Lousy Phylogenies: Phthiraptera systematics and the antiquity of lice Division of Environmental and Evolutionary Biology Institute of Biomedical and Life Sciences Graham Kerr Building University of Glasgow Scotland, UK Vincent S. Smith
Jul 01, 2015
Lousy Phylogenies:Phthiraptera systematics and the
antiquity of lice
Division of Environmental and Evolutionary BiologyInstitute of Biomedical and Life Sciences
Graham Kerr BuildingUniversity of Glasgow
Scotland, UK
Vincent S. Smith
Lice (Phthiraptera): biologyi. Diversity
• 4,384 spp “chewing lice” (3,508 bird & 402 mammal spp)• 543 spp sucking lice (812 spp mammal)
iv. Cophylogeny, cospeciation & coevolution
ii. Physical characteristics• wingless, dorsoventrally flattened, 0.3-11mm, 3 nymphal instars• feed on feathers, fur & skin debris (“chewing lice”) or blood• adaptations against host grooming
iii. Distribution• mirror host distribution worldwide in virtually every habitat• absent on Chiroptera, Cetacea, Microbiotheria, Monotremata,
Notoryctemorphia, Pholidota & Sirenia.
- 1,350 spp in 6 families- Most “primitive”
suborder- More vagile, less host specific- Widespread on birds- 2 fam. South American mammals & marsupials- 1 fam. on Australasian marsupials
- 3,060 spp., # families ?- Widespread, ~90% spp. on birds- Avian groups poorly known- Highly host specific- Niche restricted- Mammal infesting species of veterinary significance
- Just 3 species- On unrelated hosts- Acquired via shared use of watering holes?- Tiny mandibles present at end of a long rostrum pierce hosts thick skin
- 550 spp. in 16 families- Absent from birds- Well studied- Greatest medical & veterinary significance- Vectors of several important diseases- Low prevalence on healthy hosts
AmblyceraAmblycera IschnoceraIschnocera RhynchophthirinaRhynchophthirina AnopluraAnoplura
Lice (Phthiraptera): taxonomyChewing Lice“Mallophaga”
Sucking Lice(Anoplura)
Lice (Phthiraptera): phylogeny
PsocopteraPsocoptera IschnoceraIschnocera RhynchophthirinaRhynchophthirina AnopluraAnopluraAmblyceraAmblycera
Chewing Lice“Mallophaga”
Sucking Lice(Anoplura)
Kim & Ludwig, 1982(Morphology)
Parasitic Lice((Phthiraptera)
Lyal, 1985(Morphology)
GenusFamilySuborder
3
532
3,060
1,344
Rhynchophthirina
Amblycera
Ischnocera
Anoplura
MammalsBirds
Amblycera
Ischnocera
Rhyn…
Anoplura Phthiraptera:
Phylogeneticresolution, 1996
GenusFamilySuborder
3
532
3,060
1,350
Amblycera
Ischnocera
Anoplura Phthiraptera:
Phylogeneticresolution, 2003
Rhyn…
MammalsBirds
GenusFamilySuborder
3
532
3,060
1,344
Amblycera
Ischnocera
Rhyn…
Anoplura
1996GenusFamilySuborder
3
541
3,060
1,350
2003
Amblyceran Families
85
84
Grilicolinae
Gyropinae
Protogyropinae
Trimenoponidae
Ricinidae
Laemobothriidae
Boopiidae
Menoponidae
Liposcelidae (Psocoptera)
Birds Worldwide & Australasian Marsupials
South/CentralAmerican
Rodents & Marsupials
GyropidaeAnalysed by
Marshall, 2003from Clay, 1970(Morphology)
Laemobothriidae- Falconiforms
Menacanthus/Menopon-cpx.- Birds worldwide
Colpocephalum-complex- Birds worldwide
Austromenopon-complex- Aquatic birds
Dennyus-complex- Birds worldwide
Boopidae- Australasian marsupials
Ricinidae- Hummingbirds
Avian Amblycera
6457
8773
1
1
611
7561
3100 999
93853
10010012
10010015
9688
100 98
7
8
8976
4
3
5
9074
2
1
1 622
9896
11
1
11
1
523
2 80574
92755 51
13
1
2
1
2
1
2
2
1
12
