Background
Bacteria play important roles in the success and diversification of many animal groups, and insects are especially prone to establishing long-term, mutualistic endosymbioses. An estimated 10-20% of insect species, in several taxonomic orders, depend on intracellular bacterial mutualists for their viability and reproduction
1
. These obligate associates, called 'primary' (P-) endosymbionts because they are required for host survival and fecundity, often synthesize key nutrients that are lacking in the hosts' unbalanced diet (e.g., plant sap or vertebrate blood)
2
3
4
. In all cases, the bacteria live within specialized host cells called bacteriocytes and undergo maternal transmission to developing eggs or embryos. Consistent with this stable transmission through host lineages, the phylogenies of P-endosymbionts match those of their insect hosts (e.g.,
5
6
7
8
9
). This phylogenetic congruence points to host-symbiont cospeciation, which can be traced back to a single, often ancient, infection event in each host group.
Among Hymenoptera, only members of the Formicidae (ants) are known to possess bacteriocyte-associated endosymbionts. And within ants, despite the group's wide variety of symbioses with microbes
10
, only three known examples of such intracellular mutualisms exist. These three cases occur in subfamily Formicinae: Formica, Plagiolepis, and all members of the tribe Camponotini screened to date
11
12
13
14
. Although the symbioses are similar in many respects, phylogenetic analysis of bacterial 16S rDNA implies the three bacteriocyte-associated symbioses in ants evolved independently
15
.
The symbionts of Formica and Plagiolepis have not been studied in depth, but have been documented within bacteriocytes on either side of the midgut epithelium. In Formica, symbionts are found within queen ovarioles and in developing brood
12
13
16
. The bacteria are considered maternally transmitted, but their occurrence is erratic among Formica species and can vary within species depending on nutritional status
12
.
Endosymbionts in the tribe Camponotini, the focus of this study, are the best-studied bacterial mutualists in ants. The bacterium, Blochmannia, was first discovered in Camponotus
14
the second largest ant genus with ~1,000 described species worldwide
17
. The bacteria occur within ant bacteriocytes, which are intercalated among midgut epithelial cells, as well as queen and worker ovaries where symbionts infect the developing oocyte and are closely integrated with host development
13
14
18
19
. Although Blochmannia densities apparently decline in older lab-reared workers
20
, and the bacteria can be eliminated from workers treated with antibiotics
18
, we have never failed to find Blochmannia in any Camponotus worker collected in the field (unpublished data), which total many hundred samples across diverse species. The retention of many nutrient biosynthetic functions within the Blochmannia genomes implies this symbiosis plays a nutritional role
21
22
. Likewise, experimental diet treatments indicate that Blochmannia provides nutrients to the host, including amino acids
23
.
Among insects possessing long-term intracellular mutualists, which include several sap- and blood- feeding species, many Camponotus spp. stand out as true omnivores that scavenge other insects as part of their complex diet. Benefits conferred by Blochmannia might be critical during specific periods in host individual and colony development
23
24
25
(unpublished data). In addition, perhaps the symbiosis originated in an ant lineage that fed on a nutritionally unbalanced diet, such as extant arboreal Camponotus and Polyrhachis that obtain most nitrogen from plant and insect exudates
26
27
28
. Like many other ants, these arboreal species tend sap-feeding hemipterans, such as mealybugs, aphids, and psyllids, for their carbohydrate-rich excrement, or 'honeydew'
29
.
Like other P-endosymbionts, Blochmannia has codiverged with its known ant hosts, reflecting an evolutionarily stable association. Several phylogenetic analyses of symbiont and host genes have demonstrated cospeciation within Camponotus
19
30
31
. In addition, Sameshima et al.
15
showed that Blochmannia occurs in Polyrhachis and Colobopsis (currently a subgenus of Camponotus
17
but probably a separate lineage
32
), suggesting the symbiosis originated before the divergence of these three taxa, on the order of 40 MYA.
However, due to limited sampling, the actual distribution of Blochmannia throughout the Camponotini is unknown. Currently, the formal description of Camponotini includes eight extant genera: Camponotus (including subgenus Colobopsis), Polyrhachis, Calomyrmex, Echinopla, Opisthopsis, Forelophilus, Overbeckia, and Phasmomyrmex
33
. To date, Blochmannia has been detected in Camponotus (including Colobopsis) and Polyrhachis as noted above, and Stoll et al.
34
detected a Blochmannia-like bacterium in association with an Echinopla species, based on a 367-bp region of the bacterial 16S rDNA gene. Because several Camponotini genera remain unsampled, the occurrence of Blochmannia within the tribe is uncertain.
For context, Dasch
12
reported that eight genera of Camponotini possess intracellular bacterial symbionts, and this number (eight) has been cited in subsequent work. However, the genera cited by Dasch have since been reclassified as subgenera of Camponotus (i.e., Tanaemyrmex, Myrmentoma, Myrmosericus, Myrmobrachys, Myrmocladoecus, Myrmothrix, and Colobopsis)
17
.
In this study, our goals are (i) to better understand the actual host range of Blochmannia, and (ii) to identify the closest bacterial relatives and likely source of this mutualism. To this end, we screened for Blochmannia in a broader representation of Camponotini genera, including Calomyrmex, Opisthopsis, and Echinopla. We also sampled a representative of Notostigma, a genus formerly considered part of the Camponotini but recently placed in its own tribe
33
. To screen for symbionts, we amplified and sequenced a region of the 16S rDNA gene. Our results indicate that Blochmannia is more widespread within the tribe than previously documented and strongly suggest a single, ancient origin for this endosymbiosis. In addition, a close relationship with secondary endosymbionts of mealybugs suggests a potential route for the acquisition of Blochmannia. Specifically, the tribe Camponotini may have acquired its bacterial partner by tending honeydew-producing hemipterans.
Results and discussion
PCR screen for Blochmannia
We screened 53 representatives of the Camponotini for bacterial associates (Table 1). Specimens were identified minimally to subgenus (when applicable) and in most cases to species. The sample includes 42 Camponotus isolates, ten of which belong to the subgenus Colobopsis, as well as four Polyrhachis, two Calomyrmex, four Opisthopsis, and one Echinopla isolate. We also screened a representative of Notostigma, which was recently removed from the tribe
33
.
<p>Table 1</p>Ant specimens screened for bacterial associates, including 42 Camponotus specimens, ten of which belong to the subgenus Colobopsis, and representatives of Polyrhachis, Echinopla, Calomyrmex, and Opisthopsis.
Species1
ID
Subgenus2
Collector
Location
GPS
Collection code
Voucher location3
Calomyrmex albertisi
191
P. S. Ward
Australia (Qld)
13°43'S, 143°19'E
P. S. Ward #15325
UCDC
Calomyrmex laevissimus
254
P. S. Ward
Australia (Qld)
11°41'S, 142°42'E
P. S. Ward #15712
UCDC
Echinopla australis
253
P. S. Ward
Australia (Qld)
10°45'S, 142°31'E
P. S. Ward #15692
UCDC
Polyrhachis decumbens
190
Cyrtomyrma
P. S. Ward
Australia (Qld)
12°43'S, 143°17'E
P. S. Ward #15359
UCDC
Polyrhachis sp.
