Genome
Barcoding of parasitoid wasps (Braconidae and Chalcidoidea) associated with wild and cultivated olives in the Western Cape of South Africa
Journal: Genome
Manuscript ID gen-2018-0068.R3
Manuscript Type: Article
Date Submitted by the 28-Sep-2018 Author:
Complete List of Authors: Powell, Chanté; Stellenbosch University Faculty of AgriSciences, Genetics Caleca, Virgilio; University of Palermo , Department of Agricultural and Forestry SciencesDraft Sinno, Martina; University of Naples Federico II, Department of Agricultural Sciences van Staden, Michaela; Stellenbosch University Faculty of AgriSciences, Genetics van Noort, Simon; Iziko South African Museum, Department of Natural History Rhode, Clint; Stellenbosch University Faculty of Agrisciences, Genetics Department Allsopp, Elleunorah; Agricultural Research Council, Infruitec- Nietvoorbij van Asch, Barbara; Stellenbosch University Faculty of AgriSciences, Genetics;
Keyword: Braconidae, Chalcidoidea, DNA barcoding, olives, species identification
Is the invited manuscript for consideration in a Special 7th International Barcode of Life Issue? :
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1 TITLE
2 Barcoding of parasitoid wasps (Braconidae and Chalcidoidea) associated with wild and cultivated olives
3 in the Western Cape of South Africa
4 RUNNING HEAD
5 DNA barcoding of braconid and chalcid olive wasps
6 AUTHORS
7 Chante Powell1, Virgilio Caleca2, Martina Sinno3, Michaela van Staden1, Simon van Noort4, Clint
8 Rhode1, Elleunorah Allsopp5, Barbara van Asch1 9 Draft 10 AFFILIATIONS
11 1Department of Genetics, Faculty of Agrisciences, University of Stellenbosch, Stellenbosch, South
12 Africa
13 2Department of Agricultural and Forestry Sciences, University of Palermo, Italy.
14 3Department of Agricultural Sciences, University of Naples "Federico II", Naples, Italy.
15 4Division of Entomology, Department of Natural History, Iziko South African Museum, Cape Town, South
16 Africa.
17 5Agricultural Research Council, Infruitec-Nietvoorbij, Stellenbosch, South Africa.
18
19 CORRESPONDING AUTHOR
20 Barbara van Asch - [email protected]
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21 ABSTRACT
22 Wild and cultivated olives harbor and share a diversity of insects, some of which are considered
23 agricultural pests, such as the olive fruit fly. The assemblage of olive-associated parasitoids and seed
24 wasps is rich and specialized in sub-Saharan Africa, with native species possibly coevolving with their
25 hosts. Although historical entomological surveys reported on the diversity of olive wasp species in the
26 Western Cape Province of South Africa, no comprehensive study has been performed in the region in the
27 molecular era. In this study, a dual approach combining morphological and DNA-based methods was
28 used for the identification of adult specimens reared from olive fruits. Four species of Braconidae and six
29 species of Chalcidoidea were identified, and DNA barcoding methodologies were used to investigate
30 conspecificity among individuals, based on randomly selected representative specimens. Morphological 31 identifications were congruent with DNA data,Draft as NJ and ML trees correctly placed the sequences for 32 each species either at the genus or species level, depending on the available taxa coverage, and genetic
33 distances strongly supported conspecificity. No clear evidence of cryptic diversity was found. Overall
34 seed infestation and parasitism rates were higher in wild olives compared to cultivated olives, and
35 highest for Eupelmus spermophilus and Utetes africanus. These results can be used for early DNA-based
36 detection of wasp larvae in olives, and further investigating the biology and ecology of these species.
37
38 KEYWORDS
39 Braconidae, Chalcidoidea, DNA barcoding, olives, species identification
40
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41 INTRODUCTION
42 The wild olive tree (Olea europaea L. subsp. cuspidata) is closely related to the cultivated olive tree (Olea
43 europaea L. subsp. europaea var. europaea) (Green 2002). The subspecies is widely distributed on the
44 African continent from the Southern tip of Africa to South Egypt (Rubio De Casas et al. 2006) where it
45 occurs mainly in Afro-montane forests, and often near water sources; it is also present in small areas of
46 the Asian continent (Green 2002). It is known to host a wide variety of leaf, sap and fruit-feeding insects,
47 and their associated parasitoids (Silvestri 1915; Copeland et al. 2004; Mkize et al. 2008). Wild olive trees
48 are often found in close proximity to non-native cultivated olive trees in the Western Cape Province of
49 South Africa, the main commercial producer of olives, due to its typically Mediterranean climate with
50 warm, dry summers and mild, moist winters. The region comprising the Western and the Eastern Cape
51 provinces has been identified as home to a high diversity of wasp species described as natural enemies
52 of olive fruit flies and phytophagous olive seedDraft wasps (Silvestri 1913; Silvestri 1915; Neuenschwander
53 1982).
54 Two olive fruit flies, Bactrocera oleae (Rossi) and Bactrocera biguttula (Bezzi), have also been identified
55 and are presently associated with olives in Africa. Bactrocera oleae, a major pest of cultivated and wild
56 olives, is believed to have originated and disseminated in Africa, and to have accompanied the
57 geographic expansion and domestication of olive trees in the Mediterranean Basin (Zohary 1994; Nardi
58 et al. 2005; Daane & Johnson 2010; Nardi et al. 2010). Bactrocera biguttula is a closely related species
59 endemic to the continent, probably also matching the natural range of the geographic distribution of
60 wild olive trees in sub-Saharan Africa (Munro 1925; Munro 1984; Mkize et al. 2008). Infestation of
61 cultivated olives by B. biguttula has never been reported. The infestation rates of cultivated olives by B.
62 oleae in South Africa are lower than under similar conditions in the Mediterranean Basin, and the
63 limiting factors have been attributed to the action of indigenous parasitoid wasps (Neuenschwander
64 1982; Costa 1998; Hoelmer et al. 2011) and, more recently, to the specific climatic patterns of the region
65 (Giacalone 2011; Caleca et al. 2015; Caleca et al. 2017).
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66 The potential utility of parasitoid wasps for the biological control of B. oleae in the Mediterranean basin,
67 where it causes significant damage (Daane & Johnson 2010), and regions with similar climates such as
68 the Middle East and California, where invasion has occurred more recently (Rice et al. 2003; Ramezani et
69 al. 2015), has sparked interest in assembling detailed catalogues of Southern and
70 Eastern African wasp species since the early 20th century (Silvestri 1915). Surveys conducted in sub-
71 Saharan Africa have reported the presence of a distinct and broad complex of wasps, including species
72 endemic to the region (Hoelmer et al. 2011). Southern European surveys have shown wasp assemblages
73 less diverse and comprised of a smaller number of specialized species. Five parasitoid species are
74 commonly found in Southern Europe, of which four are chalcids [(Eupelmus urozonus Dalman, Pnigalio
75 mediterraneus Ferrière et Delucchi, Eurytoma martellii Domenichini, and Cyrtoptyx latipes (Rondani), and
76 only one is a braconid [(Psyttalia concolor (Szépligeti)]. Psyttalia concolor is native to North Africa and
77 some southern Italian regions or sub-regionsDraft (Sicily, southern Sardinia and southern Calabria) (Silvestri
78 1939; Caleca et al. 2017), and was purposefully imported into most of Southern Europe for the control of
79 B. oleae (Hoelmer et al. 2011; Borowiec et al. 2012).
80 Earlier studies provided the first descriptions of wasps associated with wild and cultivated olives in South
81 Africa (the Western Cape, and the Transvaal, a former province that now comprises Gauteng, Limpopo,
82 Mpumalanga and part of the North-West province), and Eritrea (Silvestri 1913; Silvestri 1915;
83 Neuenschwander 1982). A recent survey in Kenya reported wasps associated with B. oleae in wild olives,
84 but only three braconids were identified (Copeland et al. 2004). A more recent study on wild olives in the
85 Eastern Cape Province of South Africa reported the occurrence of both parasitoid and seed wasps, and
86 additionally provided estimates of relative infestation rates in wild olives. Four braconids and seven
87 chalcids were found, although some groups were only identified to genus level (Mkize et al. 2008).
88 Similar results were obtained in the Western Cape (Giacalone 2011; Caleca et al. 2017). None of these
89 works included molecular analyses, and reference DNA barcoding sequences for the majority of the
90 species reported remained unavailable.
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91 The morphological identification of small hymenopterans requires the expertise of well-trained
92 taxonomists, and is difficult to perform on immature life stages. Additional challenges result from sexual
93 dimorphisms, natural intraspecific variation, and the potential presence of cryptic species (Rowley et al.
94 2007; Al Khatib et al. 2014). DNA barcoding provides a methodological framework for identifying
95 organisms by comparing their degree of nucleotide sequence similarity (expressed as genetic distance)
96 to sets of reference taxa (Hebert et al. 2003). Sequence similarities can then be interpreted using
97 numerical methods such as hierarchical clustering of genetic distances (e.g. the Neighbour-joining
98 algorithm) and statistical evaluation of thresholds of genetic distances. The underlying assumption is that
99 interspecific genetic variation exceeds intraspecific variation.
