ◊ Example: Phylogeny of Robber Flies Ceraturgus fasciatus © Michael Thomas
  • 3. 3Kurt M. Pickett 1972 – 2011 January 2009
  • 4. . Morphological and Molecular Data 4Morphological and Molecular Data “It is still common for phylogeneticists to fear that molecular data will swamp out the signal of phenotypic characters such as morphology and behavior.” Pickett & Carpenter 2010: 13 1987
  • 5. . Morphological and Molecular Data 5Morphological and Molecular Data ◊ Kluge 1989 – Total Evidence ◊ Nixon & Carpenter 1996 – Simultaneous Analysis ◊ Freudenstein et al. 2003 › today: morphological and DNA nucleotide data › increasingly used: behavioral and ecological data › future: entire genomes, gene rearrangemant, morphology, behavior, ecology ◊ greatest explanatory power
  • 6. . Morphological and Molecular Data 6Simultaneous Analysis “Although neither of us believes that the evolutionary character content of a single nucleotide substitution, for example, is comparable to any given morphological character – most of which are the polygenic result of multiple, interacting genes – philosophical consistency dictates that we treat all characters as equal contributors to the topology.” Pickett & Carpenter 2010: 17 “Thus, here we are willingly increasing the relative power of single nucleotides or indel events to that of complex morphological characters (no doubt the result of many thousands of nucleotides). So, in effect, we are sharply minimizing the phylogenetic impact of the morphology relative to the molecular characters. As a result, none can argue that we have unfairly stacked the deck against the molecules.” Pickett & Carpenter 2010: 17
  • 7. .. Simultaneous Analyses of Insect Taxa 7Published Simultaneous Analyses – Cladistics 12 9 Number 6 44 analyses 3 insect taxa = 13 other animal taxa = 22 0 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 plant taxa = 9 Year
  • 8. .. Simultaneous Analyses of Insect Taxa 8Published Simultaneous Analyses – Insect Journals 8 6 Number 35 analyses 4 Cladistics (insect taxa) = 13 Systematic Entomology = 18 2 Insect Systematics & Evolution = 2 0 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 Invertebrate Systematics = 2 Year
  • 9. ... Methodology 9Simultaneous Analysis – traditional approach ◊ Morphological Data › primary homology statements already made by investigator (“prealigned”) static static analysis SuperMatrix in TNT ◊ Molecular Data › unaligned nucleotides › nucleotides to be aligned using traditional alignment algorithms
  • 10. ... Methodology 10Simultaneous Analysis – current approach ◊ Morphological Data › primary homology statements already made by investigator (“prealigned”) semi-dynamic semi-dynamic SuperMatrix analysis in POY ◊ Molecular Data › unaligned nucleotides › nucleotides to be aligned using dynamic homology
  • 11. ... Methodology 11Simultaneous Analysis – future approach? ◊ Morphological Data › “unaligned” character states › character states to be “aligned” using dynamic homology assignment dynamic dynamic SuperMatrix analysis in POY ◊ Molecular Data › unaligned nucleotides › nucleotides to be aligned using dynamic homology
  • 12. ... Methodology 12Optimality or Inference Criteria in Simultaneous Analyses ◊ Parsimony › morphology + molecular › static: TNT › dynamic: POY ◊ Maximum Likelihood › morphology: Mk model, No Common Mechanism › molecular: nucleotide substitution models › static: Garli, RAxML › dynamic: POY (version 5alpha) ◊ Bayesian Inference › morphology: Mk model, No Common Mechanism › molecular: nucleotide substitution models › static: MrBayes › dynamic: POY (version 5alpha), BaliPhy