189
Hagiomyrma
P. S. Ward
Australia (Qld)
13°43'S, 143°19'E
P. S. Ward #15330
UCDC
Polyrhachis cupreata
252
Hedomyrma
P. S. Ward
Australia (Qld)
16°49'S, 145°41'E
P. S. Ward #15648
UCDC
Polyrhachis foreli
255
Myrma
P. S. Ward
Australia (Qld)
16°49'S, 145°41'E
P. S. Ward #15679
UCDC
Opisthopsis haddoni
a
244
A. Andersen
Australia (NT)
12°24'S, 130°55'E
UCDC
Opisthopsis haddoni
256
P. S. Ward
Australia (Qld)
16°49'S, 145°41'E
P. S. Ward #15653-1
UCDC
Opisthopsis respiciens
192
P. S. Ward
Australia (Qld)
16°27'S, 145°22'E
P. S. Ward #15395-1
UCDC
Opisthopsis PG01b
258
P. S. Ward
Papua New Guinea
05°13'S, 145°25'E
P. S. Ward #10107
UCDC
Camponotus quercicola
228
Camponotus
S. G. Brady
USA (California)
39°14'N, 121°17'W
S. G. Brady #328
USNM
Camponotus sp.
241
Myrmaphaenus
P. S. Ward
Bolivia
13°50'S, 60°52'W
P. S. Ward #12233
UCDC
Camponotus clarithorax
233
Myrmentoma
P. S. Ward
USA (California)
32°53'N, 117°06'W
P. S. Ward #14261
UCDC
Camponotus hyatti
186
Myrmentoma
P. S. Ward
USA (California)
34°01'N, 119°48'W
P. S. Ward #14925
UCDC
Camponotus dimorphus
234
Myrmobrachys
P. S. Ward
Bolivia
17°40'S, 63°27'W
P. S. Ward #12295
UCDC
Camponotus sp.
261
Myrmobrachys
P. S. Ward
Mexico (Oaxaca)
15°40'N, 96°33'W
P. S. Ward #15578
UCDC
Camponotus sanctaefidei
240
Myrmocladoecus
P. S. Ward
Bolivia
17°27'S, 63°40'W
P. S. Ward #12423
UCDC
Camponotus suffusus
238
Myrmosaulus
P. S. Ward
Australia (SA)
32°50'S, 138°02'E
P. S. Ward #13758
UCDC
Camponotus claviscapus
227
Pseudocolobopsis
P. S. Ward
Ecuador
01°04'S, 77°37'W
P. S. Ward #11338
UCDC
Camponotus occultus
229
Pseudocolobopsis
P. S. Ward
Cuba
20°25'N, 74°34'W
P. S. Ward #14421
UCDC
Camponotus consobrinus
239
Tanaemyrmex
P. S. Ward
Australia (SA)
34°53'S, 138°43'E
P. S. Ward #13723
UCDC
Camponotus maritimus
185
Tanaemyrmex
P. S. Ward
USA (California)
37°24'N, 122°14'W
P. S. Ward #15202
UCDC
Camponotus semitestaceus
242
Tanaemyrmex
S. G. Brady
USA (California)
38°51'N, 122°24'W
S. G. Brady #123
USNM
Camponotus sp.
216
Tanaemyrmex
S.G. Brady
Brazil (São Paulo)
21°42'S, 47°28'W
S. G. Brady #344
USNM
Camponotus sp.
263
Tanaemyrmex
P.S. Ward
Mexico (Oaxaca)
16°10'N, 96°30'W
P. S. Ward #15588
UCDC
Camponotus vicinus
235
Tanaemyrmex
S. G. Brady
USA (California)
39°43'N, 122°47'W
S. G. Brady #171
USNM
Camponotus sp. cf. simillimus
199
Tanaemyrmex
D. M. Windsor
Panama (Chiriqui)
08°31'N, 82°12'W
UCDC
Camponotus lownei
230
Thlepsepinotus
P. S. Ward
Australia (SA)
32°50'S, 138°02'E
P. S. Ward #13741
UCDC
Camponotus sericeiventris
213
Myrmepomis
S. G. Brady
Brazil (São Paulo)
21°42'S, 47°28'W
S. G. Brady #343
USNM
Camponotus atriceps
203
Myrmothrix
D. M. Windsor
Panama (Veraguas)
07°55'N, 81°20'W
UCDC
Camponotus atriceps
217
Myrmothrix
S. G. Brady
Brazil (Maranhão)
08°37'S, 46°43'W
S. G. Brady #514
USNM
Camponotus atriceps
219
Myrmothrix
S. G. Brady
Brazil (São Paulo)
21°42'S, 47°28'W
S. G. Brady #339
USNM
Camponotus rufipes
220
Myrmothrix
S. G. Brady
Brazil (São Paulo)
21°42'S, 47°28'W
S. G. Brady #337
USNM
Camponotus renggeri
215
Myrmothrix
S. G. Brady
Brazil (São Paulo)
21°42'S, 47°28'W
S. G. Brady #340
USNM
Camponotus renggeri
222
Myrmothrix
S. G. Brady
Brazil (Maranhão)
08°37'S, 46°42'W
S. G. Brady #523
USNM
Camponotus sp.
221
Myrmobrachys
S. G. Brady
Brazil (Maranhão)
08°37'S, 46°43'W
S. G. Brady #516
USNM
Camponotus crassus
214
Myrmobrachys
S. G. Brady
Brazil (Maranhão)
08°41'S, 46°46'W
S. G. Brady #519
USNM
Camponotus crassus
223
Myrmobrachys
S. G. Brady
Brazil (São Paulo)
21°42'S, 47°28'W
S. G. Brady #338
USNM
Camponotus sp.
224
Myrmobrachys
S. G. Brady
Brazil (Maranhão)
08°37'S, 46°43'W
S. G. Brady #515
USNM
Camponotus latangulus
236
Myrmocladoecus
P. S. Ward
Ecuador
01°04'S, 77°37'W
P. S. Ward #11353
UCDC
Camponotus sp.
260
Myrmamblys
P. S. Ward
Indonesia (Nusa Tenggara Timur)
08°39'S, 120°05'E
P. S. Ward #15525
UCDC
Camponotus nitidior
201
Dendromyrmex
D. M. Windsor
Panama (Panama)
08°40'N, 79°55'W
UCDC
Camponotus leonardi
225
Colobopsis
S. G. Brady
Thailand (Nakhon Ratchasima)
14°30'N, 101°55'E
S. G. Brady #531
USNM
Camponotus BCA-01
188
Colobopsis
P. S. Ward
Mexico (Baja California Sur)
23°30'N, 110°04'W
P. S. Ward #15145
UCDC
Camponotus conithorax
187
Colobopsis
P. S. Ward
Australia (Qld)
12°46'S, 143°17'E
P. S. Ward #15340
UCDC
Camponotus etiolatus
264
Colobopsis
P. S. Ward
USA (Texas)
26°25'N, 98°15'W
P. S. Ward #15610
UCDC
Camponotus gasseri
243
Colobopsis
P. S. Ward
Australia (SA)
34°53'S, 138°43'E
P. S. Ward #13731
UCDC
Camponotus papago
232
Colobopsis
P. S. Ward
Mexico (Son)
28°58'N, 112°10'W
P. S. Ward #13458
UCDC
Camponotus saundersi
265
Colobopsis
D. W. Davidson
Brunei (Temburong)
04°32'N, 115°10'E
UCDC
Camponotus sp.
