DNA barcoding reveals both known and novel taxa in the Albitarsis Group (Anopheles: Nyssorhynchus) of Neotropical malaria vectors
- Freddy Ruiz-Lopez†1Email author,
- Richard C Wilkerson†1,
- Jan E Conn2, 3,
- Sascha N McKeon3,
- David M Levin1,
- Martha L Quiñones4,
- Marinete M Póvoa5 and
- Yvonne-Marie Linton†1, 6
© Ruiz-Lopez et al; licensee BioMed Central Ltd. 2012
Received: 12 September 2011
Accepted: 21 February 2012
Published: 21 February 2012
Mosquitoes belonging to the Albitarsis Group (Anopheles: Nyssorhynchus) are of importance as malaria vectors across the Neotropics. The Group currently comprises six known species, and recent studies have indicated further hidden biodiversity within the Group. DNA barcoding has been proposed as a highly useful tool for species recognition, although its discriminatory utility has not been verified in closely related taxa across a wide geographic distribution.
DNA barcodes (658 bp of the mtDNA Cytochrome c Oxidase - COI) were generated for 565 An. albitarsis s.l. collected in Argentina, Brazil, Colombia, Paraguay, Trinidad and Venezuela over the past twenty years, including specimens from type series and type localities. Here we test the utility of currently advocated barcoding methodologies, including the Kimura-two-parameter distance model (K2P) and Neighbor-joining analysis (NJ), for determining species delineation within mosquitoes of the Neotropical Albitarsis Group of malaria vectors (Anopheles: Nyssorhynchus), and compare results with Bayesian analysis.
Species delineation through barcoding analysis and Bayesian phylogenetic analysis, fully concur. Analysis of 565 sequences (302 unique haplotypes) resolved nine NJ tree clusters, with less than 2% intra-node variation. Mean intra-specific variation (K2P) was 0.009 (range 0.002 - 0.014), whereas mean inter-specific divergence were several-fold higher at 0.041 (0.020 - 0.056), supporting the reported "barcoding gap". These results show full support for separate species status of the six known species in the Albitarsis Group (An. albitarsis s.s., An. albitarsis F, An. deaneorum, An. janconnae, An. marajoara and An. oryzalimnetes), and also support species level status for two previously detected lineages - An. albitarsis G & An. albitarsis I (designated herein). In addition, we highlight the presence of a unique mitochondrial lineage close to An. deaneorum and An. marajoara (An. albitarsis H) from Rondônia and Mato Grosso in southwestern Brazil. Further integrated studies are required to confirm the status of this lineage.
DNA barcoding provides a reliable means of identifying both known and undiscovered biodiversity within the closely related taxa of the Albitarsis Group. We advocate its usage in future studies to elucidate the vector competence and respective distributions of all eight species in the Albitarsis Group and the novel mitochondrial lineage (An. albitarsis H) recovered in this study.
The need to understand the systematics of the Neotropical Albitarsis Group (Anopheles subgenus Nyssorhynchus)  is primarily driven by the operational requirement to reliably distinguish which component taxa are involved in malaria transmission. The group is of great epidemiological importance as three of the five formally described species are proven regional malaria vectors in Brazil: An. deaneorum Rosa-Freitas [2–4], An. janconnae Wilkerson and Sallum (= An. albitarsis E)  and An. marajoara Galvão and Damasceno [6–8]. The vector status of An. oryzalimnetes Wilkerson and Motoki (= An. albitarsis B), An. albitarsis Lynch-Arribálzaga and the informally named species An. albitarsis "F" , are unknown. The group, along with An. braziliensis, is easily recognized in the adult stage by a pair of white scale stripes on sternum I . The taxonomy of this group is historically complex and a comprehensive review is given in Motoki et al..
