Research Article |
Corresponding author: Luc Leblanc ( leblancl@ctahr.hawaii.edu ) Academic editor: Anthony Clarke
© 2015 Luc Leblanc, Michael San Jose, Norman Barr, Daniel Rubinoff.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Leblanc L, San Jose M, Barr N, Rubinoff D (2015) A phylogenetic assessment of the polyphyletic nature and intraspecific color polymorphism in the Bactrocera dorsalis complex (Diptera, Tephritidae). In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 339-367. https://doi.org/10.3897/zookeys.540.9786
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The Bactrocera dorsalis complex (Tephritidae) comprises 85 species of fruit flies, including five highly destructive polyphagous fruit pests. Despite significant work on a few key pest species within the complex, little has been published on the majority of non-economic species in the complex, other than basic descriptions and illustrations of single specimens regarded as typical representatives. To elucidate the species relationships within the B. dorsalis complex, we used 159 sequences from one mitochondrial (COI) and two nuclear (elongation factor-1α and period) genes to construct a phylogeny containing 20 described species from within the complex, four additional species that may be new to science, and 26 other species from Bactrocera and its sister genus Dacus. The resulting concatenated phylogeny revealed that most of the species placed in the complex appear to be unrelated, emerging across numerous clades. This suggests that they were placed in the B. dorsalis complex based on the similarity of convergent characters, which does not appear to be diagnostic. Variations in scutum and abdomen color patterns within each of the non-economic species are presented and demonstrate that distantly-related, cryptic species overlap greatly in traditional morphological color patterns used to separate them in keys. Some of these species may not be distinguishable with confidence by means other than DNA data.
Bactrocera , dorsalis , intraspecific variation, phylogenetics
Most of the Dacine fruit flies (Tephritidae: Dacini) are in the genera Bactrocera (651 described species) and Dacus (270 species), with many species (73 Bactrocera and 11 Dacus) bred from commercial/edible fruit and fleshy vegetables (
Among the pest species, Bactrocera dorsalis (Hendel) (= the Oriental fruit fly) is the most destructive and polyphagous species (
While literature abounds on the taxonomy, genetic diversity, biology and management of the economic species (
Species descriptions and illustrations in published monographs (
Our goal was to examine the B. dorsalis species complex more broadly than the few frequently targeted pest species. This is accomplished by reporting and analyzing novel molecular and morphological data on 22 non‐pest species in the complex, in the context of the main pest species and selected outgroups. These data are used to: (i) determine through phylogenetic analysis if the complex is monophyletic or polyphyletic; (ii) provide diagnostic molecular data for over 25 species for which such data is currently lacking; and (iii) determine the utility of thoracic and abdominal color/pattern variation as species level diagnostic characters.
The molecular phylogenies presented here are based on DNA sequences of 53 specimens collected in Asia, Australia, Oceania, the United States and Africa. These specimens include 47 species of Bactrocera belonging to five subgenera (including 24 species from the OFF complex), three species of Dacus, and Ceratitis capitata (Wiedemann) as the outgroup, (Table
Species, lure response, collecting locality and voucher code and GenBank accession number for sequences for the species used in this study.