Trochiloecetes rupununiRicinus fringillaeTrochiliphagus abdominalisLaemobothrion maximumTherodoxus oweniBoopia tarsataParaheterodoxus insignisLatumcephalum lesouefi/macropusParaboopia flavaRediella mirabilisActornithophilus uniseriatusPlegadiphilus threskiornisChapinia robustaBonomiella columbaePseudomenopon pilosumAncistrona vagelliDennyus hirundinisMyrsidea victrixHolomenopon brevithoracicumEidmanniella pellucidaMachaerilaemus laticorpus/latifronsAustromenopon crocatumNeomenopon pteroclurusHohorstiella lata
Osborniella crotophagaeEomenopon denticulatumPiagetiella bursaepelecaniCiconiphilus quadripustulatusCuculiphilus fasciatusArdeiphilus trochioxusOdoriphila clayae/phoeniculiPsittacomenopon poicephalusColpocephalum zebraComatomenopon elbeli/elongatum
Gruimenopon longumHoazineus armiferusMeromenopon meropisTrinoton anserinumMenacanthus stramineusColimenopon urocoliusSomaphantus lusiusAmyrsidea ventralisMenopon gallinaeNumidicola antennatus
B
L
M B
C
D
A
Liposcelis bostrychophilus
Marshall, 200344 genera, 147 char.(Morphology)
Psocoptera
Menacanthus /Menopon - complex
Ricinidae
Laemobothriidae
Boopiidae
Austromenopon- complex
Dennyus- complex
Colpocephalum- complex
• Collected Eckfeld maar nearEifel, Germany
• Middle Eocene (Middle Lutetian,44.3±0.4 Ma)
• First fossil louse
• Completes ordinal representationof fossil insects?
• Excellent preservation
• Phylogenetic affinities withmodern feather lice
• Parasite of Anseriformes orCharadriiformes
• Crown group position• Points to a long coevolutionary
history with birds• Suggests lice are very old• Useful molecular calibration point
First Fossil Louse (Amblycera: Menoponidae)
Wappler, Smith &Dalgleish , In prep.
Ischnoceran FamiliesGenusFamilySuborder
3
532
3,060
1,344
MammalsBirds
Amblycera
Ischnocera
Rhyn…
Anoplura
Ischnocera
TrichodectidaeHeptapsogasteridae
“Philopteridae”
Hopkins & Clay, 1951
cf. Eicher, 196121 families
Smith, 2000Generic level phylogeny ofGoniodidae & Heptapsogasteridae
(Morphology)
Heptapsogasteridae
Goniodidae
Avian Ischnoceran Phylogeny
Columbicola columbae
Austrogoniodes waterstoni
Harrisoniella hopkinsiHaffneria grandis
Paraclisis diomedeaPerineus nigrolimbatusHalipeurus pelagicusPhiloceanus garrodiaePseudonirmus gurltiNaubates fuliginosusPelmatocerandra setosaArdeicola smithersiAnaticola crassicornisPectinopygus bassaniPectinopygus sulaeAquanirmus australisIbidoecus plataleaeTrabeculus schillingiCraspedonirmus colymbinusQuadraceps coenocoryphaeDocophoroides brevisSaemundssonia desolataSaemundssonia haematopiPodargoecus strigoidesAlcedoecus delphaxCraspedorrhynchus platystomusStrigiphilus vapidusSturnidoecus sturniPhilopterus ornatusVernoniella guimarãesiAcidoproctus rostratusAcidoproctus hilliRallicola lugensOsculotes curtusOsculotes macropodaColoceras damicorneCampanulotes bidentatusGoniocotes gallinaeGoniodes pavonisGoniodes kéleriChelopistes guttatus
Strongylocotes angulocapitisDiscocorpus c. cephalosus
Splendoroffula ruwenzorornisOxylipeurus dentatusCuclotogaster madagascariensisLipeurus caponisDegeeriella rufaUpupicola upupaeLagopoecus affinisSyrrhaptoecus falcatusNeopsittaconirmus borgioliiParagoniocotes rotundusBrüelia semiannulataFalcolipeurus affulgeusArcholipeurus nandu
Felicola (F.) viverriculaeGeomydoecus (G.) heaneyi
Trichodectes (T.) melisBovicola limbatusDamalinia (D.) crenelata
Smith, 2001Generic level phylogenyApprox. 1/3rd of all ischnoceran genera
51 genera, 138 characters(Morphology)
Philoceanus-complex
Goniodidae
Degeeriella-complex
Trichodectidae
Lipeurus-complex
Heptap.