100 DNA barcoding in animals relies on nucleotide sequence similarity at a standard region (~650 bp) of the
101 5’-end of the mitochondrial cytochrome oxidase I gene (COI). In recent years, researchers worldwide
102 have been depositing high-quality referenceDraft sequences in public databases (e.g. Barcode of Life Data
103 System, BOLD, www.boldsystems.org) (Ratnasingham & Hebert 2007) that will increasingly allow for the
104 assignment of unknown specimens to morphologically determined taxa, the discrimination of cryptic
105 species, and the elucidation of synonymies (Hebert & Gregory 2005). Although the potential applications
106 of DNA barcoding are indisputable, methodological limitations and the nature of mitochondrial evolution
107 may restrict its applicability in particular taxa. The use of a single marker also confines the amount of
108 genetic variation, thus limiting the ability to understand the patterns of species boundaries (Dupuis et al.
109 2012). Another potential limitation of DNA barcoding based on COI sequences is the possibility that
110 ancestral polymorphic haplotypes have not sorted according to independent speciation events
111 (incomplete lineage sorting) (Ball et al. 2005). Therefore, it is advisable to combine morphological and
112 DNA-based methods for species identification, as sole reliance on either approach has limitations.
113 The aim of this study was to assess the congruence between morphological identification of braconid
114 and chalcid wasps and patterns of genetic clustering and genetic distances within and amongst groups,
115 using novel and publicly available COI sequences. The objectives included a sampling strategy that aimed
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116 at capturing the total assemblage of wasp species associated with wild and cultivated olives, and the
117 assessment of the novel sequences as representative of the species within the context of each particular
118 genus. Additionally, this work also represented an opportunity to report estimates of braconid and
119 chalcid infestation rates across the distribution range of wild and cultivated olive trees in the Western
120 Cape of South Africa, a region known to harbor a rich diversity of these parasitoid and phytophagous
121 wasps.
122
123 MATERIAL & METHODS
124 Sample collection
125 Wild and cultivated olive fruits were collected haphazardly from 16 different areas across the Western
126 Cape Province of South Africa and one area in the Eastern Cape, between March and October 2016 (Fig.
127 1). As the objective of this study was to rear,Draft identify and barcode as many parasitoids and seed wasp
128 species as possible, and fly and wasp infestation is known to be higher in wild olives, the sampling effort
129 focused particularly on wild olives. Sampling of cultivated olives included unsprayed fruit collected on
130 commercial farms, as well as in urban areas. Wild olives were collected according to accessibility in
131 diverse contexts, including the vicinity of cultivated olives, wilderness areas, and ornamental trees in
132 urban settings. Olive fruits were stored in ventilated boxes until the emergence of adults. Adult wasps
133 were euthanized by freezing, and stored individually in absolute ethanol at -20°C until DNA extraction.
134 Morphological identification of all specimens was performed on ethanol-preserved adults.
135 Morphological identification and photographic imaging
136 Braconidae were identified to the genus level using the key available in Parasitoids of Fruit infesting
137 Tephritidae (PAROFFIT) database (http://paroffit.org) (Wharton & Yoder). The genera were identified to
138 the species level following currently available descriptions (Silvestri 1913), and by comparison to
139 photographic images available on PAROFFIT. Chalcidoidea groups/species were identified as follows:
140 Eurytomidae according to Gates & Delvare (2008) and Lotfalizadeh et al. (2007); Eupelmus Dahlman
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141 according to Al Khatib et al. (2014) and Gibson & Fusu (2016), while the only way to identify specimens
142 at species level for these two families and Eulophidae was to refer to species descriptions provided by
143 Silvestri (1915). Identification of Ormyrus Westwood specimens was performed following Bouček et al.
144 (1981) and Nieves-Aldrey et al. (2007).
145 Voucher male and female representatives of each species were randomly selected for photographic
146 imaging. Specimens were washed thrice in absolute ethanol with one-hour intervals followed by an
147 additional overnight wash step. Prior to imaging, specimens were processed in a Leica EM CPD300
148 Critical Point Dryer (Leica Microsystems, Wetzlar, Germany) to maintain the integrity of morphological
149 structures. Specimens were mounted on felt tips and photographed using a Microscope EntoVision
150 Mobile Imaging System, consisting of a Leica Z16 APO zoom lens attached to a digital camera and
151 computer workstation running on the Leica Application Suite v.4.7.1 (Leica Microsystems). The images
152 were deposited onto BOLD Systems and WaspWebDraft (www.waspweb.org), an online bioinformatics
153 resource of wasps, bees, and ants documented from the Afrotropical biogeographical region. Female and
154 male specimens were deposited in the entomology collection at the Iziko South African Museum in Cape
155 Town for future reference (Table S1). DNA sequences were not generated from the deposited specimens
156 but from other specimens equally representative of each species, according to morphological
157 identifications.
158 DNA extraction, PCR amplification and sequencing
159 Individual specimens were randomly selected from the total sample of morphologically identified wasps
160 for total DNA extraction and barcoding, and were destroyed in the process. A standard phenol-
161 chloroform protocol (Sambrook et al. 1989) was used for total DNA extraction. The standard COI
162 barcoding region (~710 bp) was amplified using the universal invertebrate barcoding primers (LCO1490
163 and HCO2198) (Folmer et al. 1994) for six species (Bracon celer, Neochrysocharis formosus, Psyttalia
164 humilis, Psyttalia lounsburyi, Sycophila aethiopica, and Utetes africanus). Species-specific primers were
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165 designed for Eupelmus spermophilus (Eupel-COI-F and Eupel-COI-R), and genus-specific primers were
166 designed for Eurytoma (Euryt-COI-F2 and Euryt-COI-R2) (Table S2).
167 PCR amplifications were performed in 5 μL reactions containing 1x Kapa HiFi HotStart Ready Mix Kit
168 (KAPA Biosystems), 10 μM of each primer, and 1 μL template DNA. Thermocycling conditions were as
169 follows: initial denaturation at 95°C for 3 min; 5 cycles at 98°C for 20 s, 41°C for 15 s, and 72°C for 1min,
170 followed by 35 cycles of 98°C for 20 s, 56°C for 15 s, 72°C for 1 min; and a final extension at 72°C for 10
171 min. Amplification of the expected fragments was confirmed on a 1.5% agarose gel electrophoresis. PCR
172 products that presented non-specific bands were separated on a 0.8% agarose gel. The correct fragment
173 was then excised from the gel and purified using Zymoclean™ Gel DNA Recovery Kit (Zymo Research).
174 Sequencing was performed using the BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems)
175 at the Central Analytical Facilities of Stellenbosch University, South Africa. Sequences were manually
176 edited, and homology with known taxa wasDraft verified by BLASTn search (www.ncbi.nlm.nih.gov). All
177 sequences were translated into amino acids for the detection of premature stop codons and/or
178 frameshift mutations indicative of pseudogenes with Geneious R11 (www.geneious.com; Kearse et al.
179 2012), using the invertebrate mitochondrial genetic code.
180 Genetic clustering and estimates of sequence divergence
181 All publicly available COI sequences for the Braconidae and Chalcidoidea genera represented in this
182 study were downloaded from Genbank for estimating intra- and interspecific genetic distances, and
183 illustrating sequence clustering based on Neighbour-joining (NJ) and Maximum Likelihood (ML) methods
184 (Table S3). Sequences shorter than 500 bp, containing nucleotide ambiguities, and non-overlapping with
185 the COI region under study were excluded from downstream analyses. Only sequences identified to the
186 species level were included in the analyses, except in the case of the genus Sycophila for which only
187 sequences identified as Sycophila sp. were publicly available. To avoid excessively dense trees in the
188 genetic clustering analyses, duplicate haplotypes in the public dataset were identified and deleted using
189 Geneious R11, and a maximum of six sequences were randomly selected when a large number of
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190 representatives was available for a single species. For estimates of genetic distances, this last step was
191 not performed (i.e. duplicate sequences were not removed).
192 Nucleotide sequences were aligned with the MAFFT algorithm implemented in Geneious R11. NJ
193 clustering analyses were performed for each genus in MEGA7 (Kumar et al. 2016) using the Kimura-2-
194 parameter (K2P) model (Kimura 1980), with pairwise deletion of the only gap (a 6 bp difference between
195 braconids and chalcids representing two consecutive amino acids). ML trees were reconstructed based
196 on the same alignments with RAxML-HPC Black Box v8.2.10 (Stamatakis, 2014) using the GTRCAT
197 evolutionary model of substitution rate heterogeneity and rapid bootstrapping included in the method
198 (Stamatakis, 2006), and ran on the CIPRES Science Gateway Portal (www.phylo.org; Miller et al. 2010).