Species | Lure | Locality | Voucher | GenBank Accessions | ||
---|---|---|---|---|---|---|
Bactrocera (Bactrocera) | COI | EF-1α | Period | |||
Species in B. dorsalis complex | ||||||
B. bivittata Li & Wang | Methyl eugenol | Laos: Luang Namtha | ms1305 | KT594878 | KT594827 | KT594785 |
B. cacuminata (Hering) | Methyl eugenol | Australia: NSW, Valery | ms1997 | KT594887 | KT594822 | KT594787 |
B. carambolae Drew & Hancock | Methyl eugenol | Malaysia: Penang, Teluk Bahang | ms1439 | KF184076 | KF184222 | KF184149 |
B. dongnaiae Drew & Romig | Cue-lure | Cambodia: Koh Kong | ms1109 | KT594897 | KT594830 | KT594789 |
B. dorsalis (Hendel) (sensu stricto) | Methyl eugenol | Hawaii: Oahu, Makiki | ms0853 | KF184084 | KF184230 | KF184157 |
B. dorsalis (Hendel) (B. invadens) | Methyl eugenol | Sénégal: Ziguinchor | ms0898 | KF184092 | KF184238 | KF184165 |
B. dorsalis (Hendel) (B. papayae) | Methyl eugenol | Malaysia: Penang, Teluk Bahang | ms1428 | KF184067 | KF184213 | KF184140 |
B. fuscitibia Drew & Hancock | Cue-lure | Cambodia: Koh Kong | ms1175 | KT594899 | KT594831 | KT594790 |
B. kanchanaburi Drew & Hancock | Methyl eugenol | Cambodia: Koh Kong | ms1300 | KT594905 | KT594833 | KT594792 |
B. kohkongiae Leblanc | Cue-lure | Cambodia: Koh Kong | ms1139 | KT591145 | KT591136 | KT591129 |
B. laithieuiae Drew & Romig | Cue-lure | Cambodia: Koh Kong | ms3762 | KT594916 | KT594823 | KT594793 |
B. latilineola Drew & Hancock | Methyl eugenol | Cambodia: Koh Kong | ms1114 | KT594917 | KT594834 | KT594794 |
B. lombokensis Drew & Hancock | Cue-lure | Laos: Luang Namtha | ms1548 | KT594922 | KT594836 | |
B. melastomatos Drew & Hancock | Cue-lure | Malaysia: Kedah, Mount Jerai | ms1411 | KT594924 | KT594837 | KT594796 |
B. occipitalis (Bezzi) | Methyl eugenol | Philippines: Los Baños | ms1985 | KT594931 | KT594824 | KT594798 |
B. osbeckiae Drew & Hancock | Cue-lure | Cambodia: Koh Kong | ms1163 | KT594938 | KT594841 | KT594801 |
B. paraarecae Drew & Romig | Methyl eugenol | Laos: Luang Namtha | ms1110 | KF184040 | KF184186 | KF184113 |
B. propinqua (Hardy & Adachi) | Cue-lure | Laos: Luang Namtha | ms1167 | KF184053 | KF184199 | KF184126 |
B. quasiinfulata Drew & Romig | Cue-lure | Laos: Luang Namtha | ms1546 | KT594970 | KT594843 | KT594803 |
B. raiensis Drew & Hancock | Methyl eugenol | Laos: Luang Namtha | ms1331 | KT594972 | KT594844 | KT594804 |
B. thailandica Drew & Hancock | Cue-lure | Thailand: Chiang Mai | ms1047 | KT594985 | KT594852 | KT594812 |
B. usitata Drew & Hancock | Cue-lure | Cambodia: Koh Kong | ms1173 | KT594999 | KT594854 | KT594814 |
B. species 54 | Cue-lure | Thailand: Chiang Mai | ms1182 | KT594976 | KT594847 | KT594807 |
B. species 55 | Cue-lure | Laos: Luang Namtha | ms1181 | KT594979 | KT594848 | KT594808 |
B. species 59 | Cue-lure | Laos: Luang Namtha | ms1164 | KT594981 | KT594849 | KT594809 |
B. species 60 | Methyl eugenol | China: Jinghong | ms3633 | KT594982 | KT594850 | KT594810 |
Other species | ||||||
B. aethriobasis (Hardy) | Methyl eugenol | Cambodia: Koh Kong | ms1557 | KT594862 | KT594825 | KT594783 |
B. albistrigata deMeijere | Cue-lure | Malaysia: Penang, Teluk Bahang | ms1395 | KT594863 | KT594826 | KT594784 |
B. bhutaniae Drew & Romig | Cue-lure | Laos: Luang Namtha | ms1166 | KF184052 | KF184198 | KF184125 |
B. bryoniae (Tryon) | Cue-lure | Australia: Bundaberg | ms1515 | KT594886 | KT594828 | KT594786 |
B. correcta (Bezzi) | Methyl eugenol | Cambodia: Koh Kong | ms1093 | KT594896 | KT594829 | KT594788 |
B. kirki (Froggatt) | Cue-lure | French Polynesia: Tahiti | ms0894 | KF184090 | KF184236 | KF184163 |
B. latifrons (Hendel) | Latilure/cade oil | Hawaii: Oahu | ms0882 | KF184085 | KF184231 | KF184158 |