Recent studies using COI and white gene sequences , in addition to the complete mitochondrion DNA  for five species belonging to Albitarsis Group, suggested that An. marajoara from Manaus (Brazil) should be regarded as a separate taxon in the Group (= An. albitarsis G) [12, 13]. In the past year, two further lineages have been proposed suggesting that species discovery in the Albitarsis Group is far from complete. One, closely related to An. janconnae, was detected in the Caribbean region of Colombia based on COI, white gene and second internal transcribed spaces (ITS2) sequences . The other, closely related to An. deaneorum, was found in Acrelândia, Acre, Brazil, using white and NADH dehydrogenase subunit 6 (ND6) gene sequences . Neither of these proposed lineages was named.
Sequence data exist for mitochondrial COI[12, 13, 16, 17], NADH dehydrogenase subunit 4 (ND4) , ND6 and whole mitochondrial genomes , and the nuclear white[12, 14], ITS2 [9, 14, 18] and Dominant receptor (D2)  regions. However, a single marker is still to be identified, which can to separate all known species and recognized lineages in the Albitarsis Group to ensure accurate species identification for studies on vector competence, for accurate distribution mapping, and to facilitate vector control efforts. Early attempts to use the ITS2 as a species diagnostic marker in the group  were hampered by the inadvertent inclusion of undiscovered taxa [9, 13, 14] and extensive intragenomic variation, which rendered the proposed ITS2-PCR assay unusable .
Mitochondrial genes are considered better markers than nuclear genes because of their abundance (1000's copies per cell), lack of introns, limited exposure to recombination, and haploid mode of inheritance . DNA barcoding - which relies on the genetic variation within a standardized region of the COI gene - has been promoted as a reliable method for the identification of species in a variety of both invertebrate and vertebrate taxa . Krzywinski et al. sequenced whole mitochondrial genomes of six confirmed and putative taxa in the Albitarsis Group and showed that the 5' half of the COI "barcode region" is clearly more variable than its 3' half. COI barcoding studies of the mosquito fauna of Canada  and India , and within the genus Anopheles[24–27] have shown exceptional promise for species-level determinations. However, there has been no rigorous testing of the utility of the barcoding region in large populations of geographically widespread and closely related species such as those in the Albitarsis Group.
Herein we investigate the utility of the standard DNA COI barcode region for species identification using both the standard "simple" barcode methodology , NJ  and K2P model  to differentiate known and unknown species from 565 members of the Albitarsis Group, collected across a wide geographic range in South America in the last 20 years. For comparison, a subset of the full dataset is further investigated in a phylogenetic Bayesian framework .
Specimens and data access
Full specimen records (collection locality, coordinates, specimen identifiers, location of voucher specimens etc.) and all genetic data (edited chromatograms, consensus COI sequence files and corresponding GenBank numbers) are publicly accessible under the project code MBIK (Albitarsis Group Barcoding) on the BOLD website (http://www.boldsystems.org), as part of the Mosquito Barcoding Initiative (MBI). Collection data and distribution maps are also publicly available through MosquitoMap (http://www.mosquitomap.org). Specimens utilized in the molecular study were all morphologically verified as An. albitarsis s.l., using the original descriptions, and available keys [1, 31] and include topotypic material for An. albitarsis s.s., An. deaneorum, An. marajoara and An. oryzalimnetes, and type series material of An. janconnae. Voucher specimens and/or their DNA extracts for the majority of specimens used in this study are stored at -80°C in the archive collections of Walter Reed Biosystematics Unit, Smithsonian Institution, Museum Support Center, Suitland, Maryland, USA, or in the Culicid DNA Collection of the Molecular Systematics Laboratory, Natural History Museum, London.