199 Clade support in NJ trees was assessed by 1,000 bootstrap replications. Psyttalia humilis and B. celer
200 were used as outgroups for Chalcidoidea, and E. spermophilus and E. varicolor as outgroups for
201 Braconidae. Estimates of intra- and interspecificDraft sequence divergence, and relative standard errors were
202 estimated in MEGA7 using the K2P model.
203 Infestation rates
204 Apparent parasitism rates (APR) for Braconidae species and Neochrysocharis formosus were estimated as
205 follows: APR = total number of adult specimens of the particular species / (total number of tephritid flies
206 + total number of adult braconid and N. formosus specimens). For Chalcidoidea species, apparent seed
207 infestation rates (AIR) were estimated as: AIR = total number of adult specimens of the particular species
208 / total number of olives. For the sake of simplicity, apparent parasitism and apparent seed infestation
209 rates will be generically designated as infestation rates (IFs) in this report.
210
211 RESULTS
212 A total of 83,381 olive fruits (wild = 76,960 and cultivated = 6,421) were haphazardly collected in 16
213 areas in the Western Cape and one area in the Eastern Cape Provinces of South Africa between March
214 and October 2016 (Table S4). No adult wasp specimens were reared from wild or cultivated olive fruits 9 https://mc06.manuscriptcentral.com/genome-pubs Genome Page 10 of 48
215 collected in two areas (Tulbagh and Worcester), or from cultivated olives collected in five areas
216 (Malmesbury, McGregor, Porterville, Riebeek Kasteel and Somerset West). A total of 843 adult wasp
217 specimens was reared from wild (n = 836, 99.2%) and cultivated olives (n = 7, 0.8%). Specimens were
218 distributed among six species of Chalcidoidea and four species of Braconidae: Eupelmus spermophilus, n
219 = 321 (38.1%); Eurytoma oleae, n = 58 (6.9%); Eurytoma varicolor, n = 136 (16.1%); Sycophila aethiopica,
220 n = 50 (5.9%); Neochrysocharis formosus, n = 23 (2.7%); Ormyrus sp., n = 47 (5.6%), Psyttalia humilis, n =
221 28 (3.3%); Psyttalia lounsburyi, n = 22 (2.6%); Utetes africanus, n = 130 (15.4%); and Bracon celer, n = 28
222 (3.3%). Photographic images of one male and one female specimen representative of each species are
223 presented in Fig. 2-5. Overall, Chalcidoidea (n = 635, 75.3%) were more abundant than Braconidae (n =
224 208, 24.7%). The most abundantly reared chalcid was E. spermophilus, and the most abundant braconid
225 was U. africanus. Only three species were recovered from a total of 2,583 cultivated olives in three areas
226 (Franschhoek, Paarl and Stellenbosch): E. spermophilusDraft (n = 4), B. celer (n = 2), and P. lounsburyi (n = 1)
227 (Fig. 6).
228 PCR amplification using the universal invertebrate barcoding primers LCO1490 and HCO2198 only
229 generated the expected product in DNA samples from P. humilis, P. lounsburyi, B. celer, and S.
230 aethiopica. Eupelmus spermophilus and Eurytoma species did not consistently amplify with these
231 primers; therefore, new primers were designed for the amplification of a shorter amplicon (650 bp)
232 within the standard COI barcoding region (Table S2). The new Euryt-COI-F2 and Euryt-COI-R2 primers
233 generated non-specific products in E. varicolor; therefore, purification of the specific band from a 0.8%
234 agarose gel was performed prior to sequencing reactions. Utetes africanus also presented non-specific
235 amplifications with the universal primers, and purification of the specific band from a 0.8% agarose gel
236 was necessary.
237 One Wolbachia sequence, identified by BLASTn search during the sequence quality control procedure,
238 was unintentionally obtained from an E. spermophilus DNA sample using the universal primers. These
239 primers did not consistently generate PCR products in E. spermophilus, and were subsequently replaced
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240 by newly-designed species-specific primers (Eupel-COI-F and Eupel-COI-R, Table S2). The species-specific
241 primers were then used for generating the DNA data presented in this study, and did not amplify
242 Wolbachia sequences. Three putative pseudogene fragments, amplified from E. varicolor using the Euryt-
243 COI-F2/Euryt-COI-R2 primer pair, were also detected during the sequence quality control procedure.
244 These sequences were similar to the functional COI region, but amino acid translation showed several
245 stop codons; therefore, they were excluded from downstream analyses. Novel reference barcoding
246 sequences were generated for six of the nine species identified in this study: Bracon celer (n = 1), Utetes
247 africanus (n = 10), Eupelmus spermophilus (n = 10), Eurytoma oleae (n = 9), Eurytoma varicolor (n = 6),
248 and Sycophila aethiopica (n = 1). Additional sequences were generated for Psyttalia lounsburyi (n = 4)
249 and Psyttalia humilis (n = 3), and Neochrysocharis formosus (n = 2) (Table S5). All sequences with the
250 corresponding trace files, specimen images, GPS coordinates and biological data were deposited on
251 BOLD (projects UTET, SYCPH, PSYT, NCHRY,Draft EURYT, EUPEL and BRCN), and made publicly available. All
252 sequences were also deposited in Genbank (Table S3).
253 For an overview of the current taxonomic coverage of Braconidae and Chalcidoidea, two separate family
254 trees were constructed, with posterior condensation of species clusters into single branches (Fig. 7 and
255 8). Genus-specific trees were also constructed to provide a detailed illustration of the relationships
256 between the individual sequences generated in this study (Fig. S1-S7). Species clusters were strongly
257 supported by the NJ distance-based method, and were in agreement with the ML analysis; therefore,
258 only NJ-based trees are shown, with reference to the relevant topological differences in the text.
259 BRACONIDAE
260 Bracon celer Szépligeti (Fig. 2 A-B) represented 13.5% of the total braconids, similarly to P. humilis and P.
261 lounsburyi. Bracon celer was reared almost exclusively from wild olives, with a single specimen found in
262 cultivated olives from Paarl (Table S4). The genetic clustering analyses for the genus Bracon included 22
263 sequences distributed among nine species, with four species represented by a single sequence. NJ and
264 ML trees recovered identical topology, and showed B. celer (n = 1, this study) nested as an internal
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265 branch. The genetic clustering was consistent with species designations except for the non-monophyly
266 with strong nodal support for B. asphondyliae (Fig. S1).
267 Psyttalia humilis (Silvestri) (Fig. 2 C-D) was reared exclusively from wild olives in five areas, and
268 represented 13.5% of all braconids, while Psyttalia lounsburyi (Silvestri) (Fig. 3 A-B) was reared from
269 both cultivated (a single specimen in Paarl) and wild olives in five areas, and represented 10.6% of all
270 braconids (Table S4). The NJ and ML analyses for the genus Psyttalia included 54 sequences distributed
271 among 11 species, with only three species represented by a single sequence. The topology of the trees
272 showed monophyletic clustering of sequences in congruence with species designations (Fig. S2). The P.
273 humilis (n = 3) and P. lounsburyi (n = 4) specimens identified and sequenced in this survey grouped with
274 the publicly available sequences in their respective monophyletic clusters. The same pairs of sister
275 species were recovered in NJ and ML (e.g. P. lounsburyi/P. phaeostigma; P. humilis/P. concolor),
276 although the topology of the deeper branchesDraft differed, albeit with low statistical support. Interspecific
277 sequence divergence ranged between 8.3% for the species pair P. carinata/P. ponephoraga and 16.3%
278 for P. carinata/P. fletcheri. Intraspecific sequence divergence was estimated for six species, and
279 maximum distances were lower than 1.7% in all cases (Table S6). Intraspecific genetic distances were
280 also estimated separating the new P. lounsburyi and P. humilis sequences from the conspecific
281 sequences available on Genbank. No differences (i.e. high genetic distances) were found; therefore, the
282 public dataset did not seem to include sequences incorrectly assigned to species.
283 Utetes africanus (Szépligeti) (Fig. 3 C-D) was the most abundantly reared braconid (62.5%), and was
284 exclusively found in wild olives in nine areas (Table S4). The NJ and ML trees for the genus Utetes
285 included 52 sequences distributed among eight species, with four species represented by a single
286 sequence. U. canaliculatus (n = 34) represented 65.4% of the total sequence dataset for the genus (Fig.
287 S3). The NJ and ML trees showed the same topology, except for the position of U. magnus. A
288 polyphyletic pattern was recovered for U. canaliculatus, with a highly diverged monophyletic group
289 (cluster 3), a polyphyletic group including U. frequens (cluster 2), and a monophyletic (in NJ) or
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290 polyphyletic (in ML, where it included U. magnus) cluster 1 (Fig. S3). The maximum intraspecific genetic
291 divergence considering U. canaliculatus as a single group was 11.0%, whereas for each of the separate
292 clusters it was lower than 0.7%. The divergence was highest between cluster 3 and the other two
293 clusters, and the lowest between clusters 1 and 2 (Table S7), as suggested by the topology of the tree.