  • 13. ... Methodology 13Combining Data-sets – 1 Data-set 1 (here morphology) Data-set 2 (here nucleotide sequences)
  • 14. ... Methodology 14Combining Data-sets – 2 Data-set 1 (here morphology) Data-set 2 (here nucleotide sequences)
  • 15. .... Phylogeny of Robber Flies 15Asilidae – “robber flies” or “assassin flies” ◊ Adults & larvae predatory ◊ Adults catch generally flying prey, but some feed on resting prey ◊ 7,413 species world-wide ◊ Adults 5 – 60 mm Scleropogon duncani ◊ Speciose in arid & semi-arid environments, but also in tropical environments ◊ Many Asilidae mimic Hymenoptera Echthodopa formosa © Michael Thomas
  • 16. .... Phylogeny of Robber Flies 16Taxon and Character Sampling Morphology 158 Morphology + Molecular 77 ◊ 158 species (= 2.13 %) ◊ 77 species (= 1.04 %) ◊ 140 genera (= 26 %) ◊ 67 genera (= 12 %) ◊ 17 outgroup taxa ◊ 11 outgroup taxa ◊ 220 discrete, parsimony informative ◊ 211 discrete, parsimony informative morphological characters morphological characters ◊ 0.4% missing data ◊ 5 nuclear genes, ≈ 7,300 bp nuclear DNA ◊ new phylogenetic classification ◊ 7.25% missing data Dikow 2009 – Bulletin AMNH Dikow 2009 – Organisms, Diversity & Evolution
  • 17. .... Phylogeny of Robber Flies 17Methods ◊ MacClade + WinClada POY ◊ TNT + POY4 ◊ Ratchet, TreeDrifting, + TreeFusing ◊ TreeMap3 TNT
  • 18. .... Phylogeny of Robber Flies 18Morphology 158 Neorhynchocephalus volaticus Bathypogon nigrinus Bombylius major Phellus olgae Poecilognathus sp (El Hacha) Obelophorus terebratus Prorates sp (Escalante) Tillobroma punctipennis Apsilocephala longistylus Hypenetes stigmatias Hemigephyra atra Lycostommyia albifacies Phycus frommeri Coleomyia setigera Apiocera aldrichi Ancylorhynchus fulvicollis Apiocera painteri Scylaticus costalis Rhaphiomidas maehleri Connomyia varipennis Prolepsis tristis Neorhaphiomidas sp (Mandurah) Creolestes nigribarbis Opomydas townsendi Microstylum sp (Karkloof) Mitrodetus dentitarsis Daspletis stenoura Mydas clavatus Plesiomma sp (Guanacaste) Pseudonomoneura hirta Ospriocerus aeacus Nemomydas brachyrhynchus Scleropogon subulatus Afroleptomydas sp (Clanwilliam) Stenopogon sabaudus Perasis transvaalensis Stenopogon rufibarbis Zabrops tagax Gonioscelis ventralis Protometer sp (El Tuparro) Lestomyia fraudiger Psilocurus modestus Dasypogon diadema Laphystia aegyptiaca Saropogon dispar Laphystia tolandi Saropogon luteus Hoplistomerus nobilis Thereutria amaraca Trichardis testacea Archilestris magnificus Nusa infumata Diogmites grossus Laxenecera albicincta Neodiogmites melanogaster Blepharepium cajennensis Smeryngolaphria numitor Molobratia teutonus Orthogonis scapularis Cyrtophrys attenuatus Goneccalypsis argenteoviridis Deromyia fuscipennis Loewinella nigripes Pegesimallus laticornis Aphestia annulipes Senobasis corsair Atomosia puella Megapoda labiata Cerotainia albipilosa Pseudorus distendens Maira aenea Acnephalum cylindricum Lampria clavipes Sisyrnodytes sp (Gamka) Choerades bella Ablautus coquilletti Laphria flava Willistonina bilineata Laphria aktis Trichoura sp (Tierberg) Lamyra gulo Oligopogon sp (Cape Recife) Stiphrolamyra angularis Broticosia paramonovi Hyperechia nigripennis Dicolonus simplex Proagonistes praeceps Echthodopa pubera