DNA barcodes (658 bp, excluding primers) were generated for 565 specimens collected across South America using the published high-throughput DNA extraction and PCR amplification protocols  using the LCO1490 & HCO2198 primers of Folmer et al.. Sequencing reactions were carried out in both directions with the Big Dye® Terminator Kit on an ABI 3730 automated sequencer (PE Applied Biosystems). Sequences were edited in Sequencher™ v4.8 (Genes Codes Corporation, Ann Arbor, MI), and translated to amino acids in MacClade v.4.06 . Similarities with publicly available sequences were assessed using BLAST (Basic Local Alignment Search Tool), available at http://blast.ncbi.nlm.nih.gov/Blast.cgi, and comparisons with unpublished barcode records checked through the IDS (Identification System) of the Barcode of Life database (BOLD, available at http://www.barcodinglife.org).
To test the resolution of customarily advocated barcoding methodologies , 302 unique haplotypes (n = 565) COI barcodes were first imported into PAUP* v.4.0 . Following construction of a pairwise distance matrix using K2P , a bootstrapped  NJ tree  was generated using 1,000 replicates to produce an unrooted consensus tree. Sequence divergence was calculated in MEGA v.4.0  using the K2P model. Anopheles braziliensis Chagas [GenBank: DQ076238] and An. darlingi Root [GenBank: DQ076236] were used as outgroup taxa to the Albitarsis Group, following previously published studies [14, 16].
A Bayesian phylogenetic analysis  was carried out using five specimens from each distinctive COI lineage found by NJ-K2P analysis (including respective type localities where possible). These sequences were added to the publicly available COI sequences of [14, 16] (trimmed to 658 bp). Recently published COI data [12, 13] overlapped those already included in our dataset and were therefore not included in the analysis. MrBayes  was performed online at: http://cbsuapps.tc.cornell.edu/mrbayes.aspx. The Bayesian analysis was run for 10 million generations with two parallel searches using three heated and one cold Markov chain, with the first 5 million generations discarded as burn-in. The best-fit model HKY + I + G was selected by the AIC criterion in MrModeltest 2.3 . The trees generated were edited in Figtree v1.2.1 .
Mean pairwise nucleotide frequencies of COI barcode sequences for individuals belonging to Albitarsis Group.
No. of transitions (TS %)
No. of transversions (TV %)
Determination of barcode clusters
The analysis of COI sequences from members of the Albitarsis Group using NJ-K2P distances revealed nine distinct clusters: six of these correspond to the formerly defined species An. albitarsis s.s., An. deaneorum, An. janconnae, An. marajoara, An. oryzalimnetes and An. albitarsis F, and another to An. albitarsis G , which we believe to comprise a separate species in the Albitarsis Group along with "sp. nr. An. janconnae", named An. albitarsis I. The remaining cluster, which we believe to represent a separate lineage, is named An. albitarsis H. Currently available synonyms for the Albitarsis Group as discussed in Motoki et al. (An. albitarsis (Anopheles albitarsis var. limai Galvão and Lane, Anopheles albitarsis imperfectus Corrêa and Ramos)), An. marajoara (An. albitarsis domesticus Galvão and Damasceno) and the status An. allopha as a nomen dubium are in our opinion sustained, with none referring to the newly recognized species/lineages presented here.
The monophyly of the Albitarsis Group is strongly supported with a high P value (P = 1), which echoes earlier studies [14–17]. BLAST searches of COI sequences revealed 99-100% homology with sequences reported for An. albitarsis s.s. [GenBank: DQ076204-DQ076208], An. deaneorum [GenBank: DQ076226, DQ076230], An. janconnae [GenBank: DQ076233], An. marajoara [GenBank: DQ076216] and An. oryzalimnetes [GenBank: DQ076210-DQ076215] . This further reinforces our confidence in the identities of these taxa. The respective distributions and taxonomic positions of the informally designated taxa (An. albitarsis F, G, and I) and new lineage An. albitarsis H within the Albitaris Group are discussed in relation to earlier works below.
Anopheles albitarsis F
List of species found by country and state, belonging to Albitarsis Group.
Buenos Aires, Corrientes, Misiones
An. albitarsis s.s.
Paraná, Santa Catarina, São Paulo
An. albitarsis s.s.