294 Utetes africanus (n = 10, this study) formed a monophyletic cluster, and the sequences had high
295 similarity (maximum intraspecific distance = 0.4%).
296 CHALCIDOIDEA
297 Eupelmus spermophilus Silvestri (Fig. 4 A-B) represented 50.6% of the total chalcids, and was recovered
298 from the three areas where wasps were reared from cultivated olives, and in nine areas from wild olives
299 (Table S4). The NJ and ML trees of the genus Eupelmus included 99 sequences distributed among 37
300 species, with 18 species represented by a single sequence (Fig. S4). The general topology of the trees
301 recovered monophyletic clustering for all EupelmusDraft species, including E. spermophilus (n = 10, this
302 study), albeit with different topology and low statistical support of deeper nodes in ML and NJ.
303 Intraspecific sequence divergence was estimated for nine species (Table S8). Maximum intraspecific
304 distances ranged between 2.3% for E. spermophilus and 8.7% for E. annulatus. Interspecific sequence
305 divergence ranged between 16.9% for the species pair E. spermophilus/E. azureus, and lowest for E.
306 minozonus/E. urozonus (7.8%).
307 Eurytoma oleae Silvestri (Fig. 4 C-D) represented 9.1% of the total chalcids, and was reared exclusively
308 from wild olives in three areas (Table S4). The highest IF was found in Riversdale (1.89%), whereas the
309 average was 0.10% in the other areas. Eurytoma varicolor Silvestri (Fig. 4 E-F) was reared exclusively
310 from wild olives in five areas, and represented 21.4% of the total chalcids (Table S4). The NJ and ML trees
311 for the genus Eurytoma comprised 59 sequences distributed among 16 species, with only four species
312 represented by a single sequence. Although deeper nodes had different topologies with low statistical
313 support in NJ and ML, all species formed monophyletic clusters, including E. oleae and E. varicolor (n = 9
314 and n = 6, respectively, this study) (Fig. S5). All maximum intraspecific distances were lower than 2.7%,
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315 and interspecific distances were higher than 7.7% (E. morio/E. striolata), with the highest between E.
316 oleae and E. varicolor (18.1%) (Table S9).
317 Sycophila aethiopica (Silvestri) (Fig. 5 C-D) was reared exclusively from wild olives in four areas, and
318 represented 7.9% of the total chalcids (Table S4). The NJ and ML trees of the genus Sycophila included 71
319 sequences, with only one sequence identified to the species level (S. aethiopica, this study). Identical
320 sequence clusters were recovered in NJ and ML, albeit with different topology and low statistical support
321 of deeper nodes. Sycophila aethiopica nested in the interior branches of the trees (Fig. S6).
322 Neochrysocharis formosus (Westwood) (Fig. 5 A-B) was reared exclusively from wild olives in Paarl (n =
323 23), and represented the lowest proportion (3.6%) of the total chalcids (Table S4). A previous phylogeny
324 of Eulophidae based on morphological and molecular markers (COI and 28S rRNA D2-D5) showed that N.
325 formosus and N. clinias were a paraphyletic group with respect to Asecodes sp., although the study
326 included a single sequence for each NeochrysocharisDraft species from Italy (Burks et al. 2011). Due to the
327 poor sequence coverage of the genus Neochrysocharis, public Asecodes sequences with high quality (A.
328 lucens, n = 6) were included in the NJ and ML analyses, along with the available sequences for
329 Neochrysocharis identified to the species level (N. formosus, n = 3; and N. clinias, n = 1). The NJ and ML
330 trees recovered N. formosus (n = 2, this study) and A. lucens as sister species with high statistical
331 support. However, N. formosus HM365028 (Genbank) did not cluster with the new N. formosus
332 sequences (Fig. S7). Genetic distance estimates showed that the maximum divergence between the
333 three N. formosus sequences was 12.9% (Table S10). A closer inspection revealed that N. formosus
334 HM365028 was highly polymorphic relative to the two new N. formosus sequences, which diverged
335 between them by only 1.1%.
336 Ormyrus sp. (Fig. 5 E-F) was reared exclusively from wild olives in five areas, and represented 7.4% of the
337 total chalcids (Table S4). Identification to the genus level (Ormyrus Westwood) was performed using
338 solely morphological characters, as molecular analyses were not successful. Although PCR amplification
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339 products were generated and sequenced, BLASTn search resulted in no matches with known COI
340 sequences, or any other sequence.
341 Overall, apparent parasitism rate was the highest for U. africanus (11.80%) (Fig. S8). Psyttalia, B. celer
342 and N. formosus had approximately five-fold lower IFs (2.54% for P. humilis, 2.00% for P. lounsburyi,
343 2.54% for B. celer, and 2.09% for N. formosus). Apparent seed infestation rate was the highest for
344 Eupelmus spermophilus (0.38%). Eurytoma oleae, S. aethiopica and Ormyrus sp. had similar IFs (average
345 0.06%), and E. varicolor had an intermediate IF of 0.16%. A richer wasp assemblage was reared from wild
346 olives compared to cultivated olives, from which only two braconids (B. celer and P. lounsburyi) and one
347 chalcid (E. spermophilus) were reared at low IFs in three areas (Franschhoek, Paarl and Stellenbosch)
348 (Fig. S9 – S10).
349
350 DISCUSSION Draft
351 In this study, 10 wasp species (four braconids and six chalcids) were reared from wild and cultivated
352 olives, and identified based on morphological characters following the currently available keys. All
353 groups reported in a previous survey of wild olives performed in the Eastern Cape (Mkize et al. 2008)
354 were observed, except for N. formosus, which was only recovered in the present survey. Resolution to
355 the species level was improved for two of the genera reported in the Eastern Cape: Eurytoma, with the
356 identification of E. oleae and E. varicolor, and Sycophila, with the identification of S. aethiopica.
357 Eupelmus afer was reportedly reared in the Eastern Cape (Mkize et al. 2008), but was not identified
358 among the specimens reared in the present study.
359 The sampling strategy was haphazard and opportunistic, and not designed to consistently survey and
360 compare the assemblage of species in wild and cultivated olives in the Western Cape, but to potentiate
361 the rearing of the widest possible range of wasps for morphological species identification and DNA
362 barcoding. Some areas were visited only once, while other areas were sampled multiple times (e.g. Paarl
363 and Stellenbosch). Additionally, the number of cultivated olives collected was much lower than the
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364 number of wild olives, for which more areas were also sampled. This sampling bias was deliberate
365 because wild olives are known to harbor more olive flies, braconids and chalcids than cultivated olives.
366 The low presence of braconids in cultivated olives is most probably due to three main reasons. First,
367 olive fruit fly infestation is relatively low in the Western Cape, thus precluding high levels of parasitoid
368 wasp populations. Second, braconids have difficulty reaching the third instar fly larvae, the larval stage
369 most attacked by parasitoids, as third instar larvae feed close to the olive kernel, and the thick pulp layer
370 of cultivated olives limits the action of parasitoids. This is especially relevant in the case of Utetes
371 africanus, a species that has a very short ovipositor. As for chalcids, seed wasps attack olives when the
372 fruit is small and the kernel is still soft, but infestation is also limited because of the thicker pulp layer of
373 cultivated olives compared to wild olives. The atypical climatic conditions of extremely low rainfall in the
374 Western and the Eastern Cape Provinces since 2015 may have also contributed to the absence of wasps
375 in olives collected in five areas, and to non-representativeDraft infestation rates. Therefore, the estimates for
376 apparent parasitism and seed infestation rates here presented should be interpreted with caution.
377 However, it is relevant to note that Utetes africanus was the most abundantly reared braconid, and
378 Eupelmus spermophilus was the most abundant chalcid, with the latter the most abundant wasp overall
379 (38%). It is also relevant to note that, despite the haphazard olive sampling across the Western Cape, a
380 higher diversity of species and higher IFs were found in wild olives than in cultivated olives, as expected.
381 At least one specimen per species was sequenced for the standard barcoding COI region for all species,
382 except for Ormyrus sp. These nucleotide sequences represent the first DNA barcoding references for all
383 species except N. formosus and the two Psyttalia species, for which at least one sequence was publicly
384 available. The consistency between sequence similarity and morphological identification was then
385 investigated using K2P distances, and NJ and ML trees. Phylogenetic reconstruction and estimates of
386 genetic distances offer useful insights into evolutionary relationships among taxa, thus assisting species
387 identification, provided that the specific taxonomic group is well represented in the reference dataset
388 (Hebert et al. 2003; Ross et al. 2003; Hebert et al. 2004; Ross et al. 2008; Collins et al. 2012). This was not
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389 the case for all species identified in this study. For example, publicly available sequences for the genus
390 Sycophila, although abundant (n = 70), were not identified to the species level. The genus Bracon
391 followed a pattern of incomplete identification: 75% of the 447 public COI sequences were identified as
392 Bracon sp., and 68% of the sequences identified to the species level were duplicates (i.e. sequences with
393 identical residues), resulting in a final dataset of 22 overlapping COI sequences. Neochrysocharis was
394 similarly covered, as 34% of the public sequences were only identified to the genus level. Additionally,
395 after the removal of duplicates, 92% of the remaining 24 Neochrysocharis public sequences identified to
396 the species level had a short overlap with the standard COI barcoding region. Therefore, the final dataset
397 for the genus Neochrysocharis included only the four sequences used in the NJ and ML analyses. These
398 difficulties highlight the importance of good taxonomic coverage for the generation of reliable species
399 reference sequences. In the context of the purpose of this study, which aimed at associating
400 morphologically identified specimens with DraftDNA barcodes, phylogenetic reconstruction using the ML
401 methodology did not show improved resolution or reliability over the distance-based NJ method, as NJ
402 and ML recovered the same monophyletic species clusters with high statistical support. Deeper
403 branches, on the other hand, were as poorly supported in NJ as in ML, as expected when using relatively
404 short sequences (~500 bp) of closely related species (Min & Hickey 2007).