Andrenosoma cyrtoxys Myelaphus melas Eudioctria albius Pilica formidolosa Nannodioctria sp (formicaphaga) Dasyllis funebris Dioctria atricapillus Cophinopoda chinensis Dioctria hyalipennis Michotamia aurata Dioctria rufipes Emphysomera conopsoides Damalis sp (Palatupana) Emphysomera pallidapex Damalis monochaetes Ommatius incurvatus Damalis annulata Ommatius senex Rhipidocephala sp (Harold Johnson) Ommatius tibialis Trigonomima sp (anamaliensis) Lycomya germainii Holcocephala abdominalis Blepharotes splendidissimus Holcocephala calva Megaphorus pulchrus Acronyches maya Promachus amastrus Beameromyia bifida Apoclea algira Euscelidia pulchra Philodicus tenuipes Tipulogaster glabrata Neolophonotus bimaculatus Leptogaster arida Pogonioefferia pogonias Leptogaster cylindrica Lasiocnemus lugens Proctacanthus philadelphicus Lasiopogon aldrichii Lochmorhynchus albicans Lasiopogon cinctus1 of 720 most Eichoichemus pyrrhomystax Myaptex brachyptera Dasophrys crenulatus Nomomyia murina Townsendia albomacula Stichopogon elegantulus Stichopogon trifasciatus Stichopogon punctumparsimonious Dysmachus trigonus Tolmerus atricapillus Machimus chrysitis Machimus occidentalis Lissoteles aquilonius Afroholopogon peregrinus Dasycyrton gibbosus Cyrtopogon lateralistrees Neomochtherus pallipes Cyrtopogon rattus Afromochtherus mendax Leptarthrus brevirostris Satanas gigas Holopogon priscus Asilus crabroniformis Chrysopogon pilosifacies Codula limbipennis2760 steps Asilus sericeus Austrosaropogon nigrinus Philonicus albiceps Brachyrhopala ruficornis Congomochtherus inachus Cabasa pulchella Clephydroneura sundaica Ceraturgus fasciatus Clephydroneura sp (Kepong)CI=0.13 Nannocyrtopogon lestomyiformis Heligmonevra laevis Nicocles politus Zosteria rosevillensis Heteropogon manicatus Colepia rufiventris Metapogon punctipennis Neoitamus cyanurus Cophura brevicornisRI=0.68 Threnia carbonaria Rhabdogaster pedion yellow branches = previous taxa recovered as monophyletic
  • 19. .... Phylogeny of Robber Flies 19Morphology + Molecular 77 7.25% missing data 211 morphological characters 7,300 bp of nuclear DNA
  • 20. .... Phylogeny of Robber Flies 20Morphology + Molecular 77 Bombylius major Apsilocephala longistyla Prorates sp. (Escalante) Phycus frommeri Hemigephyra atra Apiocera painteri Opomydas townsendi ◊ Asilidae is monophyletic Mydas clavatus Mitrodetus dentitarsis Nemomydas brachyrhynchus Afroleptomydas sp. (Clanwilliam) Rhipidocephala sp. (Harold Johnson) Holcocephala calva Holcocephala abdominalis Perasis transvaalensis ◊ Different higher-level relationships Laphystia tolandi Trichardis effrena Nusa infumata Laxenecera albicincta Hoplistomerus nobilis Pilica formidolosa than in Morphology 158 hypothesis Cerotainia albipilosa Atomosia puella Stiphrolamyra angularis Lamyra gulo Laphria aktis Choerades bella Damalis monochaetes Damalis annulata Rhabdogaster pedion Acnephalum cylindricum Pegesimallus laticornis Diogmites grossus Plesiomma sp. (Guanacaste) Dasypogon diadema Saropogon luteus Lestomyia fraudiger Trichoura sp. (Tierberg) Ablautus coquilletti Molobratia teutonus Nicocles politus Leptarthrus brevirostris Cyrtopogon rattus Ceraturgus fasciatus Willistonina bilineata Eudioctria albius Dioctria hyalipennis Dioctria rufipes Dioctria atricapillus Gonioscelis ventralis Stenopogon rufibarbis Ospriocerus aeacus Tillobroma punctipennis Prolepsis tristis Microstylum sp. (Karkloof) Lycostommyia albifacies