259
Colobopsis
P. S. Ward
Indonesia (Nusa Tenggara Timur)
08°31'S, 119°52'E
P. S. Ward #15521
UCDC
Camponotus sp.
262
Colobopsis
P. S. Ward
Mexico (Oaxaca)
15°57'N, 96°28'W
P. S. Ward #15584
UCDC
Camponotus vitreus
231
Colobopsis
P. S. Ward
Australia (Qld)
12°43'S, 143°17'E
P. S. Ward #15338
UCDC
Notostigma carazzii
b, c
226
P. S. Ward
Australia (Qld)
17°26'S, 145°51'E
P. S. Ward #10006-2
UCDC
1In addition to several Camponotini specimens, we screened one isolate of Notostigma, recently removed from the Camponotini and placed in its own tribe. For nearly all samples, the 16S rDNA gene was amplified using Blochmannia-specific primers and the PCR product was sequenced directly. The three exceptions are as follows: aOverlapping primer pairs were used to amplify bacterial 16S rDNA from Opisthopsis haddoni 244; bCloning of PCR products was required for Opisthopsis PG01 and Notostigma carazzii 226; cUniversal eubacterial primers SL-SR were used to amplify bacterial 16S rDNA from Notostigma carazzii 226.
2Subgenera are listed when avaiable.
3Voucher specimens have been deposited in the Bohart Museum of Entomology, University of California, Davis (UCDC) and the National Museum of Natural History, Washington, DC (USNM).
Our screen involved PCR with primers specific to the Blochmannia 16S rDNA gene. Direct sequencing of the resulting PCR products yielded high quality data for nearly all isolates. (The few exceptions requiring alternative methods are noted as a footnote in Table 1 and detailed in the Methods section.) The Genbank accession numbers for the 52 new sequences obtained in this study are listed in boldface in Table 2. All 16S rDNA sequences from the Camponotini isolates proved to be a close match to known Blochmannia strains, as detailed in the database comparisons and phylogenetic analyses below. This indicates that our specific primers amplify a wide range of Blochmannia lineages across the tribe, but generally did not amplify other bacteria that may associate with ants in various ways (e.g., on the body surface or in the gut lumen).
<p>Table 2</p>Genbank accession numbers for 16S rDNA sequences analyzed.
Taxon1
length (bp)
Genbank Acc. No.2
Calomyrmex albertisi 191
827
GU226318
Calomyrmex laevissimus 254
787
GU226317
Camponotus atriceps 203
825
GU226311
Camponotus atriceps 217
794
GU226312
Camponotus atriceps 219
776
GU226313
Camponotus BCA-01 188
748
GU226271
Camponotus clarithorax 233
808
GU226295
Camponotus claviscapus 227
737
GU226292
Camponotus conithorax 187
682
GU226279
Camponotus consobrinus 239
772
GU226300
Camponotus crassus 214
766
GU226306
Camponotus crassus 223
755
GU226305
Camponotus etiolatus 264
743
GU226274
Camponotus gasseri 243
757
GU226278
Camponotus hyatti 186
819
GU226296
Camponotus leonardi 225
774
GU226276
Camponotus lownei 230
786
GU226302
Camponotus maritimus 185
785
GU226293
Camponotus nitidior 201
796
GU226297
Camponotus occultus 229
757
GU226291
Camponotus papago 232
772
GU226272
Camponotus quercicola 228
784
GU226268
Camponotus renggeri 215
786
GU226316
Camponotus renggeri 222
770
GU226315
Camponotus rufipes 220
784
GU226314
Camponotus sanctaefidei 240
743
GU226309
Camponotus saundersi 265
713
GU226277
Camponotus semitestaceus 242
785
GU226294
Camponotus sericeiventris 213
802
GU226304
Camponotus sp. 216
803
GU226307
Camponotus sp. 221
771
GU226303
Camponotus sp. 224
758
GU226298
Camponotus sp. 259
732
GU226275
Camponotus sp. 260
766
GU226290
Camponotus sp. 261
751
GU226299
Camponotus sp. 262
758
GU226273
Camponotus sp. 263
767
GU226308
Camponotus sp. cf. simillimus 199
825
GU226310
Camponotus suffusus 238
748
GU226301
Camponotus vicinus 235
805
GU226270
Camponotus vitreus 231ii
694
GU226280
Echinopla australis 253
773
GU226319
Opisthopsis PG01 258 -clone 1
864
GU226281
Opisthopsis PG01 258 -clone 2
864
GU226283
Opisthopsis haddoni 244
1,432
GU226284
Opisthopsis haddoni 256
768
GU226285
Opisthopsis respiciens 192
706
GU226282
Polyrhachis cupreata 252
795
GU226289
Polyrhachis decumbens 190
736
GU226288
Polyrhachis foreli 255
730
GU226286
Polyrhachis sp. 189
904
GU226287
Notostigma carazzii 226
1,202
GU226269
Camponotus americanus
1,413
41058429
Camponotus abdominalis
1,215
AJ245591
Camponotus balzani
1,509
AJ245596
Camponotus castaneus
1,513
AJ245594
Camponotus chromaiodes
1,375
41058426
Camponotus festinatus
1,402
AY196851
Camponotus floridanus
1,413
AY334381
Camponotus herculeanus
1,481
AJ250715
Camponotus laevigatus
1,373
AY334370
Camponotus ligniperdus
1,430
1212815
Camponotus nipponicus
569
AB018676
Camponotus novaeboracensis
1,376
41058429
Camponotus ocreatus
1,389
41058422
Camponotus pennsylvanicus
1,580
71795899
Camponotus rufipes
1,532
AJ245597
Camponotus sansabeanus
1,369
41058418
Camponotus sayi
1,409
41058421
Camponotus schaefferi
1,350
41058423
Camponotus sericeiventris
1,273
8250189
Camponotus silvicola
1,512
AJ245592
Camponotus socius
1,519
AJ245595
Camponotus ulcerosus
1,386
41058425
Camponotus vafer
1,410
AY334369
Camponotus vicinus
1,378
41058424
Polyrhachis dives
570
AB018678
Polyrhachis hippomanes
570
AB018679
Polyrhachis lamellidens
570
AB018680
Polyrhachis ypsilon
569
AB018681
Aquamonas haywardensis
1,522
AF015258
ant symbiont (Plagiolepis manczshurica host)
567
AB018682
ant symbiont (Plagiolepis pigmaea host)
567
AB018683
Baumannia of leafhoppers (Oncometopia orbono host)
1,408
57116285
Brenneria alni
1,501
AJ223468
Brenneria quercina
1,524
AJ223469
Citrobacter freundii
1,522
AF025365
Erwinia amylovora
1,464
AJ746201
Erwinia carotovora
1,458
U80198
Escherichia coli
1,542
U00096
Ewingella americana
1,392
EU678360
Formica fusca symbiont
568
AB018684
Hafnia alvei
1,479
M59155
Hafnia sp. 270
1,508
AM403659
Hafnia sp. NJ-71
1,522
AM419021
Hamiltonella defensa (T-type 2° symbiont of aphids)
1,447
AF293616
Klebsiella pneumoniae
1,489
AJ233420
Leminorella grimontii
1,482
AJ233421
lousefly 2° symbiont (Pseudolynchia canariensis host)
1,525
DQ115535
mealybug 2° symbiont (Amonostherium lichtensioides host)
1,504
AF476100
mealybug 2° symbiont (Antonia crawii host)
1,465
6978941
mealybug 2° symbiont (Australicoccus grevilleae host)
1,555
21717581