B. limbifera (Bezzi) | Cue-lure | Cambodia: Koh Kong | ms1108 | KT594921 | KT594835 | KT594795 |
B. nigrotibialis (Perkins) | Cue-lure | Cambodia: Koh Kong | ms1033 | KT594930 | KT594838 | KT594797 |
B. ochrosiae (Malloch) | Cue-lure | Mariana Islands: Saipan | ms1485 | KT594932 | KT594839 | KT594799 |
B. paradiospyri Chen, Zhou & Li | Methyl eugenol | Thailand: Chiang Mai | ms1470 | KT594956 | KT594842 | KT594802 |
B. rubigina (Wang & Zhao) | Cue-lure | China: Jinghong | ms3544 | KT594974 | KT594845 | KT594805 |
B. tryoni (Froggatt) | Cue-lure | French Polynesia: Tahiti | ms0892 | KF184088 | KF184234 | KF184161 |
B. tuberculata (Bezzi) | Methyl eugenol | Thailand: Chiang Mai | ms1083 | KT594998 | KT594853 | KT594813 |
B. umbrosa (Fabricius) | Methyl eugenol | Cambodia: Koh Kong | ms1002 | KF184032 | KF184178 | KF184105 |
B. wuzhishana Li & Wang | Methyl eugenol | Thailand: Chiang Mai | ms1070 | KT595000 | KT594855 | KT594815 |
B. zonata (Saunders) | Methyl eugenol | Thailand: Chiang Mai | ms1559 | KT595002 | KT594857 | KT594817 |
Bactrocera (Daculus) | ||||||
B. oleae (Gmelin) | No lure | USA: California | ms1387 | KT594933 | KT594840 | KT594800 |
Bactrocera (Notodacus) | ||||||
B. xanthodes (Broun) | Methyl Eugenol | French Polynesia: Rurutu | ms0896 | KT595001 | KT594856 | KT594816 |
Bactrocera (Sinodacus) | ||||||
B. hochii (Zia) | Cue-lure | Laos: Luang Namtha | ms1369 | KT594904 | KT594832 | KT594791 |
Bactrocera (Zeugodacus) | ||||||
B. cucurbitae (Coquillett) | Cue-lure | Cambodia: Koh Kong | ms0987 | KF184104 | KF184250 | KF184177 |
B. scutellaris (Bezzi) | Cue-lure | Thailand: Chiang Mai | ms1030 | KT594975 | KT594846 | KT594806 |
B. tau (Walker) | Cue-lure | Laos: Luang Namtha | ms1006 | KT594984 | KT594851 | KT594811 |
Genus Dacus | ||||||
D. (Didacus) ciliatus Loew | None | South Africa: Stellenbosch | ms1576 | KT595004 | KT594859 | KT594819 |
D. (Psilodacus) pullescens Munro | None | South Africa: Calitzdorp | ms1578 | KT595005 | KT594860 | KT594820 |
D. (Mellesis) sinensis Wang | Cue-lure | Laos: Luang Namtha | ms1372 | KT595006 | KT594861 | KT594821 |
Genus Ceratitis | ||||||
C. capitata (Wiedemann) | Trimedlure | Hawaii: Oahu | ms0865 | KT595003 | KT594858 | KT594818 |
Our specimens in the OFF complex were initially tentatively identified to species using available resources (
For each specimen, one to three legs were used for total genomic DNA extraction. The remainder of the specimen was deposited as a voucher in the University of Hawaii Insect Museum (UHIM) for preservation and morphological studies (Table
Sequence alignments were performed with the software package Geneious 7.1.7 (Biomatters ltd.). Heterozygosity in the nuclear genes was present in most samples. Ambiguity codes (i.e., notation according to International Union of Pure and Applied Chemistry (IUPAC)) were used to denote heterozygous base pairs, and these codes were used in the subsequent analysis. Sequence alignment for each gene was conducted in Geneious using the Muscle option with default settings (Edgar 2004). We used jModeltest and the Akaike information criterion (
Topological differences between the individual gene trees were not supported with high bootstrap values and posterior probabilities (<50% BS <0.9 PP) and overall individual gene trees were poorly resolved, with COI providing more signal for the more recent divergences (Suppl. material
Maximum likelihood tree, concatenated, based three gene (COI, period, EF-1α) dataset. Support values above branches are Maximum Likelihood Bootstrap values / Bayesian Posterior Probabilities. Scale bar indicates the number of substitutions per site. Species in the Oriental fruit fly complex are outlined in red.
