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
3
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
5
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
6
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.”
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
. Morphological and Molecular Data
7
44 analyses
insect taxa = 13
other animal taxa = 22
plant taxa = 9
Published Simultaneous Analyses – Cladistics
0
3
6
9
12
2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011
Num
ber
Year
.. Simultaneous Analyses of Insect Taxa
8
35 analyses
Cladistics (insect taxa) = 13
Systematic Entomology = 18
Insect Systematics & Evolution = 2
Invertebrate Systematics = 2
Published Simultaneous Analyses – Insect Journals
0
2
4
6
8
2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011
Num
ber
Year
.. Simultaneous Analyses of Insect Taxa
9
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
10
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
11
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
12
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
13
Combining Data-sets – 1
Data-set 1 (here morphology) Data-set 2 (here nucleotide sequences)
... Methodology
14
Combining Data-sets – 2
Data-set 1 (here morphology) Data-set 2 (here nucleotide sequences)
... Methodology
15
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
16
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◊
.... Phylogeny of Robber Flies
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◊
18
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
.... Phylogeny of Robber Flies
yellow branches = previous taxa recovered as monophyletic
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211 morphological characters 7,300 bp of nuclear DNA
.... Phylogeny of Robber Flies
Morphology + Molecular 77 7.25% missing data
20
1 most parsimonious tree27582 steps (iterative pass)
Morphology + Molecular 77Asilidae is monophyletic◊
Different higher-level relationships ◊ than in Morphology 158 hypothesis
.... Phylogeny of Robber Flies
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
21
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
.... Phylogeny of Robber Flies
Morphology + Molecular 77: Character Support
22
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
.... Phylogeny of Robber Flies
Morphology + Molecular 77: Character Support
23
220 morphological characters 7,300 bp of nuclear DNA
Morphology + Molecular 158 54.8% missing data
.... Phylogeny of Robber Flies
24
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
Cerotainia albipilosa
Perasis transvaalensis
Blepharotes splendidissimus
Phycus frommeri
Lamyra gulo
Zosteria rosevillensis
Asilus crabroniformis
Smeryngolaphria numitor
Protometer sp El Tuparro
Pogonioefferia pogonias
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
Laxenecera albicincta
Nomomyia murina
Lasiocnemus lugens
Bombylius major
Goneccalypsis argenteoviridis
Neoitamus cyanurus
Trichardis effrena
Emphysomera conopsoides
Apoclea algira
Maira aenea
Neolophonotus bimaculatus
Proctacanthus philadelphicus
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
Dasophrys crenulatus
Laphria flava
Hoplistomerus nobilis
Emphysomera pallidapex
Stiphrolamyra angularis
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)
.... Phylogeny of Robber Flies
Morphology + Molecular 158
yellow branches = taxa from Morphology 158 hypothesis recovered as monophyletic; green taxon names = Trigonomiminae
25
Laxenecera albicincta
Laxenecera albicincta
Laphystia tolandi Laphystia tolandi
Andrenosoma cyrtoxys
Andrenosoma cyrtoxys
Protometer sp ElTuparro
Protometer sp ElTuparro
Stiphrolamyra angularis
Stiphrolamyra angularis
Cerotainia albipilosa
Cerotainia albipilosa
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
Hoplistomerus nobilis
Hoplistomerus nobilis
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
Proagonistes praeceps
Proagonistes praeceps
Smeryngolaphria numitor Smeryngolaphria numitor
Goneccalypsis argenteoviridis
Goneccalypsis argenteoviridis
Loewinella nigripes
Loewinella nigripesHyperechia nigripennis
Hyperechia nigripennis
Orthogonis scapularis
Orthogonis scapularis
Morphology 158
yellow species name = molecular data
Laphriinae Morphology + Molecular 158
.... Phylogeny of Robber Flies
Morphology Only versus Morphology + Molecular
26
Philodicus tenuipes
Philodicus tenuipes
Clephydroneura sp Kepong
Clephydroneura sp Kepong
Myaptex brachyptera
Myaptex brachyptera
Promachus amastrus
Promachus amastrus
Heligmonevra laevis
Heligmonevra laevis
Nomomyia murina Nomomyia murina
Asilus crabroniformis
Asilus crabroniformis
Dysmachus trigonus
Dysmachus trigonus
Pogonioefferia pogonias
Pogonioefferia pogonias
Neoitamus cyanurus
Neoitamus cyanurus
Tolmerus atricapillus
Tolmerus atricapillus
Clephydroneura sundaica
Clephydroneura sundaica
Megaphorus pulchrus
Megaphorus pulchrus
Colepia rufiventris
Colepia rufiventris
Zosteria rosevillensis
Zosteria rosevillensis
Congomochtherus inachus
Congomochtherus inachus
Neolophonotus bimaculatus
Neolophonotus bimaculatus
Blepharotes splendidissimus
Blepharotes splendidissimus
Apoclea algira
Apoclea algira
Machimus occidentalis
Machimus occidentalis
Dasophrys crenulatus
Dasophrys crenulatus
Neomochtherus pallipes
Neomochtherus pallipes
Satanas gigas
Satanas gigas
Lycomya germainii
Lycomya germainii
Afromochtherus mendax
Afromochtherus mendax
Proctacanthus philadelphicus
Proctacanthus philadelphicus
Machimus chrysitis
Machimus chrysitis
Lochmorhynchus albicans
Lochmorhynchus albicans
Asilus sericeus
Asilus sericeus
Threnia carbonaria
Threnia carbonaria
Philonicus albiceps
Philonicus albiceps
Eichoichemus pyrrhomystax
Eichoichemus pyrrhomystax
Morphology 158
yellow species name = molecular data
Asilinae Morphology + Molecular 158
.... Phylogeny of Robber Flies
Morphology Only versus Morphology + Molecular
27
Ommatius tibialis Ommatius tibialis
Asilinae
Asilinae
Laphriinae Leptogastrinae
Ommatius incurvatus
Ommatius incurvatusMichotamia aurata
Michotamia aurata
Emphysomera conopsoides
Emphysomera conopsoides
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
.... Phylogeny of Robber Flies
Morphology Only versus Morphology + Molecular
28
Taxon Morphology 158
Morphology + Molecular 77
Morphology + Molecular 158
Asilinae √ √ √Bathypogoninae monogeneric unavailable monogeneric
Brachyrhopalinae √ — —Dasypogoninae √ — —Dioctriinae √ √ —Laphriinae √ √ √Leptogastrinae √ √ √Ommatiinae √ √ —Phellinae √ unavailable √Stenopogoninae √ — —Stichopogoninae √ √ —Tillobromatinae √ — —Trigonomiminae √ — —Willistonininae √ — —
√ monophyletic— non-monophyletic
.... Phylogeny of Robber Flies
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◊
30
AcknowledgmentsWilli Hennig Society◊
U.S. National Science Foundation (DDIG DEB 0608258, REVSYS DEB 0919333)◊
Cornell University, AMNH, FMNH◊
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