mealybug 2° symbiont (Cyphonococcus alpinus host)
1,559
21717584
mealybug 2° symbiont (Dysmicoccus brevipes host)
1,517
AF476103
mealybug 2° symbiont (Melanococcus albizziae host)
1,528
AF476106
mealybug 2° symbiont (Paracoccus nothofagicola host)
1,570
21717591
mealybug 2° symbiont (Planococcus citri host)
1,560
21717589
Pasteurella multocida
1,432
AY507110
Pectobacterium carotovorum
1,544
BX950851
Photorhabdus luminescens
1,545
BX571861
Plesiomonas shigelloides
1,499
X60418
Pseudomonas aeruginosa
1,536
AE004883
psyllid 2° symbiont (Aphalaroida inermis host)
1,513
8575696
psyllid 2° symbiont (Blastopsylla occidentalis host)
1,511
AF263558
Rahnella aquatilis
1,520
X79939
Rahnella sp. NJ-8
1,506
AM419020
Regiella insecticola (U-type 2° symbiont of aphids)
1,387
AF293623
Salmonella typhimurium
1,544
AE008857
Serratia marcescens
1,505
AJ233431
Shigella flexneri
1,541
AE015280
Sodalis glossinidius, 2° symbiont of tsetse flies - GM-SG1
1,507
AY861701
Sodalis glossinidius, 2° symbiont of tsetse flies - str. 'morsitans'
1,511
AP008232
tephritid fruit fly symbiont (Noeeta pupillata host)
1,313
EF469633
Vibrio cholerae
1,535
AE004096
weevil symbiont (Sitophilus oryzae) host
1,512
AF548137
weevil symbiont (Sitophilus oryzae) host, strain SFr
1,461
AF005235
weevil symbiont (Sitophilus zeamais host)
1,509
AF548142
Xenorhabdus nematophilus
1,497
X82251
Yersinia pestis
1,585
AE013985
Yersinia sp.
1,506
AJ011333
1Bacterial sequences from Camponotini are labeled by the ant host species.
2The 52 new sequences obtained in this study are listed in boldface.
The 16S rDNA amplified from an outgroup related to this tribe (Notostigma) did not match Blochmannia. In addition, previous work has screened other members of the subfamily Formicinae for bacterial symbionts and failed to detect Blochmannia. The bacterial symbiont in Formica and Plagiolepis is not Blochmannia, as we have verified in our phylogenetic analysis here. Moreover, we were unable to amplify Blochmannia from a specimen of Oecophylla smaradina (unpublished data).
Database comparisons
We compared new sequences to Genbank and to the Ribosomal Database Project (RDP, release 10.5)
35
. These searches are based on sequence similarity and provide a very rough idea of taxonomic affiliation. Most new bacterial 16S rDNA sequences from the Camponotini most closely matched published Blochmannia in both databases. (Please see additional file 1 for a list of top matches.) These include isolates of Calomyrmex and Opisthopsis, where Blochmannia has not been detected before, and Echinopla, where a short, Blochmannia-like sequence was noted once previously
34
. For an additional four sequences, Blochmannia was the top match in one of the two databases, and nearly the top in the other database. Four members of the Colobopsis subgenus most closely match other members of the Enterobacteriaceae. Nonetheless, subsequent phylogenetic analysis (below) groups these Colobopsis associates with Blochmannia with very high confidence, illustrating the approximate nature of the similarity-based database searches. The bacterial associate of Notostigma carazzii did not match Blochmannia in either database.
<p>Additional file 1</p>
Database matches for 52 new bacterial 16S rDNA sequences obtained in this study. The vast majority of sequences most closely matched a published Blochmannia 16S rDNA sequence in NCBI (compared using BLASTn) and/or the Ribosomal Database Project (RDP; compared using SeqMatch).
Click here for file
Phylogenetic results
Gamma-Proteobacteria analysis: Camponotini isolates group with known Blochmannia strains
To test for the monophyly of presumed Blochmannia isolates and to position this group within the gamma-Proteobacteria, we estimated the phylogeny of 16S rDNA using Bayesian and maximum likelihood (ML) approaches. Taxa included candidates for the closest relatives of Blochmannia, based on matches in databases such as Genbank, the RDP
35
, and ARB
36
. Bayesian posterior probabilities were higher than ML bootstrap values, as expected based on previous studies
37
. As a consequence, the Bayesian consensus tree (Figure 1) showed higher resolution than did the ML bootstrap consensus tree. (The ML tree of the gamma-Proteobacteria dataset is presented as additional file 2.) Both methods support the monophyly of known Blochmannia isolates and newly sampled Camponotini associates (Bayesian posterior probability of 1.00 and bootstrap support of 78%). The phylogenies also illustrate that Plagiolepis and Formica endosymbionts represent independent lineages within the gamma-Proteobacteria, as suggested in an earlier study based on a smaller taxon sample
15
. Interestingly, the Notostigma isolate is closely related to Blochmannia but clearly falls outside of that clade. This absence of Blochmannia is consistent with the removal of Notostigma from the Camponotini and assignment to its own tribe
32
33
. Whether the Notostigma isolate represents a symbiosis or casual bacterial associate is uncertain.
<p>Figure 1</p>Relationships among diverse gamma-Proteobacteria, estimated from a region of the 16S rDNA gene
Relationships among diverse gamma-Proteobacteria, estimated from a region of the 16S rDNA gene. Within Blochmannia, taxa are labeled by the ant host from which the bacterial gene was amplified. These and other ant symbionts are noted in boldface. The phylogeny was estimated using Bayesian methods. The topology shown reflects the majority-rule consensus of post-burnin trees, and posterior probabilities are given at nodes. The results support the monophyly of known Blochmannia isolates and newly sampled Camponotini associates (posterior probability of 1.00), demonstrating for first time that Calomyrmex, Echinopla, and Opisthopsis possess bacterial associates that are members of the same clade as known Blochmannia strains. Blochmannia occurs within a large, diverse, and strictly-endosymbiotic group that includes a wide range of insect endosymbionts. Plagiolepis and Formica endosymbionts do not group with Blochmannia, showing independent origins of intracellular endosymbioses within ants.