405 Overall, we found complete concordance between morphological identification of specimens, sequence
406 clusters on NJ and ML trees, and genetic distances for six species (Eupelmus spermophilus, Eurytoma
407 oleae, Eurytoma varicolor, Psyttalia humilis, Psyttalia lounsburyi and Utetes africanus) of the ten species
408 reared from olives. No clear evidence for cryptic diversity was found, as these species formed
409 monophyletic clusters with high statistical support, and maximum intraspecific genetic distances were
410 within the range of the commonly used barcoding thresholds of 2-3%, and lower than 1.3% in all cases,
411 except for Eurytoma oleae (2.7%). Interestingly, the maximum intraspecific genetic distance in Eupelmus
412 spermophilus was 2.3%, the lowest in the genus Eupelmus, for which high intraspecific divergence was
413 found, the most striking case being E. annulatus (8.7%).
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414 BRACONIDAE
415 Bracon celer is an idiobiont ectoparasitoid of third (last) instar olive fruit fly larva, and the only Bracon
416 species known to be an olive fruit fly parasitoid (Silvestri 1913). In sub-Saharan Africa, B. celer has been
417 reported in Kenya, Ethiopia, Namibia, and South Africa (Silvestri 1913; Silvestri 1915; Neuenschwander
418 1982; Mkize et al. 2008; Daane et al. 2011). The genus was previously found to be monophyletic with
419 high statistical support, using 658 bp COI sequences (Matsuo et al. 2016). Our NJ and ML analyses
420 recovered B. asphondilae and B. tamabae as non-monophyletic with low statistical support, probably
421 due to the shorter COI region utilized (547 bp). Only one B. celer specimen was sequenced in this study,
422 therefore precluding estimates of intraspecific variation. However, B. celer nested as an interior tree
423 branch, suggesting that it can be used as a reference for the species.
424 Psyttalia lounsburyi and Psyttalia humilis are endoparasitoids of tephritids endemic to sub-Saharan
425 Africa. The two species have been found inDraft South Africa, Namibia and Kenya (Copeland et al. 2004; Mkize
426 et al. 2008; Rugman-Jones et al. 2009; Daane et al. 2011), and both have been tested as exotic biocontrol
427 agents of B. oleae in Europe and California, albeit with limited success (Daane et al. 2008; Borowiec et al.
428 2012). Previous studies of the genus Psyttalia based on COI sequences showed monophyly of Psyttalia
429 species, including P. lounsburyi and P. humilis (Cheyppe-Buchmann et al. 2011; Borowiec et al. 2012;
430 Schuler et al. 2016), and phylogenetic reconstruction based on COI and 28sD2 sequences provided
431 further support (Rugman-Jones et al. 2009). Our NJ and ML analyses and the estimates of intra- and
432 interspecific genetic distances support the morphological identification of the specimens analyzed in this
433 study, and the utility of standard DNA barcoding for the molecular identification of species belonging to
434 the genus Psyttalia, at least for those with good intraspecific coverage.
435 Utetes africanus is a parasitoid reported in South Africa, Namibia and Kenya (Silvestri 1913; Copeland et
436 al. 2004; Mkize et al. 2008; Daane et al. 2011). It has been reported as being more abundant in wild
437 olives than in cultivated olives (Neuenschwander 1982; Mkize et al. 2008; Giacalone 2011; Caleca et al.
438 2017), most likely because its short ovipositor is unable to reach fly larvae buried deep inside the pulp of
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439 the large fruit of cultivated olives. The genus Utetes was shown to be polyphyletic (Hamerlinck et al.
440 2016), and three main clusters were recovered for U. canaliculatus with an exact correspondence
441 between microsatellite genetic distances and a COI maximum parsimony tree (Hood et al. 2015). Our NJ
442 and ML trees also recovered non-monophyly for the genus, the same three U. canaliculatus clusters, and
443 inconsistency between species designations and sequence clustering (e.g. U. tabellariae was positioned
444 within U. canaliculatus in cluster 2). Comparison of genetic distances suggested that U. canaliculatus
445 cluster 3 represents an evolutionary unit highly diverged from U. canaliculatus clusters 1 and 2. In
446 agreement with the morphological identification, U. africanus was a monophyletic cluster with low
447 intraspecific divergence (0.4%), thus supporting the use of these sequences as references for the species.
448 CHALCIDOIDEA
449 Eupelmus spermophilus was found “emerging from the seeds of wild olive fruits” (Silvestri 1915). This
450 species was previously reported in Eritrea, Draftand in the Western and Eastern Cape Provinces of South
451 Africa (Silvestri 1915; Mkize et al. 2008). In agreement with previous phylogenetic analyses focusing on
452 the Eupelmus urozonus species complex (Al Khatib et al. 2014; Al Khatib et al. 2016), our NJ and ML trees
453 showed concordance between monophyletic clustering and morphological identification for the genus
454 Eupelmus, including E. spermophilus. Interspecific genetic distances were generally high, and supported
455 the species designations. Interspecific divergence was exceptionally low for E. urozonus/E. minozonus
456 (7.8%), suggesting a more recent divergence for this pair, represented as sister clades in the NJ tree.
457 Maximum intraspecific genetic distances within this genus were exceptionally high for some species,
458 suggesting the presence of cryptic diversity. For example, E. annulatus had a maximum intraspecific
459 genetic distance of 8.7%), and the sequences were distributed between two well-supported clades
460 composed by E. annulatus 1, 2 and 3, and E. annulatus 5, 6 and 7 (Fig. S4). The mean genetic distance
461 between the two clades was 7.2%, and the maximum within-clade distance was lower than 3.1%, thus
462 suggesting that not all sequences designated as E. annulatus are conspecific. Although this was not the
463 case for E. spermophilus (2.3%, this study), a pattern of high maximum intraspecific distances (4.0 - 8.7%)
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464 was found for the all Eupelmus species reported in a previous assessment of this genus, except for E.
465 minozonus and E. gemellus (2.7%) (Al Khatib et al. 2014).
466 Eurytoma oleae and Eurytoma varicolor were reported to develop on the seeds of olives, and the
467 species may be phytophagous seed wasps or parasitoids of seed wasps (Silvestri 1915; Neuenschwander
468 1982). Both species were previously found in Eritrea and South Africa (Western Cape) (Silvestri 1915).
469 Eurytoma oleae was also identified in a previous study in the Eastern Cape, as well as a Eurytoma sp. that
470 most likely represented E. varicolor (Mkize et al. 2008). The geographic range of Eurytoma species
471 associated with olive trees probably extends to Kenya, where unidentified Eurytomidae were reportedly
472 reared from wild olives (Copeland et al. 2004). Our NJ and ML analyses recovered monophyletic clusters
473 in accordance with species designations, including E. oleae and E. varicolor. As maximum intraspecific
474 genetic distances in the genus Eurytoma ranged between 0.4 and 1.5%, future investigation of potential
475 cryptic diversity in E. oleae using additionalDraft genetic markers may be warranted. The range of interspecific
476 genetic distances (>10.2%) support the utilization of the standard barcoding COI region for species
477 identification within this genus.
478 Sycophila aethiopica is possibly a parasitoid of seed wasps (Silvestri 1915). The species was previously
479 reported in Eritrea and South Africa (Western Cape) (Silvestri 1915; Neuenschwander 1982), and most
480 probably reported in the Eastern Cape as Sycophila sp. (Mkize et al. 2008). Sycophila aethiopica was
481 represented by a single sequence generated in this study, and none of the publicly available sequences
482 were identified to the species level, therefore hampering estimation of intra- and interspecific
483 divergences, and specific NJ clustering. However, the single Sycophila aethiopica sequence nested within
484 the interior branches of the NJ and ML trees, thus supporting its utility as reference for the species. The
485 genus Sycophila was shown to be monophyletic using nuclear markers (28S and 18S rRNA), and non-
486 monophyletic using mitochondrial markers (16S and COI) (Chen et al. 2004). The low statistical support
487 for the deeper-level divergences in the NJ and ML trees also suggest that future phylogenetic
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488 reconstructions may have to include a combination of nuclear and mitochondrial sequences for the
489 recovery of reliable branching patterns within this genus.