Saemundssonia-complex
Philopterus-complex
Multiple clades of liceon the same host
A. Circumfasciate Head
B. Non-Circumfasciate Head
N I N II N III Adult
C. Wing Lice D. Body Lice E. Head Lice
Characters Defining Major Ischnoceran Clades
Philoceanus-complex
Goniodidae
Degeeriella-complex
Trichodectidae
Lipeurus-complex
Heptap.
Saemundssonia-complex
Philopterus-complex
WingLice
WingLice
CI: 0.5RI: 0.95
HeadLice
BodyLiceCircumfasciate
Non-circumfasciate
CI: 1.0RI: 1.0
Characters Defining Major Ischnoceran Clades
Multiple cladesoccupy differenthost niches
• Incongruent with molecular data• Morphological convergence• Molecular data suggests many of
these pairs are more closely related
• Character displacement?
• Sympatric speciation?
Problems with Morphology!Smith et al, 2003
Rhynchophthirina: HaematomyzidaeGenusFamilySuborder
3
532
3,060
1,344
Amblycera
Ischnocera
Anoplura
Rhynchophthirina
Rhynchophthirina: Haematomyzidae• Just 3 species in 1 family• Present on elephants, wart hog & bush
pig (perhaps also mammoths?)• Monophyly & sister placement with
Anoplura well supported• Chewing lice (have outwardly opposing
mandibles)• Pool blood feeders (telmophages) cf
vessel feeding Anoplura• Spread via shared use of watering holes?• Possible cryptic species?
(morphologically identical species onAfrican & Asian elephants)
• Specimens hard to come by!
Haematomyzus elephantisHaematomyzus elephantisex Asian / African elephantex Asian / African elephant
Haematomyzus elephantisHaematomyzus hopkinsiHaematomyzus porci
Part of Smith, in prep.51 genera, 76 species184 characters(Morphology)
3
532
3,060
1,344
Amblycera
Ischnocera
Rhyn…
Anoplura
Anopluran Families
Anoplura At least 15distinct families
Anoplura:familial phylogeny
• 541spp. in 15 families• Patchily distributed across
mammals
Based on Kim, 198847 genera, 39 characters(Morphology)
• Monophyly of all 15 familiessupported
• 3 basal clades• Many lice of host groups
(including Primates) paraphyletic
Kim’s datasetre-analysed:
Kim, 1988 reanalysedStrict Consensus
• Length=219 (CI=0.26, RI=0.62)
OUTGROUP
“Polyplacidae” 1
“Polyplacidae” 2
“Polyplacidae” 3
Hoplopleuridae
“Polyplacidae” 4-12
Echinophthiriidae
Enderleinellidae
“Linognathidae” 1
Neolinognathidae
“Linognathidae” 2
Pedicinidae
Pthiridae
“Polyplacidae” 13
Ratemiidae
Hamophthiriidae
Hybophthiridae
Pediculidae
Pecaroecidae
Haematopinidae
Microthoraciidae
“Polyplacidae” 1
“Polyplacidae” 2
“Polyplacidae” 3
“Polyplacidae” 4-12
“Linognathidae” 1
“Linognathidae” 2
“Polyplacidae” 13
• Paraphyly of 2 of the 5 familiesthat were not monogenic
• Only 3 other nodes arecompatible with Kim’s tree
• Just 1 node agrees with Kim’soriginal tree!