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<p>Additional file 2</p>
Maximum likelihood phylogeny of gamma-Proteobacteria, estimated from a region of the 16S rDNA gene. Within Blochmannia, taxa are labeled by the ant host from which the bacterial gene was amplified. The topology reflects the majority-rule consensus tree of 100 bootstrap replicates. Bootstrap values ≥70% are marked. (All unmarked nodes have bootstrap values of 50%-69%.)
Click here for file
These results demonstrate for the first time that Calomyrmex, Echinopla, and Opisthopsis possess bacterial associates that are part of the same clade as known Blochmannia strains, consistent with a single origin of endosymbiosis in the Camponotini. Although additional Camponotini taxa remain to be screened from more rarely collected genera, we predict that Blochmannia will be pervasive throughout the tribe. The three Camponotini genera not included in our study (Forelophilus, Overbeckia, and Phasmomyrmex) together comprise only six living species and represent a comparatively small component of the overall diversity within the tribe. Indeed, current taxonomy suggests that Forelophilus and Overbeckia may be synonymous with Camponotus
33
.
This discovery of Blochmannia in diverse Camponotini genera helps to refine the questions we ask about the evolution of this association. For example, it remains mysterious why the mutualism became established in this group, but apparently not in other ant clades. What is distinct about Camponotini? This remains an open question. Studying the full range of hosts will highlight conspicuous exceptions, where the life history or physiology of ants may impact the symbiosis. For example, while Blochmannia may be involved in claustral founding of new colonies
38
, Polyrhachis shows instances of semi-claustral founding, the only known example in a formicine ant
39
. In addition, in a tribe in which the metapleural gland is often missing
33
, any role of symbionts in pathogen defense may be particularly important (D. E. Wheeler and J. F. A. Traniello, pers. comm.). This gland is a structure unique to ants whose external secretions have been hypothesized to serve antiseptic functions, although other functions have been proposed that involve chemical defense, recognition odor, and territorial marking (U. Mueller, pers. comm.). The metapleural gland is present in workers from the vast majority of ant genera, including Calomyrmex, Opisthopsis and Echinopla, but is absent from Polyrhachis and most species of Camponotus. It is known to be present in the workers of at least 13 Camponotus species including C. gigas
40
, C. thadeus
41
, C. sericeus
42
, and ten species of Camponotus (Myrmonesites) from Madagascar (B. Fisher and U. Mueller, pers. comm.). These exceptions to the rule offer natural experiments to explore the influence of host biology on symbiont persistence and functions.
Our phylogenetic analysis of gamma-Proteobacteria position Blochmannia within a large, diverse group of insect endosymbionts (Figure 1). This group includes many secondary symbionts of sap-feeding mealybugs, psyllids, and aphids. In our analyses, a group of secondary symbionts of mealybugs are the closest relatives of Blochmannia. This group represents one of at least four distinct acquisitions of gamma-Proteobacterial symbionts by mealybugs
43
. The most recent common ancestor (MRCA) of Blochmannia is reconstructed with very high likelihood to be endosymbiotic, with a proportional likelihood of 0.9999 under both Mk1 model and AsymmMk model (expressed as the proportion of the total probability of 1.0). Similarly, the ancestral node representing the MRCA of Blochmannia and the four closely-related mealybug endosymbionts is inferred to have been endosymbiotic (proportional likelihood 0.9999 under both models).
Camponotini is one of the major ant groups that commonly tend mealybugs, aphids, and other hemipterans for their carbohydrate-rich honeydew
29
44
and may have acquired Blochmannia through this route. Ants and hemipterans have a long history of association, with fossil evidence for this relationship occurring in Baltic (~44 MYA) and Dominican (15-20 MYA) amber deposits
45
46
. Ants often have been observed to scavenge or kill the hemipterans that they tend and transport the bodies to their nests, presumably to help feed their colonies
47
48
49
50
. Repeated consumption by ant larvae, the only stage that can ingest particulate matter, may have selected for sequestration of a hemipteran symbiont. Feeding interactions have been implicated in the horizontal transmission of other endosymbiotic bacteria in insects including Wolbachia
51
and Rickettsia
52
although definitive experimental evidence for the successful establishment of an endosymbiont via this pathway remains lacking
52
.
Blochmannia-focused analysis
We performed a more focused phylogenetic analysis that included new bacterial sequences obtained here, as well as 28 published Blochmannia sequences. We analyzed the data with and without mealybug endosymbionts as outgroups. Using Bayesian approaches, the unrooted (Figure 2) and rooted (Figure 3) phylogenies resolved four subgroups within Blochmannia that match genus-level distinctions among their ant hosts: Polyrhachis, Camponotus subgenus Colobopsis (called Colobopsis here, for brevity), Opisthopsis, and a fourth group composed of Camponotus, Calomyrmex, and Echinopla. In rooted Bayesian trees, each subgroup was resolved with high confidence (posterior probabilities of 0.97-1.00). The ML analyses gave similar results but with lower confidence. Unrooted and rooted ML trees of Blochmannia are presented in additional files 3 and 4, respectively.
<p>Figure 2</p>Blochmannia phylogeny estimated from a region of the 16S rDNA gene, analyzed without outgroups
Blochmannia phylogeny estimated from a region of the 16S rDNA gene, analyzed without outgroups. The analysis includes 50 new bacterial sequences from Camponotini and 28 published Blochmannia sequences. Taxon groups are labeled by the ant host from which the bacterial gene was amplified. The phylogeny was estimated using Bayesian methods, and the topology shown reflects the majority-rule consensus of post-burnin trees. Both this unrooted and rooted (Figure 3) phylogenies resolved four major lineages within Blochmannia: Polyrhachis, Colobopsis, Opisthopsis, and a fourth group composed of Camponotus, Calomyrmex, and Echinopla. In this unrooted tree, only the posterior probabilities of major nodes are marked. Relationships within major groups resemble those in the rooted tree (Figure 3). Taxon names were removed for clarity, and we refer the reader to the rooted tree for these data.
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<p>Figure 3</p>Blochmannia phylogeny estimated from a region of the 16S rDNA gene, analyzed with outgroups
Blochmannia phylogeny estimated from a region of the 16S rDNA gene, analyzed with outgroups. The analysis includes 50 new bacterial sequences from Camponotini, 28 published Blochmannia sequences, and four mealybug endosymbionts that we found to be the closest relatives to Blochmannia. Taxa are labeled by the ant host from which the bacterial gene was amplified. The phylogeny was estimated using Bayesian methods, and the topology shown reflects the majority-rule consensus of post-burnin trees. Posterior probabilities of all nodes are marked. Taxon names of new samples are followed by a sample ID number, whereas published Blochmannia sequences are not. Like the unrooted tree (Figure 2), this rooted phylogeny resolved four major lineages within Blochmannia: Polyrhachis, Colobopsis, Opisthopsis, and a fourth group comprised of Camponotus, Calomyrmex, and Echinopla.
