tdikow hennig 2011

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Torsten DikowBiodiversity Synthesis Center Field Museum of Natural History Chicago, IL, USA

Molecules and morphology: insights from phylogenetic analyses of insect taxa

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OverviewMorphological and Molecular Data ◊

Simultaneous Analyses of Insect Taxa ◊

Methodological Considerations◊

Example: Phylogeny of Robber Flies◊

Efferia sp.

Ceraturgus fasciatus © Michael Thomas

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Kurt M. Pickett 1972 – 2011

January 2009

4. Morphological and Molecular Data

Morphological and Molecular Data

1987

“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

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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◊

. Morphological and Molecular Data

Morphological and Molecular Data

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Simultaneous 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.”


“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.”


. Morphological and Molecular Data

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44 analyses

insect taxa = 13

other animal taxa = 22

plant taxa = 9

Published Simultaneous Analyses – Cladistics

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3

6

9

12

2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011

Num

ber

Year

.. Simultaneous Analyses of Insect Taxa

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35 analyses

Cladistics (insect taxa) = 13

Systematic Entomology = 18

Insect Systematics & Evolution = 2

Invertebrate Systematics = 2

Published Simultaneous Analyses – Insect Journals

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2

4

6

8

2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011

Num

ber

Year

.. Simultaneous Analyses of Insect Taxa

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Simultaneous Analysis – traditional approach

Morphological Data ◊ › primary homology statements already made by investigator (“prealigned”)

Molecular Data ◊ › unaligned nucleotides › nucleotides to be aligned using traditional alignment algorithms

static SuperMatrix

static analysis in TNT

... Methodology

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Simultaneous Analysis – current approach

Morphological Data ◊ › primary homology statements already made by investigator (“prealigned”)

Molecular Data ◊ › unaligned nucleotides › nucleotides to be aligned using dynamic homology

semi-dynamic SuperMatrix

semi-dynamic analysis in POY

... Methodology

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Simultaneous Analysis – future approach?

Morphological Data ◊ › “unaligned” character states › character states to be “aligned” using dynamic homology assignment

Molecular Data ◊ › unaligned nucleotides › nucleotides to be aligned using dynamic homology

dynamic SuperMatrix

dynamic analysis in POY

... Methodology

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Optimality or Inference Criteria in Simultaneous AnalysesParsimony ◊

› morphology + molecular › static: TNT › dynamic: POY

... Methodology

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

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Combining Data-sets – 1

Data-set 1 (here morphology) Data-set 2 (here nucleotide sequences)

... Methodology

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Combining Data-sets – 2

Data-set 1 (here morphology) Data-set 2 (here nucleotide sequences)

... Methodology

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Scleropogon duncani

Asilidae – “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◊

Speciose in arid & semi-arid environments, ◊ but also in tropical environments

Many Asilidae mimic Hymenoptera◊

Echthodopa formosa © Michael Thomas

.... Phylogeny of Robber Flies

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Morphology 158

158 species ◊ (= 2.13 %)

140 genera ◊ (= 26 %)

17 outgroup taxa◊

220 discrete, parsimony informative ◊ morphological characters

0.4% missing data◊

new phylogenetic classification◊

Taxon and Character SamplingMorphology + Molecular 77

77 species ◊ (= 1.04 %)

67 genera ◊ (= 12 %)