Summary statistics of genetic variability, based on COI gene sequences, for non-economic species in the B. dorsalis complex.
Species | Sample size | Haplotypes (Nh) | Haplotype diversity (h) | Nucleotide diversity (pi) | Segregating sites (s) |
---|---|---|---|---|---|
B. bhutaniae | 33 | 25 | 0.966 | 0.02557 | 86 |
B. bivittata | 10 | 9 | 0.978 | 0.00320 | 10 |
B. cacuminata | 11 | 4 | 0.491 | 0.00161 | 5 |
B. fuscitibia | 6 | 5 | 0.933 | 0.00676 | 14 |
B. kanchanaburi | 15 | 13 | 0.981 | 0.00768 | 31 |
B. kohkongiae | 22 | 17 | 0.952 | 0.00472 | 23 |
B. latilineola | 4 | 3 | 0.833 | 0.00320 | 5 |
B. melastomatos | 8 | 4 | 0.643 | 0.00127 | 4 |
B. osbeckiae | 35 | 13 | 0.704 | 0.00717 | 18 |
B. paraarecae | 5 | 5 | 1.000 | 0.01536 | 29 |
B. propinqua | 24 | 23 | 0.996 | 0.01047 | 40 |
B. thailandica | 56 | 13 | 0.386 | 0.00145 | 24 |
B. usitata | 5 | 5 | 1.000 | 0.01076 | 17 |
Color patterns of scutum and/or abdomen (Figures
Variation in color pattern of scutum and abdomen in Bactrocera latilineola Drew and Hancock (A–E) (11 specimens examined and 4 sequenced) and B. melastomatos Drew and Hancock (F–O) (46 specimens examined and 8 sequenced). Voucher codes are: A ms1114 B ms2025 C ms2025 D ms2024 E ms1299 F ms1415 G ms1416 H ms1410 I ms1412 J ms1411 K ms1416 L ms1417 M ms1413 N ms1410 O ms1411.
Variation in color pattern of scutum and abdomen in Bactrocera osbeckiae Drew and Romig (100 specimens examined and 39 sequenced). Voucher codes are: A ms1161 B ms3559 C ms3558 D ms3553 E ms3555 F ms3561 G ms1163 H ms3785 I ms3764 J ms3768 K ms1153 L ms3758 M ms3554 N ms1180 O ms1138 P ms3555 Q ms3784 R ms3560 S ms1154 T ms3768.
Scutum and abdomen of: A Bactrocera dongnaiae Drew and Romig (ms1158; 7 specimens examined and 3 sequenced) B B. laithieuiae Drew and Romig (ms3762; 1 specimen examined and sequenced) C B. lombokensis Drew and Hancock (ms1548; 1 specimen examined and sequenced) D B. quasiinfulata Drew and Romig (ms3455; 4 specimens examined and sequenced) E B. raiensis Drew and Hancock (ms1331; 2 specimens examined and 1 sequenced) F B. rubigina (Wang and Zhao) (ms3543; 259 specimens examined and 27 sequenced) G B. usitata Drew and Hancock (ms2039; 27 specimens examined and 6 sequenced).
Scutum, abdomen and wing costal region of: A–C Bactrocera species 54 (ms1798 (wing, scutum), ms3777 (abdomen); 7 specimens examined and sequenced) D–F B. species 55 (ms3575; 7 specimens examined and sequenced) G–I B. species 59 (ms1164; 1 specimen examined and sequenced) J–L B. species 60 (ms3730; 3 specimens examined and sequenced).