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<p>Additional file 3</p>
Maximum likelihood phylogeny of Blochmannia, estimated without outgroups. Taxa are labeled by the ant host from which the bacterial gene was amplified. The topology reflects the majority-rule consensus tree of 100 bootstrap replicates. In this unrooted tree, only bootstrap values of deep nodes are marked. Otherwise, relationships resemble those in the fully-labeled rooted tree (see additional file 4).
Click here for file
<p>Additional file 4</p>
Maximum likelihood phylogeny of Blochmannia, estimated with outgroups. Taxa are labeled by the ant host from which the bacterial gene was amplified. The topology reflects the majority-rule consensus tree of 100 bootstrap replicates. In this rooted tree, bootstrap values ≥70% are marked. (All unmarked nodes have bootstrap values of 50%-69%.) Outgroup taxa are four mealybug endosymbionts that we found to be the closest relatives to Blochmannia. Support for the monophyly of subgenus Colobopsis is 55%.
Click here for file
In an analysis of ant relationships, Brady et al.
32
found strong support for the grouping of Polyrhachis with Camponotus + Calomyrmex, the relationship reflected in schematic tree A (Figure 4). While the rooting of the Camponotini was uncertain, it may occur along the Opisthopsis lineage
32
. By contrast, our 16S rDNA dataset does not distinguish relationships among major subgroups within Blochmannia. For example, we considered the three possible unrooted trees for these four lineages (trees A-C; Figure 4). The Shimodaira-Hasegawa (SH) test indicated the data cannot distinguish among the three possible unrooted topologies (Table 3). To test whether our dataset can resolve the root position, we also used the SH test to evaluate the relative support for 15 trees that represent the alternative rootings of trees A-C. The data do not reject any of the 15 alternative trees, and thus cannot reject any hypotheses for relationships among major Blochmannia lineages (Table 4). Additional data from rDNA genes or other Blochmannia loci will be necessary to resolve ancient divergences within this mutualism.
<p>Table 3</p>Results of the Shimodaira-Hasegawa (SH) test indicate the data cannot reject any of the three alternative unrooted Blochmannia phylogenies.
Constraint tree1
-ln L
Diff -ln L
p-value2
A
8785.83
0.52
0.67
B
8785.31
(best)
C
8785.97
0.66
0.74
1The four major Blochmannia lineages may be related in three possible ways, reflected in three unrooted trees A-C (see Figure 4).
2Non-significant results indicate that the likelihood score does not differ significantly from that of the "best" tree (topology B).
<p>Table 4</p>Results of the Shimodaira-Hasegawa (SH) test indicate the data cannot reject any of the 15 alternative rooted Blochmannia phylogenies.
Constraint tree1
Root Position2
-ln L
Diff -ln L
p-value3
A
Camp+Cal+Echin
9895.98
3.63
0.86
A
Colob
9892.35
(best)
A
Mid
9900.48
8.14
0.80
A
Opis
9899.04
6.69
0.82
A
Poly
9899.24
6.90
0.84
B
Camp+Cal+Echin
9895.73
3.38
0.88
B
Colob
9896.81
4.46
0.85
B
Mid
9894.59
2.24
0.97
B
Opis
9895.78
3.44
0.95
B
Poly
9893.82
1.47
0.90
C
Camp+Cal+Echin
9895.18
2.84
0.91
C
Colob
9894.88
2.53
0.94
C
Mid
9896.98
4.64
0.88
C
Opis
9906.04
13.69
0.66
C
Poly
9898.01
5.66
0.81
1Each of the three unrooted trees (A-C, see Figure 4) has five possible root positions, for 15 possible rooted trees.
2The root position indicates the lineage to which outgroup taxa (mealybug endosymbionts) were attached, with "mid" indicating the internal branch.
3Non-significant results indicate that the likelihood score does not differ significantly from that of the "best" tree (topology A-Colob).
<p>Figure 4</p>Schematic trees reflecting the possible relationships among the four well-supported Blochmannia lineages detected here
Schematic trees reflecting the possible relationships among the four well-supported Blochmannia lineages detected here. For four lineages, three possible unrooted trees exist (A, B, C), each with five possible root positions, or 15 trees total. The Shimodaira-Hasegawa test indicated that we cannot distinguish among the three possible unrooted or 15 possible rooted topologies (see text and Tables 3, 4).
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Agreement of bacterial and ant relationships
Agreement of the Blochmannia and host phylogeny is expected, given that several previous studies demonstrate host-symbiont cospeciation in this mutualism
15
19
30
31
. While a formal cospeciation analysis is beyond the scope of this study, the Blochmannia phylogeny suggests host-symbiont congruence at taxonomic levels previously unexamined. At the tribe level, we detected Blochmannia only in association with Camponotini, and not, for example, in Notostigma. At the genus level, the major groups within Blochmannia match distinctions among the ant hosts. In a comprehensive phylogenetic analysis of ants, Brady et al.
32
confirmed that Camponotus is a polyphyletic assemblage. Colobopsis, although still formally considered a subgenus of Camponotus
17
, constitutes a distinct group that is separated from Camponotus by intervening genera. Here, we found an identical pattern in the 16S rDNA of associated Blochmannia. That is, Blochmannia from ants in the subgenus Colobopsis formed a group that is distinct from other Camponotus. In addition, the close relationship of bacteria from Calomyrmex and Camponotus matches the affiliation of these ant genera
32
53
.
At shallower taxonomic levels, many well-resolved species-level relationships among Blochmannia agree with known or predicted host relationships. Congruence has already been documented in previous cospeciation studies of many species included here
15
19
30
31
. In addition, our new data illustrate further examples of recently-diverged Blochmannia strains from ant hosts that are close relatives
54
. Examples include C. quercicola and C. castaneus, C. rufipes and C. floridanus, C. hyatti and C. sayi, C. balzani and C. silvicola, and the group containing C. sansabeanus, C. maritimus, C. semitestaceus and C. vicinus. Although Camponotus subgenera are often polyphyletic and not always good predictors of host relationships
31
54
, notably the Blochmannia of C. claviscapus and C. occultus, both members of the subgenus Pseudocolobopsis, are sister taxa. Furthermore, Blochmannia sampled from the same Camponotus species but from different geographic areas are always closely related, usually as a strongly supported monophyletic unit.
Caveats: Strengths and limitations of molecular data
The molecular approach presented here has clear advantages. This approach let us screen for symbionts using one or few host specimens, infer relationships among the bacteria detected, and place newly-discovered isolates within a broader phylogenetic context. However, based on DNA sequence data alone, it is difficult to make strong conclusions about the type of association between Blochmannia and the additional genera sampled here. For instance, it is impossible to say for certain that the bacteria form stable, obligate, intracellular relationships in each host genus - i.e., that the type of mutualism well-characterized in Camponotus also occurs in Opisthopsis, Calomyrmex, and Echinopla. A complete characterization of Blochmannia in these genera is beyond the scope of the current study, but ideally will include additional representatives of each genus to test for symbiont persistence and stability, and will be coupled with ultrastructural work to document the location of bacteria within host tissues or cells. Such characterizations will be a fruitful area for future research.