11 outgroup taxa◊

211 discrete, parsimony informative ◊ morphological characters

5 nuclear genes, ≈ 7,300 bp nuclear DNA◊

7.25% missing data◊


Dikow 2009 – Bulletin AMNH Dikow 2009 – Organisms, Diversity & Evolution

17.... Phylogeny of Robber Flies

Methods

TNT

POY

MacClade + WinClada◊

TNT + POY4◊

Ratchet◊ , TreeDrifting, + TreeFusing

TreeMap3◊

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Morphology 158Neorhynchocephalus volaticusBombylius majorPoecilognathus sp (El Hacha)Prorates sp (Escalante)Apsilocephala longistylusHemigephyra atraPhycus frommeriApiocera aldrichiApiocera painteriRhaphiomidas maehleriNeorhaphiomidas sp (Mandurah)Opomydas townsendiMitrodetus dentitarsisMydas clavatusPseudonomoneura hirtaNemomydas brachyrhynchusAfroleptomydas sp (Clanwilliam)Perasis transvaalensisZabrops tagaxProtometer sp (El Tuparro)Psilocurus modestusLaphystia aegyptiacaLaphystia tolandiHoplistomerus nobilisTrichardis testaceaNusa infumataLaxenecera albicinctaSmeryngolaphria numitorOrthogonis scapularisGoneccalypsis argenteoviridisLoewinella nigripesAphestia annulipesAtomosia puellaCerotainia albipilosaMaira aeneaLampria clavipesChoerades bellaLaphria flavaLaphria aktisLamyra guloStiphrolamyra angularisHyperechia nigripennisProagonistes praecepsAndrenosoma cyrtoxysPilica formidolosaDasyllis funebrisCophinopoda chinensisMichotamia aurataEmphysomera conopsoidesEmphysomera pallidapexOmmatius incurvatusOmmatius senexOmmatius tibialisLycomya germainiiBlepharotes splendidissimusMegaphorus pulchrusPromachus amastrusApoclea algiraPhilodicus tenuipesNeolophonotus bimaculatusPogonioefferia pogoniasProctacanthus philadelphicusLochmorhynchus albicansEichoichemus pyrrhomystaxMyaptex brachypteraDasophrys crenulatusNomomyia murinaDysmachus trigonusTolmerus atricapillusMachimus chrysitisMachimus occidentalisNeomochtherus pallipesAfromochtherus mendaxSatanas gigasAsilus crabroniformisAsilus sericeusPhilonicus albicepsCongomochtherus inachusClephydroneura sundaicaClephydroneura sp (Kepong)Heligmonevra laevisZosteria rosevillensisColepia rufiventrisNeoitamus cyanurusThrenia carbonaria

Bathypogon nigrinusPhellus olgaeObelophorus terebratusTillobroma punctipennisHypenetes stigmatiasLycostommyia albifaciesColeomyia setigeraAncylorhynchus fulvicollisScylaticus costalisConnomyia varipennisProlepsis tristisCreolestes nigribarbisMicrostylum sp (Karkloof)Daspletis stenouraPlesiomma sp (Guanacaste)Ospriocerus aeacusScleropogon subulatusStenopogon sabaudusStenopogon rufibarbisGonioscelis ventralisLestomyia fraudigerDasypogon diademaSaropogon disparSaropogon luteusThereutria amaracaArchilestris magnificusDiogmites grossusNeodiogmites melanogasterBlepharepium cajennensisMolobratia teutonusCyrtophrys attenuatusDeromyia fuscipennisPegesimallus laticornisSenobasis corsairMegapoda labiataPseudorus distendensAcnephalum cylindricumSisyrnodytes sp (Gamka)Ablautus coquillettiWillistonina bilineataTrichoura sp (Tierberg)Oligopogon sp (Cape Recife)Broticosia paramonoviDicolonus simplexEchthodopa puberaMyelaphus melasEudioctria albiusNannodioctria sp (formicaphaga)Dioctria atricapillusDioctria hyalipennisDioctria rufipesDamalis sp (Palatupana)Damalis monochaetesDamalis annulataRhipidocephala sp (Harold Johnson)Trigonomima sp (anamaliensis)Holcocephala abdominalisHolcocephala calvaAcronyches mayaBeameromyia bifidaEuscelidia pulchraTipulogaster glabrataLeptogaster aridaLeptogaster cylindricaLasiocnemus lugensLasiopogon aldrichiiLasiopogon cinctusTownsendia albomaculaStichopogon elegantulusStichopogon trifasciatusStichopogon punctumLissoteles aquiloniusAfroholopogon peregrinusDasycyrton gibbosusCyrtopogon lateralisCyrtopogon rattusLeptarthrus brevirostrisHolopogon priscusChrysopogon pilosifaciesCodula limbipennisAustrosaropogon nigrinusBrachyrhopala ruficornisCabasa pulchellaCeraturgus fasciatusNannocyrtopogon lestomyiformisNicocles politusHeteropogon manicatusMetapogon punctipennisCophura brevicornisRhabdogaster pedion