Haematomyzus elephantisHaematomyzus hopkinsi
Pthirus gorillaePthirus pubisPediculus schaeffiPediculus humanusPediculus mjobergiPediculus humanus var. americanusScipio aulacodiScipio tripedatusNeolinognathus sp.Neolinognathus elephantuliSolenopotes muntiacusProlinognathus aethiopicusProlinognathus ferrisiLinognathus setosusLinognathus aepycerusLinognathus africanusLatagophthirus rauschiEchinophthirius horridusLepidophthirus macrorhiniAntarctophthirus callorhiniAntarctophthirus microchirProechinophthirus fluctusProechinophthirus zumptiJohnsonpthirus chlorotalpaeJohnsonpthirus heliosciuriLemurphthirus galagusLemurphthirus stigmosusLinognathoides laeviusculusSathrax durusNeohaematopinus callosciuriNeohaematopinus inornatusAbrocomaphthirus chilensisCtenophthirus cercomydisProenderleinellus calvaPolyplax abyssinicaPolyplax spinulosaDocophthirus acinetusEulinognathus denticulatusHaemodipsus leporisHaemodipsus lyriocephalusLagidiophthirus parvusFahrenholzia ferrisiFahrenholzia pinnataGaleophthirus caviaePhthirpediculus brygooiPhthirunculus sumatranusAtopophthirus emersoniMicrophthirus uncinatusEnderleinellus osborniWerneckia nigeriensisHoplopleura acanthopusParadoxophthirus emarginataHoplopleura pacificaHoplopleura irritansPterophthirus audaxPterophthirus splendidaAncistroplax crociduraeHaematopinoides squamosusTyphlomyophthirus bifoliatusSchizophthirus graphiuriSchizophthirus pleurophaeus
Haematomyzus porciMicrothoracius cameliRatemia squamulataHamophthirius galeopitheciHybophthirus notophallusHaematopinus asiniHaematopinus suisPecaroecus javaliiPedicinus ferrisiPedicinus patas
Anoplura:phylogeny
Haematomyzidae
Linognathidae
“Polyplacidae” 1Neolinognathidae
Enderleinellidae
Hoplopleuridae
“Polyplacidae” 2
“Polyplacidae” 3
Echinophthiriidae
MicrothoraciidaeRatemiidaeHamophthiriidaeHybophthiridae
HaematopinidaePecaroecidae
PedicinidaePthiridae
Pediculidae
Smith, in prep.51 genera, 76 species184 characters(Morphology)
• Why are rodents so lousy?
• Why are other mammalsrelatively louse free cf. birds
• Good evidence forcophylogeny in some clades
• Comparative studies underwayusing these trees
Louse Molecular Studies
Nuclear
- EF1-α (350-450bp)- 18S rRNA (1500+bp)- Wingless, PEPCK, DDC
• Hard to amplify• Multiple copies• RNA alignment issues• Utility varies between genes &
taxa
Mitochondrial
- COI (400-1500bp)- 12S rRNA (450bp)- Cyt. B (450bp)- ND4 (500bp)
• Easy to amplify• Limited phylogenetic utility
outside families• Often restricted to use within
closely related genera
Need New Genes!