Amazonas, Bahia, Pará
An. albitarsis G
Mato Grosso, Rondônia
An. albitarsis H
Mato Grosso, Rondônia, Paraná
Amapá, Roraima, Pará
Amapá, Mato Grosso, Pará, Rondônia
Espirito Santo, Bahia, Ceará, Mato Grosso Pará, Rio de Janeiro, Rondônia, São Paulo
Antioquia, Norte de Santander
An. albitarsis I
Meta, Norte de Santander, Vichada
An. albitarsis F
An. albitarsis s.s.
St. George East, St. Andrew/St.David
An. albitarsis F
An. albitarsis F
An. albitarsis I
Morphologically, An. albitarsis F is similar to the proven malaria vector An. marajoara, thus the wider distribution of this cryptic taxon in Venezuela and Trinidad is of epidemiological significance. Based on morphology and RAPD profiling , An. marajoara was believed to be the only member of the Albitarsis Group present in western Venezuela , where it is a proven secondary vector of Plasmodium vivax 210 . However, these studies predate the discovery of An. albitarsis F and it is not known if the species-diagnostic RAPD assay (developed for the four known members of the Albitarsis Group at that time)  could distinguish An. marajoara from An. albitarsis F. Given the data presented herein, it seems likely that "An. marajoara" reported in Venezuela  corresponds to An. albitarsis F. It is also probable that "population C" from Venezuela and Colombia [41, 42] identified on the basis of chromosomal analysis, may also be An. albitarsis F. Further sampling is needed to assess the true identity of An. albitarsis s.l. in Venezuela and assess whether An. albitarsis F is the only member of the group present there, or whether An. marajoara and An. albitarsis F are sympatric in that country. This is also true for the population of An. marajoara in Trinidad, which is regarded as a secondary vector in the region . An ecological study stated that An. marajoara was identified from the island based on RAPD profiles and ITS2 sequences , yet our data clearly show all samples tested from Trinidad to be An. albitarsis F. Concurrent species determination, distribution mapping and vector incrimination studies are needed to assess the true impact of An. marajoara and An. albitarsis F on malaria transmission across their range.
Anopheles albitarsis G
Mean COI genetic intra-specific distance within An. albitarsis G was 0.010, whereas mean inter-specific divergence within the Albitarsis Group were four-fold higher (0.041) (Figure 2, Figure 3), and well above accepted species delimitation divergence thresholds routinely employed in DNA barcoding [22–27]. Based on consistent differences in DNA sequence in one individual (C10 [GenBank: DQ076225]) from four different DNA markers , Wilkerson et al. first suggested the presence of hidden genetic diversity within An. marajoara from Manaus, Brazil. Bayesian analysis of the entire COI gene showed that sample C10 grouped closest with An. deaneorum, but with low support (P = 0.69) . Because of this, these authors questioned the validity of An. deaneorum arguing: "if An. deaneorum is a separate species from An. marajoara, then An. marajoara may consist of two or more species in Amazonian Brazil". The presence of An. albitarsis G as a cryptic species in the Albitarsis Group was later confirmed in further DNA studies [12, 13]. BLAST of our An. albitarsis G sequences returned 100% homology with GenBank: DQ076225 (C10, from Manaus, Brazil, as An. marajoara) and GenBank: DQ076217 (C2, from Itaituba, Brazil, as An. marajoara) . GenBank: DQ076221 (Itaituba, Brazil)  still shows deviation in the Bayesian phylogeny. However, at this time we are unable to assess whether this reflects further hidden genetic diversity, whether these differences are due to poor sequence quality in the first instance, or are indeed real and reflective of geographic distance as all other specimens sequenced are from Manaus, Brazil (Figure 4). Further sampling from Itaituba and other localities is needed.