1 of 720 most parsimonious trees2760 stepsCI=0.13RI=0.68


yellow branches = previous taxa recovered as monophyletic

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211 morphological characters 7,300 bp of nuclear DNA


Morphology + Molecular 77 7.25% missing data

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1 most parsimonious tree27582 steps (iterative pass)

Morphology + Molecular 77Asilidae is monophyletic◊

Different higher-level relationships ◊ than in Morphology 158 hypothesis


Bombylius majorApsilocephala longistylaProrates sp. (Escalante)Phycus frommeriHemigephyra atraApiocera painteriOpomydas townsendiMydas clavatusMitrodetus dentitarsisNemomydas brachyrhynchusAfroleptomydas sp. (Clanwilliam)Rhipidocephala sp. (Harold Johnson)Holcocephala calvaHolcocephala abdominalisPerasis transvaalensisLaphystia tolandiTrichardis effrenaNusa infumataLaxenecera albicinctaHoplistomerus nobilisPilica formidolosaCerotainia albipilosaAtomosia puellaStiphrolamyra angularisLamyra guloLaphria aktisChoerades bellaDamalis monochaetesDamalis annulataRhabdogaster pedionAcnephalum cylindricumPegesimallus laticornisDiogmites grossusPlesiomma sp. (Guanacaste)Dasypogon diademaSaropogon luteusLestomyia fraudigerTrichoura sp. (Tierberg)Ablautus coquillettiMolobratia teutonusNicocles politusLeptarthrus brevirostrisCyrtopogon rattusCeraturgus fasciatusWillistonina bilineataEudioctria albiusDioctria hyalipennisDioctria rufipesDioctria atricapillusGonioscelis ventralisStenopogon rufibarbisOspriocerus aeacusTillobroma punctipennisProlepsis tristisMicrostylum sp. (Karkloof)Lycostommyia albifaciesScylaticus costalisConnomyia varipennisLasiopogon cinctusLasiopogon aldrichiiStichopogon punctumStichopogon trifasciatusStichopogon elegantulusEuscelidia pulchraBeameromyia bifidaLeptogaster cylindricaLeptogaster aridaTipulogaster glabrataLasiocnemus lugensEmphysomera pallidapexEmphysomera conopsoidesOmmatius tibialisAfroestricus chiastoneurusProctacanthus philadelphicusPogonioefferia pogoniasPhilodicus tenuipesPromachus amastrusMegaphorus pulchrusNeolophonotus bimaculatusDasophrys crenulatusNeoitamus cyanurusClephydroneura sp. (Kepong)Dysmachus trigonusPhilonicus albicepsMachimus occidentalisTolmerus atricapillusAsilus sericeusAsilus crabroniformis

yellow branches = taxa from Morphology 158 hypothesis recovered as monophyletic

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Proctacanthus philadelphicus

Pogonioefferia pogonias

Philodicus tenuipes

Promachus amastrus

Megaphorus pulchrus

Neolophonotus bimaculatus

Dasophrys crenulatus

Neoitamus cyanurus

Clephydroneura sp. (Kepong)

Dysmachus trigonus

Philonicus albiceps

Machimus occidentalis

Tolmerus atricapillus

Asilus sericeus

Asilus crabroniformis

206

0146

2

133

3110

1172

1

133

2

EF-1α

18S28SAATSCAD

morphological autapomorphies

Asilinae ◊ › molecular characters enhance resolution


Morphology + Molecular 77: Character Support

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Laphriinae ◊ › only supported by morphological autapomorphies

Perasis transvaalensis

Laphystia tolandi

Trichardis effrena

Nusa infumata

Laxenecera albicincta

Hoplistomerus nobilis

Pilica formidolosa

Cerotainia albipilosa

Atomosia puella

Stiphrolamyra angularis

Lamyra gulo

Laphria aktis

Choerades bella

EF-1α

18S28SAATSCAD

morphological autapomorphies

193

3

42

1 188

2

187

2

186

2

164

2

162

2

161

2

160

2

45

2

220

2

17

1

18

1

172

3166

1

158

1

150

1

140

3

137

4

57

5

50

1

96

3

45

1

47

1


Morphology + Molecular 77: Character Support

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220 morphological characters 7,300 bp of nuclear DNA