Despite these caveats, the demonstrated specificity of Blochmannia makes its detection in additional host genera compelling. When a symbiont group is already well described, the presence of that symbiont is frequently based on molecular data alone, even when it is detected in new hosts. In addition, our results support the hypothesis that Blochmannia is monophyletic and evolved more than 40 MYA from an ancient, diverse clade consisting of intracellular endosymbionts. This pattern lends further support to the view that newly-discovered Blochmannia lineages within the Camponotini also live within cells. Moreover, the general agreement of host and symbiont phylogenies bolsters the view that these bacterial associates form meaningful, stable associations with their hosts.
Conclusions
Our molecular screen and phylogenetic analysis of ant-associated bacteria revealed four important results.
(i) We demonstrated for the first time that Calomyrmex and Opisthopsis possess bacterial associates that are members of the same clade as known Blochmannia strains. Furthermore, we confirmed a similar finding for Echinopla. These results significantly expand the range of known hosts of this symbiont and suggest the mutualism is more ancient and diverse than previously documented. Consistent with the recent removal of Notostigma from the Camponotini
33
, we were unable to detect Blochmannia in a specimen of this genus. Although additional Camponotini genera remain to be screened (Forelophilus, Overbeckia, and Phasmomyrmex), we predict that Blochmannia will be pervasive throughout the Camponotini.
(ii) The three known bacteriocyte-associated symbionts in ants evolved independently in Formica, Plagiolepis, and the Camponotini. The three symbionts constitute distinct lineages within the gamma-Proteobacteria.
(iii) Blochmannia is positioned within a diverse, strictly endosymbiotic bacterial group and is reconstructed with very high likelihood to have originated from an endosymbiotic ancestor. This larger bacterial group includes endosymbionts of mealybugs, psyllids, lice, weevils, Plagiolepis, and tsetse flies. Our analysis suggests that a group of secondary symbionts of mealybugs constitute the closest relatives to Blochmannia, based on available sequence data, and suggest a possible origin for the ant mutualism. Unlike primary symbionts such as Blochmannia, secondary symbionts form dynamic associations and are known to transfer among distinct insect species and, occasionally, among insect superfamilies
55
. Camponotini might have acquired the bacteria by tending mealybugs or other sap-feeding hemipterans for their carbohydrate-rich honeydew.
(iv) We found that the phylogeny of Blochmannia agrees with known relationships among Camponotini hosts at taxonomic levels previously unexamined. We detected four robust groups within Blochmannia: isolates from Polyrhachis, Colobopsis, Opisthopsis, and a fourth group composed of Camponotus (excluding Colobopsis), Calomyrmex, and Echinopla. Our data further support Colobopsis as a lineage distinct from remaining Camponotus.
Exciting areas for future research include testing the prediction that Blochmannia are pervasive throughout the Camponotini, by characterizing microbial associates of unsampled genera and by documenting the tissue- and cellular location of bacteria detected. Additional phylogenetic analysis, ideally based on expanded molecular and morphological datasets, will shed light on the deep divergences among Camponotini genera and whether hosts and symbionts codiverged in the earliest stages of this ancient mutualism.
Methods
Molecular methods
For each ant sample, genomic DNA was prepared from whole ants or from only the gaster (QIAGEN DNeasy kit). In nearly all cases, single worker ants were used. Rarely, two or more ant individuals from the same colony were combined for a given DNA prep, particularly when ants were small. For samples that gave very low yields of DNA, we amplified the DNA using GenomiPhi (GE Life sciences). As a positive control for DNA quality and quantity, we PCR-amplified a 1.3-kb region of cytochrome oxidase I and II (COI/II). Nearly all samples gave a visible COI/II product. These PCR products generally were not sequenced for this study, but rather served as an indicator of high-quality DNA.
We used primers designed to match Blochmannia 16S rDNA to screen for this endosymbiont across ant specimens. These specific primers (Bloch16S-462F 5-AAACCCTGATGCAGCTATACCGTGTGTG-3', and Bloch16S-1299R 5'-CCATTGTAGCACGTTTGTAGCCCTACTCA-3') produce a PCR product of ~840 bp
31
. 16S rDNA PCR reactions were repeated in large-scale (50 uL) format and the products purified (Promega Wizard PCR purification kit). PCR products were sequenced directly in both directions on an ABI 3730×l automated sequencer using Big Dye v3.0 (Applied Biosystems). This approach gave high quality DNA sequences for nearly all samples. All sequences were assembled and edited using PHRED, PHRAP and CONSED. DNA assemblies were checked by eye and any ambiguous base calls were re-sequenced or changed to N. Most sequences obtained were ~750-800 bp, slightly shorter than the PCR product itself.
Three isolates required the use of alternative primer pairs and/or cloning, in order to obtain high quality data. These few exceptions are noted in the footnote in Table 1 and detailed here. First, for Opisthopsis PG01, the PCR product generated from Blochmannia-specific primers was cloned (Invitrogen TOPO TA kit). Six clones were selected for sequencing with M13F and M13R primers and showed considerable variation. Two sequences had a highest BLASTn hits to known Blochmannia isolates, and were included in the phylogenetic analyses presented here; the remaining four sequences showed closest BLASTn hits to bacteria from soils. While the latter four sequences might represent meaningful bacterial associates, we favor the conservative interpretation that they reflect environmental contaminants. Notably, we found significant variation between the two Blochmannia clones. Because two Opisthopsis PG01 individuals were pooled for the gDNA preparation (one worker and one pupa), it is possible that this reflects standing genetic variation between host individuals, a subject for future investigation.
Two samples (Notostigma carazzii 226 and Opisthopsis haddoni 244) did not give detectable PCR products with the Blochmannia-specific primers. For Notostigma carazzii 226, we used the eubacterial 16S primers SL and SR
31
to amplify a 1,202 bp fragment that was subsequently cloned and sequenced with M13F and M13R primers. Among the eight clones sequenced, only minor variation was observed, likely reflecting cloning artifacts. The single sequence used in our phylogenetic analyses was selected for its length and high quality. Finally, for Opisthopsis haddoni 244, we generated two overlapping PCR products using the primers 16S_10F (5'-AGTTTGATCATGGCTCAGATTG-3') + 23S_480R (5'-CACGGTACTGGTTCACTATCGGTC-3'), and 16S_777F (5'-AGCAAACAGGATTAGATACCC-3') + SR; these were sequenced directly to generate a 1,432-bp fragment.
Among the bacterial 16S rDNA sequences from Camponotini, all matched known Blochmannia, based on database comparisons and/or phylogeny reconstructions (see Results). Only three specimens, Camponotus latangulus 236, Campontous sp. 241, and Camponotus dimorphus 234, failed to work in our molecular screen. These isolates did not generate PCR for host COI/II, our positive control for DNA quality. In addition, a C. vitreus worker that we initially sampled apparently possessed two bacterial associates: Blochmannia, as well as an isolate that matched the soil bacterium Chromohalobacter. To test whether the latter was a persistent bacterial associate or contaminant, we screened a second C. vitreus worker collected from the same colony. The second worker (C. vitreus 231ii) possessed only Blochmannia and is included in the phylogenetic analyses here.