Scylaticus costalis Connomyia varipennis Lasiopogon cinctus Lasiopogon aldrichii Stichopogon punctum Stichopogon trifasciatus Stichopogon elegantulus Euscelidia pulchra Beameromyia bifida Leptogaster cylindrica Leptogaster arida Tipulogaster glabrata Lasiocnemus lugens Emphysomera pallidapex Emphysomera conopsoides Ommatius tibialis Afroestricus chiastoneurus Proctacanthus philadelphicus Pogonioefferia pogonias Philodicus tenuipes Promachus amastrus Megaphorus pulchrus Neolophonotus bimaculatus Dasophrys crenulatus Neoitamus cyanurus Clephydroneura sp. (Kepong) 1 most parsimonious tree Dysmachus trigonus Philonicus albiceps Machimus occidentalis Tolmerus atricapillus 27582 steps (iterative pass) Asilus sericeus Asilus crabroniformis yellow branches = taxa from Morphology 158 hypothesis recovered as monophyletic
  • 21. .... Phylogeny of Robber Flies 21Morphology + Molecular 77: Character Support ◊ Asilinae › molecular characters enhance resolution 133 Proctacanthus philadelphicus 3 Pogonioefferia pogonias 110 206 146 Philodicus tenuipes 1 0 2 172 Promachus amastrus 1 Megaphorus pulchrus Neolophonotus bimaculatus 18S Dasophrys crenulatus Neoitamus cyanurus 28S 133 Clephydroneura sp. (Kepong) 2 AATS Dysmachus trigonus Philonicus albiceps CAD Machimus occidentalis EF-1α Tolmerus atricapillus Asilus sericeus morphological autapomorphies Asilus crabroniformis
  • 22. .... Phylogeny of Robber Flies 22Morphology + Molecular 77: Character Support ◊ Laphriinae › only supported by morphological autapomorphies 45 Perasis transvaalensis 42 193 2 Laphystia tolandi 1 3 160 161162164186187188 Trichardis effrena 2 2 2 2 2 2 2 220 18S 2 Nusa infumata Laxenecera albicincta 28S 17 18 172 Hoplistomerus nobilis AATS 1 1 3 57137 140 150 158 166 50 Pilica formidolosa Cerotainia albipilosa 1 CAD 5 4 3 1 1 1 Atomosia puella 47 Stiphrolamyra angularis EF-1α 1 Lamyra gulo morphological autapomorphies 45 96 1 3 Laphria aktis Choerades bella
  • 23. .... Phylogeny of Robber Flies 23Morphology + Molecular 158 54.8% missing data 220 morphological characters 7,300 bp of nuclear DNA
  • 24. .... Phylogeny of Robber Flies 24Morphology + Molecular 158 Neorhynchocephalus volaticus Bombylius major Sisyrnodytes sp Gamka Poecilognathus sp El Hacha Acnephalum cylindricum Apsilocephala longistyla Rhabdogaster pedion Prorates sp Escalante Afroholopogon peregrinus Phycus frommeri Dasycyrton gibbosus Hemigephyra atra Codula limbipennis Apiocera painteri Chrysopogon pilosifacies Apiocera aldrichi Damalis sp Palatupana Rhaphiomidas maehleri Damalis monochaetes Neorhaphiomidas sp Mandurah Damalis annulata Mitrodetus dentitarsis Archilestris magnificus Opomydas townsendi Diogmites grossus Mydas clavatus Neodiogmites melanogaster Pseudonomoneura hirta Blepharepium cajennensis Nemomydas brachyrhynchus Plesiomma sp Guanacaste Afroleptomydas sp Clanwilliam Dasypogon diadema Rhipidocephala sp HaroldJohnson Lestomyia fraudiger Trigonomima sp anamaliensis Saropogon luteus Holcocephala calva Saropogon dispar Holcocephala abdominalis Thereutria amaraca Perasis transvaalensis Cabasa pulchella Zabrops tagax Brachyrhopala ruficornis Psilocurus modestus Austrosaropogon nigrinus Protometer sp El Tuparro Senobasis corsair Laphystia tolandi Deromyia fuscipennis Laphystia aegyptiaca Cyrtophrys attenuatus Trichardis effrena Pegesimallus laticornis Laxenecera albicincta Pseudorus distendens Hoplistomerus nobilis Megapoda labiata Nusa