Morphology + Molecular 158 54.8% missing data


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Microstylum sp Karkloof

Heteropogon manicatus

Lestomyia fraudiger

Ancylorhynchus fulvicollis

Connomyia varipennis

Scleropogon subulatus

Metapogon punctipennis

Leptarthrus brevirostris

Damalis sp Palatupana

Cyrtopogon lateralis

Broticosia paramonovi

Archilestris magnificus

Damalis monochaetes

Molobratia teutonus

Damalis annulata

Cyrtopogon rattus

Chrysopogon pilosifacies

Eudioctria albius

Pegesimallus laticornis

Dicolonus simplex

Ospriocerus aeacus

Stenopogon sabaudus

Ceraturgus fasciatus

Rhabdogaster pedion

Sisyrnodytes sp Gamka

Senobasis corsair

Gonioscelis ventralis

Saropogon luteus

Cabasa pulchella

Hypenetes stigmatias

Myelaphus melas

Codula limbipennis

Scylaticus costalis

Daspletis stenoura

Dioctria rufipes

Plesiomma sp Guanacaste

Dasycyrton gibbosus

Phellus olgae

Prolepsis tristis

Cyrtophrys attenuatus

Thereutria amaraca

Nannodioctria sp formicaphaga

Coleomyia setigera

Lycostommyia albifacies

Pseudorus distendens

Blepharepium cajennensis

Ablautus coquilletti

Bathypogon nigrinus

Creolestes nigribarbis

Acnephalum cylindricum

Nicocles politus

Deromyia fuscipennis

Diogmites grossus

Dioctria hyalipennis

Tillobroma punctipennis

Dioctria atricapillus

Saropogon dispar

Neodiogmites melanogaster

Megapoda labiata

Austrosaropogon nigrinus

Stenopogon rufibarbis

Afroholopogon peregrinus

Brachyrhopala ruficornis

Obelophorus terebratus

Oligopogon sp Cape Recife

Cophura brevicornis

Willistonina bilineata

Dasypogon diadema

Nannocyrtopogon lestomyiformis

Echthodopa pubera

Afromochtherus mendax

Holopogon priscus

Nusa infumata

Clephydroneura sundaica

Prorates sp Escalante

Stichopogon punctum

Orthogonis scapularis

Machimus occidentalisTolmerus atricapillus

Mydas clavatus

Neorhaphiomidas sp Mandurah

Lissoteles aquilonius

Lasiopogon cinctus

Trigonomima sp anamaliensisRhipidocephala sp HaroldJohnson

Pilica formidolosa

Rhaphiomidas maehleri

Colepia rufiventris

Lycomya germainii

Laphystia tolandi

Aphestia annulipes

Eichoichemus pyrrhomystax


Perasis transvaalensis

Blepharotes splendidissimus

Phycus frommeri

Lamyra gulo

Zosteria rosevillensis


Smeryngolaphria numitor

Protometer sp El Tuparro


Dysmachus trigonus

Afroleptomydas sp Clanwilliam

Michotamia aurata

Choerades bella

Machimus chrysitis

Hemigephyra atra

Philodicus tenuipesMegaphorus pulchrus

Clephydroneura sp Kepong

Mitrodetus dentitarsis

Psilocurus modestus

Laphria aktis

Proagonistes praeceps

Stichopogon elegantulus

Myaptex brachyptera

Laphystia aegyptiaca

Leptogaster arida

Apsilocephala longistyla

Threnia carbonaria

Poecilognathus sp El Hacha

Congomochtherus inachus

Afroestricus chiastoneurus

Lasiopogon aldrichii

Acronyches maya

Leptogaster cylindrica

Neomochtherus pallipes

Zabrops tagax

Trichoura sp Tierberg

Beameromyia bifida

Atomosia puella

Ommatius tibialis

Townsendia albomacula


Nomomyia murina

Lasiocnemus lugens

Bombylius major

Goneccalypsis argenteoviridis

Neoitamus cyanurus

Trichardis effrena

Emphysomera conopsoides

Apoclea algira

Maira aenea



Satanas gigas

Holcocephala abdominalis

Opomydas townsendi

Nemomydas brachyrhynchus

Philonicus albiceps

Pseudonomoneura hirta

Dasyllis funebris

Cophinopoda chinensis

Neorhynchocephalus volaticus

Holcocephala calva

Asilus sericeus

Lampria clavipes

Stichopogon trifasciatus

Apiocera aldrichi


Laphria flava


Emphysomera pallidapex


Hyperechia nigripennis

Andrenosoma cyrtoxys

Ommatius incurvatus

Heligmonevra laevis

Lochmorhynchus albicans

Euscelidia pulchra

Apiocera painteri

Loewinella nigripes

Tipulogaster glabrata

Promachus amastrus

1 most parsimonious tree28773 steps (iterative pass)