Scutum color and variation followed three basic patterns among species for which series of specimens were examined. In B. bhutaniae (Figure
Abdomen color for almost all species and variants followed the basic “T-shaped” pattern typical of the B. dorsalis complex, i.e. a black band across the base of tergum III, a narrow to broad medial longitudinal black band covering the entire length of terga III to V, and narrow to broadly expanded lateral black markings on terga III to V. Medial band was broad and lateral markings generally broad along margins of tergum III and narrower on terga IV and V in B. bhutaniae (Figure
The concatenated tree demonstrates that the OFF complex is a highly polyphyletic assemblage of unrelated species. Consistent with other published studies, the methyl eugenol responsive B. dorsalis, B. carambolae, B. occipitalis, B. cacuminata, and B. raiensis, form a well-defined monophyletic unit (
The widespread conformity of unrelated species to the dorsalis-like appearance is unclear. Color patterns in Dacine fruit flies are assumed to mimic wasps (
Except for a handful of well-studied species (e.g. B. dorsalis, B. carambolae, B. cacuminata), the definitions and concepts for the majority of the OFF complex species were based on morphology (mainly color patterns), lure response, and generally limited host fruit records. Only now are we starting to better characterize these species with molecular tools. Most of the non-economic species described by
Attraction of B. osbeckiae to cue-lure is a new lure record. Morphological variation in our cue-lure trapped specimens (Figure
Four species, consistent in appearance with the definition of the OFF complex, could not clearly be identified and are referred to here as numbered species. Species 54 (from Chiang Mai, Thailand) and 55 (Luang Nam Tha, Laos and Jinghong, China) look very similar (Figure
Bactrocera dorsalis, B. invadens and B. papayae were recently declared conspecific, and are genetically indistinguishable (
The high degree of intraspecific variation in color pattern severely limits the reliability of dichotomous and interactive keys. The range of variation differs considerably among species, with extreme cases like the scutum of B. dorsalis (
The OFF complex was defined by
Collecting trips in Asia were funded through USDA-ARS Specific Cooperative Agreements 58-5320-9-382 and 58-5320-4-018, managed by the University of Hawaii’s College of Tropical Agriculture and Human Resources (UH-CTAHR). A study trip in Australia was covered by Farm Bill funding (project 3.0251), through a Cooperative Agreement between USDA and UH-CTAHR. Additional support was provided by USDA-NIFA Hatch projects HAW00942-H and HAW00956-H, administered UH-CTAHR. We also thank Anthony R. Clarke for reviewing an earlier version of the manuscript and Richard A.I. Drew and David L. Hancock for their insight, mentoring and long hours discussing the relationships among species in the OFF complex and the higher classification of dacine fruit flies. Desley Tree and Justin Bartlett provided access to the impressive QDAF fruit fly collection in Brisbane. The use or mention of a trademark or proprietary product does not constitute an endorsement, guarantee, or warranty of the product and does not imply its approval to the exclusion of other suitable products by the U.S. Department of Agriculture, an equal opportunity employer.
Figure S1
Data type: TIF File Format
Explanation note: Maximum likelihood tree, based the COI gene dataset. Support values above branches are Maximum Likelihood Bootstrap values / Bayesian Posterior Probabilities. Scale bar indicates the number of substitutions per site. Species in the Oriental fruit fly complex are outlined in red.
Figure S2
Data type: TIF File Format
Explanation note: Maximum likelihood tree, based the EF-1α gene dataset. Support values above branches are Maximum Likelihood Bootstrap values / Bayesian Posterior Probabilities. Scale bar indicates the number of substitutions per site. Species in the Oriental fruit fly complex are outlined in red.
Figure S3
Data type: TIF File Format
Explanation note: Maximum likelihood tree, based the period gene dataset. Support values above branches are Maximum Likelihood Bootstrap values / Bayesian Posterior Probabilities. Scale bar indicates the number of substitutions per site. Species in the Oriental fruit fly complex are outlined in red.