infumata Oligopogon sp Cape Recife Smeryngolaphria numitor Molobratia teutonus Stiphrolamyra angularis Ablautus coquilletti Lamyra gulo Nannocyrtopogon lestomyiformis Maira aenea Metapogon punctipennis Lampria clavipes Heteropogon manicatus Choerades bella Nicocles politus Laphria flava Cophura brevicornis Laphria aktis Leptarthrus brevirostris Hyperechia nigripennis Holopogon priscus Dasyllis funebris Cyrtopogon rattus Pilica formidolosa Cyrtopogon lateralis Proagonistes praeceps Ceraturgus fasciatus Andrenosoma cyrtoxys Broticosia paramonovi Orthogonis scapularis Lycostommyia albifacies Loewinella nigripes Hypenetes stigmatias Goneccalypsis argenteoviridis Connomyia varipennis Aphestia annulipes Scylaticus costalis Cerotainia albipilosa Ancylorhynchus fulvicollis Atomosia puella Tillobroma punctipennis Lasiopogon cinctus Coleomyia setigera Lasiopogon aldrichii Prolepsis tristis Trichoura sp Tierberg Creolestes nigribarbis Townsendia albomacula Microstylum sp Karkloof Lissoteles aquilonius Daspletis stenoura Stichopogon trifasciatus Bathypogon nigrinus Stichopogon punctum Phellus olgae Stichopogon elegantulus Obelophorus terebratus Acronyches maya Gonioscelis ventralis Euscelidia pulchra Stenopogon rufibarbis Beameromyia bifida Stenopogon sabaudus Leptogaster cylindrica Scleropogon subulatus Leptogaster arida Ospriocerus aeacus Tipulogaster glabrata Willistonina bilineata Lasiocnemus lugens Dicolonus simplex Michotamia aurata Echthodopa pubera Emphysomera pallidapex Myelaphus melas Emphysomera conopsoides Eudioctria albius Ommatius tibialis Nannodioctria sp formicaphaga Afroestricus chiastoneurus Dioctria hyalipennis Ommatius incurvatus Dioctria rufipes Cophinopoda chinensis Dioctria atricapillus Neolophonotus bimaculatus Dasophrys crenulatus Pogonioefferia pogonias Proctacanthus philadelphicus Lochmorhynchus albicans Eichoichemus pyrrhomystax Promachus amastrus Megaphorus pulchrus Philodicus tenuipes Apoclea algira Blepharotes splendidissimus Lycomya germainii Satanas gigas Nomomyia murina Colepia rufiventris Threnia carbonaria Neoitamus cyanurus Zosteria rosevillensis Heligmonevra laevis Clephydroneura sundaica Clephydroneura sp Kepong Myaptex brachyptera Dysmachus trigonus Philonicus albiceps Congomochtherus inachus Machimus chrysitis Machimus occidentalis Tolmerus atricapillus Asilus sericeus 1 most parsimonious tree 28773 steps (iterative pass) Asilus crabroniformis Neomochtherus pallipes Afromochtherus mendax yellow branches = taxa from Morphology 158 hypothesis recovered as monophyletic; green taxon names = Trigonomiminae
  • 25. .... Phylogeny of Robber Flies 25Morphology Only versus Morphology + Molecular Morphology 158 Laphriinae Morphology + Molecular 158 Perasis transvaalensis Perasis transvaalensis Zabrops tagax Zabrops tagax Protometer sp ElTuparro Psilocurus modestus Psilocurus modestus Protometer sp ElTuparro Laphystia aegyptiaca Laphystia aegyptiaca Laphystia tolandi Laphystia tolandi Hoplistomerus nobilis Trichardis effrena Trichardis effrena Laxenecera albicincta Nusa infumata Hoplistomerus nobilis Laxenecera albicincta Nusa infumata Smeryngolaphria numitor Smeryngolaphria numitor Orthogonis scapularis Stiphrolamyra angularis Goneccalypsis argenteoviridis Lamyra gulo Loewinella nigripes Maira aenea Aphestia annulipes Lampria clavipes Atomosia puella Choerades bella Cerotainia albipilosa Laphria flava Maira aenea Laphria aktis Lampria clavipes Hyperechia nigripennis Choerades bella Dasyllis funebris Laphria flava Pilica formidolosa Laphria aktis Proagonistes praeceps Lamyra gulo Andrenosoma cyrtoxys Stiphrolamyra angularis Orthogonis scapularis Hyperechia nigripennis Loewinella nigripes Proagonistes praeceps Goneccalypsis argenteoviridis Andrenosoma cyrtoxys Aphestia annulipes Pilica formidolosa Cerotainia albipilosa Dasyllis funebris Atomosia puella yellow species name = molecular data