Anopheles albitarsis H
This novel mitochondrial lineage was detected in 42 specimens collected in Rondônia and Mato Grosso, Brazil. COI sequences showed highest similarity with An. marajoara and An. deaneorum (0.020 and 0.024, respectively), both values being significantly higher than its intra-specific divergence (0.010) (Figure 2, Figure 3). BLAST of our sequences revealed 99% homology with GenBank: DQ076222 from Matupá and GenBank: DQ076223 from Peixoto de Azevedo (both Mato Grosso, Brazil) and GenBank: DQ076224 from Ariquemes, Rondônia, Brazil (as An. marajoara samples C7, C8 and C9) . These three samples were shown to form a cluster distinct from An. marajoara, which is further supported in our Bayesian analysis (Figure 4).
Based on sequence variation, the barcoding community generally accept species delineation if the intraspecific variation is less than 1%, while the inter-specific variation is at least 2% different from its nearest congener [22–27, 44]. Average inter-specific divergences between known taxa in the Albitarsis Group is 0.036, however, inter-specific values between An. deanorum, An. marajoara and Anopheles albitarsis H are much lower, ranging from 0.020 - 0.025. Our COI data supports the suggestion of Lehr et al., exposing this grouping as cryptic complex in its own right within the Albitarsis Group. The status of the mitochondrial lineage An. albitarsis H is far from resolved. Further detailed ecological, genetic and morphological studies are necessary before we can speculate whether this lineage is reflective of a new species within the Albitarsis Group.
The presence of a cryptic species near to An. deaneorum (using ND6 and white gene sequences ) and near to An. marajoara (by allozymes and mtDNA RFLPs ), were detected in populations of An. albitarsis s.l. from the same and neighbouring localities to where An. albitarsis H was detected in this study.
Anopheles albitarsis I
Brochero et al. first reported An. albitarsis F in Vichada, Colombia (east of the Cordillera Oriental) in sympatry with another taxon determined as An. marajoara based on morphological keys . Microsatellite analysis of five populations of An. marajoara in Colombia revealed two incompletely isolated gene pools separated by the eastern Andean cordillera . Using the entire COI, white gene and ITS2 sequences, Gutierrez et al. reported a new lineage in the Albitarsis Group closely related to An. janconnae from northwestern Colombia. Sequences generated in our study share 99% homology with these COI sequences [GenBank: GQ153597-GQ153610] , and this cluster was highly supported in our Bayesian analysis (P = 0.99) (Figure 5). We clearly show that the lineage previously reported by Gutierrez et al. as sp. nr. An. janconnae in the Caribbean region of Colombia and by Brochero et al. as An. marajoara, is a separate species in the Albitarsis Group, which we call An. albitarsis I.
Despite the small sample size analysed, this species is clearly distinct from other members of the Albitarsis Group based on COI sequence data, with an intra-specific divergence of 0.008 and mean inter-specific divergence of 0.044 (0.027 with An. albitarsis F - 0.053 with An. marajoara) (Figure 2). That the sister taxon An. albitarsis F and An. albitarsis I were detected in sympatry in the geographically separate localities of Tibú, Norte de Santander, Colombia and Rio Socuavo, Zulia, Venezuela (Figure 5), provides further evidence to support their separate species status within the Albitarsis Group.
Distribution of Albitarsis Group in South America based on COI sequences
Locality data for all molecularly confirmed Neotropical Albitarsis Group specimens used in this study (n = 565) and correlated COI data from previous studies [14, 16] were plotted using the mapping methodology developed by Foley  (Figure 5). This figure shows the distributions of An. albitarsis F and An. albitarsis I to be restricted to northern South America (Colombia, Venezuela and Trinidad), whereas An. albitarsis s.s. is found in southern Brazil, northern Argentina and Paraguay. Anopheles marajoara is present in the central east and west region of Brazil and An. deaneorum is in southwestern Brazil. Anopheles oryzalimnetes has a wide distribution in Brazil, mainly in the central region (Figure 5). Three species in the Albitarsis Group and the new lineage An. albitarsis H appear endemic only to Brazil to date: An. marajoara (Amapá, Mato Grosso, Pará, Rondônia), An. janconnae is present in northern Brazil (Roraima and Pará states), An. albitarsis G in Amazonian Brazil (Amazonas and Pará states) and An. albitarsis H in Rondônia and Mato Grosso, Brazil. Some species and lineages were found to be sympatric: for example, An. marajoara with An. oryzalimnetes and An. janconnae in Pará, Brazil; An. albitarsis H, An. deaneorum, An. marajaora and An. oryzalimnetes in Mato Grosso, Brazil; An. oryzalimnetes and An. albitarsis in São Paulo, Brazil, amongst others (Figure 5).