Morphology + Molecular 158

yellow branches = taxa from Morphology 158 hypothesis recovered as monophyletic; green taxon names = Trigonomiminae

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Laphystia tolandi Laphystia tolandi



Protometer sp ElTuparro

Protometer sp ElTuparro





Dasyllis funebris

Dasyllis funebris

Laphystia aegyptiaca Laphystia aegyptiaca

Laphria aktis

Laphria aktis

Pilica formidolosa

Pilica formidolosaLaphria flava

Laphria flava

Atomosia puella

Atomosia puella

Choerades bella

Choerades bella

Maira aenea

Maira aenea



Aphestia annulipes

Aphestia annulipes

Psilocurus modestus

Psilocurus modestus

Lampria clavipes

Lampria clavipes

Trichardis effrena

Trichardis effrena

Perasis transvaalensis Perasis transvaalensis

Lamyra gulo

Lamyra gulo

Nusa infumata

Nusa infumata

Zabrops tagax Zabrops tagax



Smeryngolaphria numitor Smeryngolaphria numitor



Loewinella nigripes

Loewinella nigripesHyperechia nigripennis

Hyperechia nigripennis



Morphology 158

yellow species name = molecular data

Laphriinae Morphology + Molecular 158


Morphology Only versus Morphology + Molecular

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Philodicus tenuipes

Philodicus tenuipes



Myaptex brachyptera

Myaptex brachyptera

Promachus amastrus

Promachus amastrus

Heligmonevra laevis

Heligmonevra laevis

Nomomyia murina Nomomyia murina



Dysmachus trigonus

Dysmachus trigonus



Neoitamus cyanurus

Neoitamus cyanurus





Megaphorus pulchrus

Megaphorus pulchrus

Colepia rufiventris

Colepia rufiventris









Apoclea algira

Apoclea algira







Satanas gigas

Satanas gigas

Lycomya germainii

Lycomya germainii





Machimus chrysitis

Machimus chrysitis



Asilus sericeus

Asilus sericeus

Threnia carbonaria

Threnia carbonaria

Philonicus albiceps

Philonicus albiceps



Morphology 158

yellow species name = molecular data

Asilinae Morphology + Molecular 158



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Ommatius tibialis Ommatius tibialis

Asilinae

Asilinae

Laphriinae Leptogastrinae

Ommatius incurvatus

Ommatius incurvatusMichotamia aurata

Michotamia aurata



Emphysomera pallidapex

Emphysomera pallidapexCophinopoda chinensis

Cophinopoda chinensis

Afroestricus chiastoneurus Afroestricus chiastoneurus

Morphology 158 Morphology + Molecular 158

yellow species name = molecular data, green branches = Ommatiinae

Ommatiinae



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Taxon Morphology 158



Asilinae √ √ √Bathypogoninae monogeneric unavailable monogeneric

Brachyrhopalinae √ — —Dasypogoninae √ — —Dioctriinae √ √ —Laphriinae √ √ √Leptogastrinae √ √ √Ommatiinae √ √ —Phellinae √ unavailable √Stenopogoninae √ — —Stichopogoninae √ √ —Tillobromatinae √ — —Trigonomiminae √ — —Willistonininae √ — —

√ monophyletic— non-monophyletic


29..... Summary

SummaryTotal 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◊

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AcknowledgmentsWilli Hennig Society◊

U.S. National Science Foundation (DDIG DEB 0608258, REVSYS DEB 0919333)◊

Cornell University, AMNH, FMNH◊

tdikow hennig 2011

Career

morphology data

molecular data kluge

combining data

thatmolecular data

molecular static

molecular characters

dna nucleotide data

molecular data5morphological