490 Neochrysocharis formosus (formerly N. formosa) is a non-specialized endoparasitoid with worldwide
491 distribution except for Australia (Chien & Ku 2001). This species was also previously found in the Western
492 Cape in several areas (including Paarl) (Neuenschwander 1982), but it was not reported in the Eastern
493 Cape (Mkize et al. 2008). The classification of genera and species in the tribe Entedonini is controversial,
494 particularly in the case of small-bodied species, such as Neochrysocharis. Neochrysocharis (N. formosus
495 HM365028 and N. clinias HM365038) was previously shown to be, with respect to Asecodes,
496 paraphyletic in molecular analyses, paraphyletic in combined (molecular and morphological) parsimony
497 analysis, and monophyletic in combined Bayesian analysis (Burks et al. 2011). The inclusion of the N.
498 formosus Nf21 and N. formosus Nf18 sequences recovered the paraphyly of the genus Neochrysocharis
499 with regards to Asecodes. Additionally, bothDraft the trees and the estimates of genetic divergence indicated
500 that the Neochrysocharis COI sequence dataset is composed of two different species, with one species
501 represented by N. formosus HM365028, and the other represented by N. formosus Nf21 and N. formosus
502 Nf18 identified in this study. Deeper molecular coverage of species will be necessary to resolve
503 taxonomic classifications within this group.
504 Ormyrus and similar species are considered to be parasitoids attacking seed wasps both in Eritrea and in
505 the Western Cape (Silvestri 1915), and no ormyrids are known to parasitize B. oleae. Ormyrus sp. was
506 reportedly reared from wild and cultivated olives in the Western and the Eastern Cape (Neuenschwander
507 1982; Mkize et al. 2008; Giacalone 2011). Several attempts were made to obtain PCR products from
508 Ormyrus sp. without success, suggesting that specific primers may have to be designed for future
509 analysis.
510 Wolbachia and pseudogenes
511 Unintended amplification and sequencing of two types of fragments non-representative of the barcoding
512 COI region occurred in some DNA extracts. One Wolbachia sequence, the most common bacterial
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513 endosymbionts in arthropods, was sequenced from E. spermophilus. This is known to occur when
514 attempting PCR amplification of insect COI with universal primers from total genomic DNA (Smith et al.
515 2012). Procedures for the quality control of the data (e.g. BLASTn searches) are mandatory to prevent
516 false results in downstream assessments of genetic variation and phylogenetic reconstructions. Putative
517 pseudogene fragments, possibly nuclear pseudogenes of mitochondrial origin (NUMTs), were also
518 obtained with the genus-specific primers (Euryt-COI-F2/Euryt-COI-R2) in three E. varicolor samples. This
519 could be explained by the non-specificity of the primers for E. varicolor, as these were designed based on
520 E. oleae sequences. PCR amplification of NUMTs is known to occur frequently in DNA barcoding of
521 insects, and quality control for their identification (e.g. amino acid translation) can greatly contribute to
522 detect and purge these sequences from COI datasets (Leite 2012).
523 The present assessment of wasp species associated with wild and cultivated olives represents a
524 comprehensive coverage of the rich endemicDraft parasitoid and seed wasp diversity in South African olives.
525 Sub-Saharan African Braconidae are particularly interesting, due to their potential use as exotic
526 biocontrol agents for controlling olive fly populations in regions where this pest lacks specialized natural
527 enemies (e.g. California). The assemblage of Chalcidoidea associated with olives remains poorly studied,
528 and details of the specific biology remain unknown for several species. For example, Eupelmus
529 spermophilus, Eurytoma oleae, Eurytoma varicolor, Sycophila aethiopica and Ormyrus sp. have been
530 variously reported as possible seed wasps, parasitoids of olive fruit flies, or hyperparasitoids. DNA
531 analyses can be applied to the identification of immature insect life stages such as eggs, larvae, nymphs
532 or pupae, otherwise often impossible to identify morphologically. This is particularly pertinent for the
533 early detection of invasions, disseminations and infestation outbreaks of agricultural pests. In the
534 particular case of olives, methodologies inspired by DNA barcoding for species identification could also
535 be used in the analyses of insect material collected from the interior of the fruits to elucidate the elusive
536 lifestyle of the wasps and other insect groups associated with wild and cultivated olive trees.
537
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538 ACKNOWLEDGEMENTS
539 The authors are grateful to numerous olive growers and landowners for allowing the collection of
540 samples on their properties. Emma Cook is acknowledged for assistance in laboratory work. This study
541 was funded by the National Research Foundation (FBIP - Small Grants and Biodiversity Surveys,
542 FBIS150603118644, Grant 98112), the National Research and Technology Fund of South Africa
543 (Reference RTF150428117617; Grant 98590), and Stellenbosch University (Staff Grant, Research Sub-
544 committee B).
545
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636 Hoelmer, K.A., Kirk, A.A, Pickett, C.H., Daane, K.M., and Johnson, M.W. 2011. Prospects for improving
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641 divergence and the multiplicative origin of community diversity. Proc. Natl. Acad. Sci. USA. 112(44):
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693 through a multi-regional host shift to cultivated olives: comparative dating using complete mitochondrial
694 genomes. Mol. Phyl. Evol. 57(2): 678–686. doi:10.1016/j.ympev.2010.08.008. PMID: 20723608.
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696 Nardi, F., Carapelli, Dallai, R., Roderick, G.K.Draft and Frati, F. 2005. Population structure and colonization
697 history of the olive fly, Bactrocera oleae (Diptera, Tephritidae). Mol. Ecol. 14(9): 2729–2738. doi:
698 10.1111/j.1365-294X.2005.02610.x. PMID: 16029474.
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700 Neuenschwander, P., 1982. Searching parasitoids of Dacus oleae (Gmel.) (Dipt., Tephritidae) in South
701 Africa. Zeit. Ang. Entomol. 94(1): 509–522. doi:10.1111/j.1439-0418.1982.tb02598.x.
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703 Nieves-Aldrey, J.L., Hernández Nieves, M., and Gómez, J.F. 2007. A new afrotropical species
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705 10.3989/graellsia.2007.v63.i1.80.
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707 Ramezani, S., Blibech, I., Trindade-Rei, F., van Asch, B. and Teixeira da Costa, L. 2015. Bactrocera oleae
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711 Ratnasingham, S. and Hebert, P.D. 2007. Bold: The Barcode of Life Data System
712 (http://www.barcodinglife.org). Mol. Ecol. Notes. 7(3): 355-364. doi:10.1111/j.1471-8286.2007.01678.x.
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715 Rice, R.E., Philips, P.A., Stewart-Leslie, J., Sibbett, G.S. 2003. Olive fruit fly populations measured in
716 Central and Southern California. Calif. Agric. 57(4): 122–127.
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718 Ross, H.A., Lento, G.M., Dalebout, M.L., Goode, M., Ewing, G., McLaren, P., et al. 2003. DNA Surveillance:
719 Web-based molecular identification of whales, dolphins, and porpoises. J. Heredity, 94(2): 111–114.
720 doi:10.1093/jhered/esg027. PMID: 12721222.
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722 Ross, H.A., Murugan, S. and Li, W.L.S. 2008. Testing the reliability of genetic methods of species
723 identification via simulation. Syst. Biol. 57(2): 216–230. doi:10.1080/10635150802032990. PMID:
724 18398767.
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726 Rowley, D.L., Coddington, J.A., Gates, M.W., Norrbom, A.L., Ochoa, R.A., Vandenberg, N.J., et al. 2007.
727 Vouchering DNA-barcoded specimens: test of a nondestructive extraction protocol for terrestrial
728 arthropods. Mol. Ecol. Notes. 7(6): 915–924. doi:10.1111/j.1471-8286.2007.01905.x.
729
730 Rubio De Casas, R., Besnard, G., Schönswetter, P., Balaguer, L. and Vargas, P. 2006. Extensive gene flow
731 blurs phylogeographic but not phylogenetic signal in Olea europaea L. Theo. App. Genet. 113(4): 575–
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734 Rugman-Jones, P.F., Wharton, R., van Noort, T. and Stouthamer, R. 2009. Molecular differentiation of
735 the Psyttalia concolor (Szépligeti) species complex (Hymenoptera: Braconidae) associated with olive fly,
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737 10.1016/j.biocontrol.2008.12.005.
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742 Schuler, H., Kern, P., Arthofer, W., Vogt, H., Fischer, M., Stauffer, C., et al. 2016. Wolbachia in parasitoids
743 attacking native European and introduced Eastern cherry fruit flies in Europe. Environ. Entomol. 45(6):
744 1424–1431. doi:10.1093/ee/nvw137. PMID: 28028089.