  • 26. .... Phylogeny of Robber Flies 26Morphology Only versus Morphology + Molecular Morphology 158 Asilinae Morphology + Molecular 158 Lycomya germainii Neolophonotus bimaculatus Blepharotes splendidissimus Dasophrys crenulatus Megaphorus pulchrus Pogonioefferia pogonias Promachus amastrus Proctacanthus philadelphicus Apoclea algira Lochmorhynchus albicans Philodicus tenuipes Eichoichemus pyrrhomystax Neolophonotus bimaculatus Promachus amastrus Pogonioefferia pogonias Megaphorus pulchrus Proctacanthus philadelphicus Philodicus tenuipes Lochmorhynchus albicans Apoclea algira Eichoichemus pyrrhomystax Blepharotes splendidissimus Myaptex brachyptera Lycomya germainii Dasophrys crenulatus Satanas gigas Nomomyia murina Nomomyia murina Machimus chrysitis Colepia rufiventris Machimus occidentalis Threnia carbonaria Satanas gigas Neoitamus cyanurus Asilus crabroniformis Zosteria rosevillensis Asilus sericeus Heligmonevra laevis Neomochtherus pallipes Clephydroneura sundaica Afromochtherus mendax Clephydroneura sp Kepong Philonicus albiceps Myaptex brachyptera Congomochtherus inachus Dysmachus trigonus Clephydroneura sundaica Philonicus albiceps Clephydroneura sp Kepong Congomochtherus inachus Heligmonevra laevis Machimus chrysitis Zosteria rosevillensis Machimus occidentalis Colepia rufiventris Tolmerus atricapillus Neoitamus cyanurus Asilus sericeus Threnia carbonaria Asilus crabroniformis Dysmachus trigonus Neomochtherus pallipes Tolmerus atricapillus Afromochtherus mendax yellow species name = molecular data
  • 27. .... Phylogeny of Robber Flies 27Morphology Only versus Morphology + Molecular Morphology 158 Ommatiinae Morphology + Molecular 158 Laphriinae Leptogastrinae Asilinae Michotamia aurata Cophinopoda chinensis Emphysomera pallidapex Ommatius incurvatus Emphysomera conopsoides Ommatius tibialis Ommatius tibialis Afroestricus chiastoneurus Afroestricus chiastoneurus Michotamia aurata Ommatius incurvatus Emphysomera conopsoides Cophinopoda chinensis Emphysomera pallidapex Asilinae yellow species name = molecular data, green branches = Ommatiinae
  • 28. .... Phylogeny of Robber Flies 28Taxon Morphology Morphology + Molecular Morphology + Molecular 158 77 158Asilinae √ √ √Bathypogoninae monogeneric unavailable monogenericBrachyrhopalinae √ — —Dasypogoninae √ — —Dioctriinae √ √ —Laphriinae √ √ √Leptogastrinae √ √ √Ommatiinae √ √ —Phellinae √ unavailable √Stenopogoninae √ — —Stichopogoninae √ √ —Tillobromatinae √ — — √ monophyleticTrigonomiminae √ — — — non-monophyleticWillistonininae √ — —
  • 29. ..... Summary 29Summary ◊ Total evidence strongest hypothesis › largest taxonomic coverage › largest amount of data ◊ Combined morphological and molecular data not used for phylogeny too often ◊ Several simultaneous analysis methods available ◊ Completeness of matrix might affect results
  • 30. 30Acknowledgments ◊ Willi Hennig Society ◊ U.S. National Science Foundation (DDIG DEB 0608258, REVSYS DEB 0919333) ◊ Cornell University, AMNH, FMNH