Database comparisons
New bacterial 16S rDNA sequences were compared to all sequences in two comprehensive databases. First, we identified closest matches in the Ribosomal Database Project (RDP, release 10.5; http://rdp.cme.msu.edu/) using the Sequence Match utility
35
. This allowed us to compare our new sequences to 671,510 high quality Bacterial SSU sequences. In addition, we used BLASTn for a more general comparison of our new sequences to all sequences in Genbank. These searches are based on DNA sequence similarity and provide a very rough prediction of taxonomic affiliation. The advantage of this approach is the ability to search numerous 16S rDNA sequences very rapidly. The disadvantage is that the similarity results are not always good indicators of phylogenetic relationships. Nonetheless, these broad comparisons helped us to identify the closest non-Blochmannia outgroups to include in phylogenetic analysis.
Phylogenetic analysis
Taxon selection
Taxa were selected according to the goals of two phylogenetic analyses. (i) Gamma-Proteobacteria analysis. First, we explored the broad placement of Blochmannia 16S rDNA sequences, including new sequences obtained here, within the gamma-Proteobacteria. This analysis (a) tested whether newly discovered bacterial associates of Camponotini form a monophyletic group that includes known Blochmannia, (b) identified the closest relative to Blochmannia, and (c) tested whether Plagiolepis and Formica endosymbionts group with Blochmannia or, alternatively, represent distinct symbiont acquisitions in ants. The full, 99-taxon dataset for this gamma-Proteobacteria analysis included representatives of new and published Blochmannia sequences, endosymbionts of other insects, non-endosymbiotic Enterobacteriaceae, and divergent outgroup taxa. To identify the immediate relatives of Blochmannia, we included its closest matches in databases such as Genbank, the Ribosomal Database Project
35
, and ARB
36
. We deliberately excluded the exceptionally AT-rich primary endosymbionts (e.g., Wigglesworthia, Buchnera, Carsonella) to reduce biases resulting from extreme base compositions, especially the artefactual grouping of AT-rich sequences
56
57
. In addition, initial analyses showed their phylogenetic positions were unstable across the tree.
(ii) Blochmannia-focused analysis. Second, we explored relationships among Blochmannia in a targeted analysis of 78 bacterial isolates from Camponotini, including the previously unsampled host genera, Calomyrmex, Echinopla, and Opisthopsis. We analyzed Blochmannia sequences with and without sequences of four mealybug endosymbionts that proved to be the closest outgroups in the gamma-Proteobacteria analysis above.
Sequence alignment
16S rDNA sequences were aligned using SILVA INcremental Aligner, or SINA http://www.arb-silva.de/aligner/
36
. The alignment was examined carefully and any regions considered ambiguous were excluded from analysis. This 16S rDNA alignment, with ambiguous regions marked, is provided in nexus format as additional file 5. After excluding ambiguous regions, alignment lengths were 1,510 sites (599 of which were variable) for the gamma-Proteobacteria analysis and 1,547 sites (429 variable) for the Blochmannia-focused analysis. At 700-800 bp, many Blochmannia sequences were considerably shorter than the full alignment length and thus included stretches of missing data. However, we chose to analyze a longer region to retain as much information as possible.
<p>Additional file 5</p>
MacClade file (nexus format) of the 16S rDNA sequence alignment analyzed here. Ambiguous (excluded) regions in the alignment are marked as character sets. Sequences used in phylogenetic analyses are marked as distinct taxon sets.
Click here for file
Phylogenetic reconstruction
For both the gamma-Proteobacteria and Blochmannia-focused analyses, datasets were analyzed using Modeltest 3.7 to determine the appropriate model of sequence evolution
58
. Based on the hierarchical likelihood ratio test (hLRT) results, the most appropriate model for both datasets is the General Time Reversible model with invariant sites and rate variation among sites (GTR+I+G).
We performed phylogenetic analysis with Bayesian and maximum likelihood (ML) methods. Bayesian analysis. Using the parallel version of MrBayes v3.1.2, we implemented a GTR model with unequal base frequencies, portion of invariant sites estimated from the data, rate variation among sites according to the gamma distribution, and noninformative priors. We simultaneously performed two independent runs, each with four incrementally heated Markov Chain Monte Carlo (MCMC) chains starting from a random tree. Analyses were run for 10 million generations with trees sampled every 100 generations. Stationarity of log likelihood (-lnL) was confirmed by plotting the -lnL scores versus the number of generations. Discarding the first 90,000 trees provided a very conservative 90% burn-in, as -lnL was stationary well before this point. Posterior probabilities were determined by constructing a 50% majority-rule tree of the 10,000 trees sampled after the burn-in. To assess whether Bayesian runs had adequate convergence and mixing for a given data set, we confirmed that the convergence diagnostic PSRF (pscale reduction factor) approached or reached one in all cases, indicating convergence of the two independent runs. In addition, we used Compare and other functions available in AWTY (Are We There Yet; http://ceb.scs.fsu.edu/awty) to confirm convergence
59
.
Maximum likelihood analysis
We performed ML analysis using GARLI Version 0.96 (Beta) https://www.nescent.org/wg_garli/. We used the default GTR model, in light of Modeltest results supporting a relatively complex model. Base frequencies and the portion of invariant sites were estimated from the data, and rates among sites were allowed to vary according to a discrete gamma distribution (4 categories). The runs were terminated when no topology with an lnL increase of 0.01 or greater had been found in 20,000 generations. We used these parameters to find the trees with the highest likelihood score and to perform bootstrap analyses of 100 replications.
We used likelihood tests to compare alternative hypotheses regarding: (i) possible relationships among the four deep Blochmannia lineages, represented by three unrooted trees, and (ii) the 15 various attachments of outgroups to the unrooted Blochmannia trees (three unrooted trees × five possible root attachments = 15). We first estimated the most likely tree (using GARLI as described above) under the appropriate topological constraints (e.g., the unrooted trees A-C shown in Figure 3, and the 15 possible attachments of outgroups to those unrooted trees). We then compared these ML trees using the Shimodaira-Hasegawa (SH) test
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as implemented by PAUP version 4.0b10 for Unix
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. These SH tests involved optimizing each data set across the topologies being compared, using the GTR model described above, then evaluating whether the -lnL of a given dataset differed significantly between the "best" versus alternative topologies. The SH test was performed with all taxa in the Blochmannia-focused analysis.
Ancestral state reconstruction
We used ancestral state reconstruction to infer the history of endosymbiosis in this group, using the Bayesian majority consensus tree with branch lengths and employing the maximum likelihood methods provided by Mesquite v.2.6
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. Taxa were coded as either endosymbiotic or non-endosymbiotic. We employed two different models of character evolution, the Mk1 model which uses a single parameter for the rate of change and the AsymmMk model which uses two parameters and thus allows for a bias in gains versus losses.