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746 Silvestri, F. 1913. Viaggio in Africa per cercare parassiti di mosche dei frutti. Boll. Lab. Zoo. Gen. Agr. R.
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749 Silvestri, F. 1915. Contributo alla conoscenza degli insetti dell’ olivo dell’ Eritrea e dell’ Africa meridionale.
750 Boll. Lab. Zoo. Gen. Agr. Portici, 9: 240–334.
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752 Silvestri F. 1939. La lotta biologica contro le mosche dei frutti della famiglia Trypetidae. In Proceedings of
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755 Smith, M.A., Bertrand, C., Crosby, K., Eveleigh, E.S., Fernandez-Triana, J., Fisher, B.L., et al. 2012.
756 Wolbachia and DNA barcoding insects: patterns, potential, and problems. PLoS ONE. 7(5). doi:
757 10.1371/journal.pone.0036514. PMID: 22567162.
758
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759 Stamatakis, A. 2006. Phylogenetic models of rate heterogeneity: a high performance computing
760 perspective. In Proceedings of the 20th IEEE International Parallel & Distributed Processing Symposium
761 (IPDPS2006). Washington: IEEE Computer Society Press. pp. 278–286. doi:10.1109/IPDPS.2006.1639535.
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763 Stamatakis, A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large
764 phylogenies. Bioinformatics, 30(9): 1312-3. doi:10.1093/bioinformatics/btu033. PMID: 24451623.
765
766 Thompson, J.D., Higgins, D.G. and Gibson, T.J. 1994. CLUSTAL W: improving the sensitivity of progressive
767 multiple sequence alignment through sequence weighting, position-specific gap penalties and weight
768 matrix choice. Nucleic Acids Res. 22(22): 4673–4680. PMID: 7984417.
769
770 Wharton, R. and Yoder, M. Parasitoids of Fruit-InfestingDraft Tephritidae [online]. Available from
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772
773 Zohary, D. 1994. The wild genetic resources of the cultivated olive. Acta Hortic. 356: 62-65. doi:
774 10.17660/ActaHortic.1994.356.12.
775
776
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777 MAIN FIGURE LEGENDS
778
779 Figure 1. Areas of collection of wild and cultivated olives in the Western Cape (16) and in the Eastern
780 Cape (1) Provinces of South Africa. Pie charts represent the relative proportion of Braconidae and
781 Chalcidoidea species reared from olives collected in each area. The size of the circles is proportional to
782 the total number of adult wasp specimens recovered from each area. Black dots represent collection
783 areas from which no specimens were reared.
784
785 Figure 2. A) Bracon celer female; B) Bracon celer male; C) Psyttalia humilis female; D) Psyttalia humilis
786 male.
787
788 Figure 3. A) Psyttalia lounsburyi female; B)Draft Psyttalia lounsburyi male. C) Utetes africanus, female; D)
789 Utetes africanus male.
790
791 Figure 4. A) Eupelmus spermophilus female; B) Eupelmus spermophilus male; C) Eurytoma oleae female;
792 D) Eurytoma oleae male; E) Eurytoma varicolor female; F) Eurytoma varicolor male.
793
794 Figure 5. A) Neochrysocharis formosus female; B) Neochrysocharis formosus male; C) Sycophila
795 aethiopica female; D) Sycophila aethiopica male; E) Ormyrus sp. female; and F) Ormyrus sp. male.
796
797 Figure 6. Relative proportions of adult braconid and chalcid wasps reared from wild and cultivated olives
798 collected in 16 areas in the Western Cape Province and one area in the Eastern Cape Province of South
799 Africa.
800
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801 Figure 7. Neighbour-joining (K2P) tree of the family Braconidae, based on a 485 bp alignment of 128 COI
802 sequences and two outgroups, with pairwise deletion of sites. Values indicate nodal bootstrap support
803 (1,000 replicates). The scale bar represents the percentage of sequence divergence. Species surveyed in
804 this study are shown in bold underlined. Triangles represent condensed species clades.
805
806 Figure 8. Neighbour-joining (K2P) tree of the superfamily Chalcidoidea, based on a 460 bp alignment of
807 225 COI sequences and two outgroups, with pairwise deletion of sites. Values indicate nodal bootstrap
808 support (1,000 replicates). The scale bar represents the percentage of sequence divergence. Species
809 surveyed in this study are shown in bold underlined. Triangles represent condensed species clades.
810
811 Draft
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812 SUPPLEMENTARY TABLE AND FIGURE LEGENDS
813
814 Table S1. List of specimens of Braconidae and Chalcidoidea wasps associated with wild and cultivated
815 olives in the Western Cape Province of South Africa, as deposited in the entomology collection at the
816 Iziko South African Museum in Cape Town.
817
818 Table S2. List of primers used for the PCR amplification and bidirectional sequencing of the barcoding
819 region of the COI gene in Braconidae and Chalcidoidea wasps reared from wild and cultivated olives in
820 the Western Cape and Eastern Cape Provinces of South Africa. *Previously published (Folmer et al,
821 1994); **Developed in this study.
822
823 Table S3. List of publicly available and newDraft COI sequences of Braconidae and Chalcidoidea used in the NJ
824 and ML analyses of wasps reared from wild and cultivated olives in the Western and the Eastern Cape
825 Provinces of South Africa, with Genbank accession numbers and BOLD identification numbers.
826 Sequences generated in this study are shown in bold underlined.
827
828 Table S4. Number of tephritid flies, and braconid and chalcid adult specimens reared from wild and
829 cultivated olives, and apparent parasitism and seed wasp estimates of infestation rates in 16 areas in the
830 Western Cape and one area in the Eastern Cape (Grahamstown) Provinces of South Africa. AIR %* -
831 Apparent seed infestation rate, calculated as the total number of adult specimens of the particular
832 species / total number of olives at each collection site and date. APR %* - Apparent parasitism rate,
833 calculated as the total number of adult braconid and Neochrysocharis formosus specimens / (total
834 number of tephritid flies + total number of braconids + N. formosus) at each collection site and date. Nd
835 – No data.
836
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837 Table S5. Specimen data of Braconidae and Chalcidoidea adult specimens reared from wild and
838 cultivated olives collected in 17 areas in the Western Cape and Eastern Cape Provinces of South Africa,
839 and used for DNA barcoding and phylogenetic analyses. Geographic coordinates indicate the site of olive
840 collection. Primer pair codes can be found in Table S1. Nd – No data.
841
842 Table S6. a), b) and c) Minimum, maximum and mean intraspecific p-distances (K2P) for Psyttalia species
843 based on a 609 bp alignment of 63 COI sequences, with pairwise deletion of sites. n - Number of
844 sequences used in estimates for each species; d), e) and f) Mean interspecific and intergroup p-distances
845 (K2P) for Psyttalia species based on a 609 bp alignment of 63 COI sequences, with pairwise deletion of
846 sites. Standard errors are shown above the diagonal.
847
848 Table S7. a) Minimum, maximum and meanDraft intraspecific p-distances (K2P) for two Utetes species based
849 on a 515 bp alignment of COI sequences, with pairwise deletion of sites. n - Number of sequences used
850 in estimates for each species; b) Mean interspecific p-distances (K2P) for U. africanus and three U.
851 canaliculatus NJ clusters (see Fig. S3) based on a 515 bp alignment of COI sequences, with pairwise
852 deletion of sites. Standard errors are shown above the diagonal.
853
854 Table S8. a) Minimum, maximum and mean intraspecific p-distances (K2P) for nine Eupelmus species
855 based on a 532 bp alignment of 150 COI sequences, with pairwise deletion of sites. n - Number of
856 sequences used in estimates for each species; b) Mean interspecific p-distances (K2P) for nine Eupelmus
857 species based on a 532 bp alignment of 150 COI sequences, with pairwise deletion of sites. Standard
858 errors are shown above the diagonal.
859
860 Table S9. a) Minimum, maximum and mean intraspecific p-distances (K2P) for seven Eurytoma species
861 based on a 530 bp alignment of 74 COI sequences, with pairwise deletion of sites. n - Number of
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862 sequences used in estimates for each species; b) Mean interspecific p-distances (K2P) for seven
863 Eurytoma species, based on a 532 bp alignment of 74 COI sequences, with pairwise deletion of sites.
864 Standard errors are shown above the diagonal.
865
866 Table S10. Minimum, maximum and mean intraspecific p-distances (K2P) for Neochrysocharis based on
867 633 bp alignments of COI sequences, with pairwise deletion of sites. n - Number of sequences used in
868 estimates for each group. na – not applicable.
869
870 Figure S1. Neighbour-joining (K2P) tree of the Bracon genus, based on a 524 bp alignment of 22 COI
871 sequences and two outgroups, with pairwise deletion of sites. Values indicate nodal bootstrap support
872 (1,000 replicates). The scale bar represents the percentage of sequence divergence. Sequences
873 generated in this study are shown in bold underlinedDraft.