Whilst this study significantly contributes to the verified distribution of members of the Albitarsis Group, it is important to note that samples were not available from Bolivia, Costa Rica, French Guiana, Guatemala, Guyana, Panama, Peru, Suriname and Uruguay, where species of the Group have previously been reported . We advocate the utility of the COI barcoding region for the correct species identification of An. albitarsis s.l. specimens in these regions, allowing complete species level distribution maps to be constructed for all eight species and the new lineage recognised in this study.
The results reported here using COI barcoding of specimens collected over 20 years from a wide geographic range in South America (Argentina, Brazil, Colombia, Paraguay, Trinidad and Venezuela), including topotypic specimens of the formally described taxa, helped resolve the taxonomic status and the distribution of the Albitarsis Group in South America. Contrary to intra-specific variation detected in previous studies using ITS2 , we consider the COI barcode region to be a robust marker of choice for species delimitation in the Albitarsis Group, not least because amplification of a short region (658 bp) yielded similar results to studies based on the entire mitochondria  or full COI gene [12, 14, 16]. We now consider the following species to comprise the Albitarsis Group: An. albitarsis s.s., An. deaneorum, An. janconnae, An. marajoara, An. oryzalimnetes, An. albitarsis F, An. albitarsis G and An. albitarsis I. In addition, we uncovered a new mitochondrial lineage, An. albitarsis H, which requires further sampling and sequencing of additional markers before its true species status can be resolved. This first comprehensive study of species in the Albitarsis Group across a wide geographic range in South America and provides a firm systematic basis for future studies that ideally should include ecology, biogeography, population genetics analysis, and vector incrimination of these species, particularly in malaria endemic regions where some of these new taxa may be acting as vectors.
This study forms part of the larger objectives of the Mosquito Barcoding Initiative (MBI), led by the senior authors YML & RCW. This investigation received financial support from: supporters of the Natural History Museum, London to further the activities of the Mosquito Barcoding Initiative (to YML); the UNICEF/UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (TDR) (grant A50252 to YML), Consortium for the Barcode of Life (CBOL) (to YML & RCW) and The Sloane Foundation (to YML & RCW); from the National Institute of Health (NIH), USA, (grant 2R01AI054139 to JEC) and COLCIENCIAS (grant 110134319196 to MLQ). We gratefully acknowledge Dr. Marta Moreno (Griffin Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA), Izis M. Carvalho and Galiza Primo (Instituto Evandro Chagas, Ananindeua, PA, Brazil) for their invaluable field assistance; Andrea Ormos for molecular laboratory support (Laboratories of Analytical Biology, Smithsonian Institution, Washington DC, USA), Dr. Desmond Foley (WRBU, Smithsonian Institution, Washington DC, USA) for elaboration of the map; Dr. Shazia Mahamdallie for helpful suggestions and discussions and Dr. Helena Brochero (Universidad Nacional de Colombia, Bogotá D.C., Colombia) for donation of An. albitarsis F samples.
This research was performed under a Memorandum of Understanding between the Walter Reed Army Institute of Research and the Smithsonian Institution, with institutional support provided by both organizations. The material to be published reflects the views of the authors and should not be construed to represent those of the Department of the Army or the Department of Defense. This manuscript was prepared while YML held a National Research Council Research Associateship Award at the Walter Reed Army Institute of Research.
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