Lice
all sitespos. 1pos. 2pos. 3
all sitespos. 1pos. 2pos. 3
all sitespos. 1pos. 2pos. 3
11
0.12129.9
11
0.15169.78
11
0.000144.79
0.0180.0130.0160.41
0.0160.0390.017
0.80.250.20
0.00012.49
55.676.97.5
316.861.525.68.8
212.24.15.01.018.0
Physconelloidinae
Columbicola
aphids
DataSet
Sites Ratio(COI:EF1α)COI EF1-α
Rate Parameter
Relative Substitution Rate(Mit. COI vs nuc. EF1-α)
Louse 12SSecondary
Structure
mit. 12S rRNAColumbicola columbae
Austrogoniodes cristati
Naubates prioni
Halipeurus pelagicus
Naubates harrisoni
Rallicola columbiana
Austrophilopterussubsimilis
Austrogoniodes cristati
Austrogoniodes waterstoni
Oxylipeurus chiniri
Campanulotes bidentatus
Austrophilopterussubsimilis
Page et al, 2002
0
20
40
60
80
100
120
Length
35 40 45 50 55 60 65 70 75 800123456789
10
Length
020406080
100120140160180200
Length
15 20 2530 35 40 45 50 55 60 65 70 75 80 850
2
4
6
8
10
12
14
Length
Segment 3: 38'-39' Segment 5: 34'-33'
0
20
40
60
80
100
120
140
160
Length
5 10 15 20 25 30 35 40 450
2
4
6
8
10
12
Length
Segment 2: 36-38Segment 1: 33-33'
0
20
40
60
80
100
120
140
160
Length
insects
2102202302402502602702802903003103200
1
2
3
4
5
6
7
Length
lice
12S LengthVariation
Insects vs.LicePage et al, 2002
cox1 cox2
atp8
atp6 cox3
nad3 nad5 nad4
nad4
L
nad6 cob nad2 rrnL rrnS nad2
L2 KD G HARNS1EF TP VS2 L1IQM WCY
cox1 cox3 nad1 cob nad4
nad4
L
nad2
nad3nad5 cox2 rrnL rrnS atp6
atp8
nad6
S2 L2 KNAY QV PTDIFS1CMWERII GL1
Gene arrangement of Heterodoxus macropus (Amblycera)
Inferred gene arrangement of ancestral insect
Adapted fromAdapted from Shao Shao, Campbell & Barker, 2001, Campbell & Barker, 2001
Louse Mitochondrial Genome
Louse Molecular Studies
Nuclear
- EF1-α (350-450bp)- 18S rRNA (1500+bp)- Wingless, PEPCK, DDC
• Hard to amplify• Multiple copies• RNA alignment issues• Utility varies between genes &
taxa
Mitochondrial
- COI (400-1500bp)- 12S rRNA (450bp)- Cyt. B (450bp)- ND4 (500bp)
• Easy to amplify• Limited phylogenetic utility
outside families• Often restricted to use within
closely related genera
Need New Genes!
ISCHNOCERA
AMBLYCERA
ANOPLURA
RHYN… Louse NuclearGenes
CruickshankCruickshank et al, 2001 et al, 2001
• 350 bp single copy EF1-α• Limited phylogenetic utility
above families
What Not to do!
Phylogenetic Utility 18S rRNA
Smith et al, 2003
• Much recent progress on basal phthirapteran phylogeny• Monophyly of suborders well supported• Complex pattern of host-louse relationships• Distinctive molecular evolution in lice• Incongruence between molecules & morphology
Ongoing Questions…
• To what extent do lice cospeciate with their hosts?• Why are some hosts more lousy than others?• How old are the major louse clades?• Are Phthiraptera truly paraphyletic?
Conclusions…
Acknowledgements
CollaborationStephen BarkerDale Clayton Tom FordKevin JohnsonRod PageIsabel MarshallDavid Reed
FundingWellcome Trust, UKNatural Environment Research Council, UK
0.60.50.40.30.20.100
100
200
300
ML Corrected Divergences(EF1-α 3rd Positions)
ML
Cor
rect
ed D
iver
genc
es(C
OI 3
rd P
ositi
ons)
Slopeapproximatesrelative rate
Around 1000:1 !!!
Pairwise ML Corrected Distances for 3rd Sites(Nuclear EF1-α against Mit. COI)
Johnson et al, 2003
18S – not a panacea for basal louse Phylogeny!
Unc
orre
cted
NJ
Bay
esia
n
0.10.1
AnopluraAnoplura
Ischnocera
Ischnocera
Amblycera
Amblycera
Liposcelis sp.
Liposcelis sp.Trogiomorph Psocoptera Trogiomorph Psocoptera