874
875 Figure S2. Neighbour-joining (K2P) tree of the Psyttalia genus, based on a 524 bp alignment of 54 COI
876 sequences and two outgroups, with pairwise deletion of sites. Values indicate nodal bootstrap support
877 (1,000 replicates). The scale bar represents the percentage of sequence divergence. Sequences
878 generated in this study are shown in bold underlined.
879
880 Figure S3. Neighbour-joining (K2P) tree of the Utetes genus, based on a 485 bp alignment of 52 COI
881 sequences and two outgroups, with pairwise deletion of sites. Values indicate nodal bootstrap support
882 (1,000 replicates). The scale bar represents the percentage of sequence divergence. Sequences
883 generated in this study are shown in bold underlined.
884
885 Figure S4. Neighbour-joining (K2P) tree of the Eupelmus genus, based on a 545 bp alignment of 99 COI
886 sequences and two outgroups, with pairwise deletion of sites. Values indicate nodal bootstrap support
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887 (1,000 replicates). The scale bar represents the percentage of sequence divergence. Sequences
888 generated in this study are shown in bold underlined.
889
890 Figure S5. Neighbour-joining (K2P) tree of the Eurytoma genus, based on a 536 bp alignment of 51 COI
891 sequences and two outgroups, with pairwise deletion of sites. Values indicate nodal bootstrap support
892 (1,000 replicates). The scale bar represents the percentage of sequence divergence. Sequences
893 generated in this study are shown in bold underlined.
894
895 Figure S6. Neighbour-joining (K2P) tree of the Sycophila genus, based on a 549 bp alignment of 71 COI
896 sequences and two outgroups, with pairwise deletion of sites. Values indicate nodal bootstrap support
897 (1,000 replicates). The scale bar represents the percentage of sequence divergence. Sequences
898 generated in this study are shown in bold underlinedDraft.
899
900 Figure S7. Neighbour-joining (K2P) tree of the Neochrysocharis genus and the sister group Asecodes
901 lucens, based on a 561 bp alignment of 10 COI sequences and two outgroups, with pairwise deletion of
902 sites. Values indicate nodal bootstrap support (1,000 replicates). The scale bar represents the percentage
903 of sequence divergence. Sequences generated in this study are shown in bold underlined.
904
905 Figure S8a. Overall apparent parasitism rate (%) in wild and cultivated olives collected across all 17 areas
906 in the Western Cape and the Eastern Cape Provinces of South Africa. Overall apparent parasitism rate =
907 total number of adult braconid and Neochrysocharis formosus* specimens / (total number of tephritid
908 flies + the total number of adult braconid and N. formosus* specimens). *Neochrysocharis formosus is a
909 chalcid wasp with a parasitoid lifestyle.
910
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911 Figure S8b. Overall apparent seed infestation rate (%) in wild and cultivated olives collected across all 17
912 areas in the Western Cape and the Eastern Cape Provinces of South Africa. Overall apparent seed
913 infestation rate = total number of adult chalcid specimens / total number of wild and cultivated olives.
914
915 Figure S9. Apparent parasitism and apparent seed infestation rates (%) in cultivated olives collected from
916 three areas in the Western Cape Province of South Africa. Apparent parasitism rate = number of adult
917 braconid specimens / (number of tephritid flies + number of adult braconid specimens). Apparent seed
918 infestation rate = number of adult chalcid specimens / number of cultivated olives. Bracon celer (BR) and
919 Psyttalia lounsburyi (PL) are braconid wasps. Eupelmus spermophilus (ES) is a chalcid wasp.
920
921 Figure S10. Apparent parasitism and seed infestation rates (%) in wild olives collected from 11 areas in
922 the Western Cape Province and one area inDraft the Eastern Cape Province of South Africa. Apparent
923 parasitism rate = number of adult braconid and Neochrysocharis formosus* specimens / (number of
924 tephritid flies + number of adult braconid and N. formosus* specimens). Apparent seed infestation rate =
925 number of adult chalcid specimens / number of wild olives. Bracon celer (BR), Psyttalia humilis (PS),
926 Psyttalia lounsburyi (PL) and Utetes africanus (UA) are braconid wasps. Eupelmus spermophilus (ES),
927 Eurytoma oleae (EYO), Eurytoma varicolor (EYV), Sycophila aethiopica (SY) and Ormyrus sp. (OR) are
928 chalcid wasps. *Neochrysocharis formosus (NF) is a chalcid wasp with a parasitoid lifestyle.
929
930
931
932
933
934
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936
Draft
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Eupelmus spermophilus Eurytoma oleae Eurytoma varicolor Sycophila aethiopica SOUTH AFRICA NORTHERN CAPE Psyttalia humilis SOUTH AFRICA Psyttalia lounsburyi Bracon celer Neochrysocharis formosus Utetes africanus Ormyrus striatus
Riebeek Kasteel Draft
Porterville Malmesbury Tulbagh WESTERN CAPE EASTERN CAPE Paarl Grahamstown Worcester
Franschhoek Brackenfell Bonnievale Stellenbosch Riversdale Cape Town Swellendam McGregor
Stanford INDIAN OCEAN https://mc06.manuscriptcentral.com/genome-pubs Somerset West 100 km Genome Page 42 of 48
Draft
Figure 2. A) Bracon celer female; B) Bracon celer male; C) Psyttalia humilis female; D) Psyttalia humilis male.
220x165mm (300 x 300 DPI)
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Draft
Figure 3. A) Psyttalia lounsburyi female; B) Psyttalia lounsburyi male. C) Utetes africanus, female; D) Utetes africanus male.
220x165mm (300 x 300 DPI)
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Draft
Figure 4. A) Eupelmus spermophilus female; B) Eupelmus spermophilus male; C) Eurytoma oleae female; D) Eurytoma oleae male; E) Eurytoma varicolor female; F) Eurytoma varicolor male.
220x248mm (300 x 300 DPI)
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Draft
Figure 5. A) Neochrysocharis formosus female; B) Neochrysocharis formosus male; C) Sycophila aethiopica female; D) Sycophila aethiopica male; E) Ormyrus sp. female; and F) Ormyrus sp. male.
220x248mm (300 x 300 DPI)
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Draft
https://mc06.manuscriptcentral.com/genome-pubs Page 47 of 48 99 Genome Utetes canaliculatus
Utetes magnus
Utetes frequens Utetes canaliculatus 10 99 Utetes canaliculatus 95 Utetes juniperi 100 Utetes rosicola Utetes anastrephae
Utetes africanus 100 Utetes canaliculatus 100 Bracon greeni 100 Bracon atrator
Bracon intercessor 100 Bracon crassicornis 80 100 Bracon kopelkei Draft95 Bracon picticornis Bracon celer Br02 87 Bracon asphondylae 9 100 99 Bracon tamabae Bracon asphondylae 100 100 98 Psyttalia carinata Psyttalia ponerophaga 100 Psyttalia phaeostigma 86 100 99 Psyttalia fletcheri Psyttalia incisi Psyttalia cf. perproxima PFRJ-2008 100 Psyttalia cosyrae 100 Psyttalia lounsburyi 100 Psyttalia perproxima 100 Psyttalia concolor
95 Psyttalia humilis 100 Eurytoma spermophilus ES99 100 Eurytoma oleae EY14
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Sycophila sp.
Sycophila aethiopica SY50 Sycophila sp. 83 Sycophila sp.
Sycophila sp. 99 Eurytoma striolata Eurytoma morio 99 Eurytoma oleae 99 Eurytoma maura 99 Eurytoma afra 99 Eurytoma gigantea Eurytoma juniperina Eurytoma discordans Eurytoma aciculata 99 Eurytoma laricis 99 Eurytoma arctica Eurytoma longavena 99 Eupelmus varicolor 99 99 Eupelmus spermophilus Eupelmus matranus Eupelmus testaceiventris Eupelmus linearis 99 Eupelmus cushmani Eupelmus falcatus Eupelmus phragmitis Draft Eupelmus fuscipennis Eupelmus cicadae Eupelmus juniperinus thuriferae Eupelmus atropurpureus Eupelmus seculatus Eupelmus microzonus 99 Eupelmus tibicinis Eupelmus muellneri Eupelmus simizonus Eupelmus vesicularis 9 Eupelmus pini 99 99 82 Eupelmus gemellus Eupelmus martellii Eupelmus acinellus 99 Eupelmus annulatus 99 99 Eupelmus vindex Eupelmus azureus 99 Eupelmus cerris 99 Eupelmus confusus Eupelmus pistaciae 99 Eupelmus fulgicalvus 99 Eupelmus fulvipes 99 99 Eupelmus kiefferi Eupelmus tremulae 99 93 Eupelmus opacus 91 Eupelmus priotoni 97 Eupelmus purpuricollis 99 Eupelmus janstai 99 Eupelmus minozonus 98 Eupelmus urozonus 99 Neochrysocharis formosus HM365028 Neochrysocharis clinias HM365038 Neochrysocharis formosus 99 Psyttalia humilis Ps24 99 https://mc06.manuscriptcentral.com/genome-pubsBracon celer Br02
0.05