Cryptic species within cryptic moths: new species of Dunama Schaus (Notodontidae, Nystaleinae) in Costa Rica

A re-analysis of the data in Sharkey et al.'s (2021) minimalist revision reveals that BINs do not deserve names, but BOLD Systems needs a stronger commitment to open science

Halting biodiversity decline is one of the most critical challenges for humanity, but monitoring biodiversity is hampered by taxonomic impediments. One impediment is the large number of undescribed species (here called "dark taxon impediment") whereas another is caused by the large number of superficial species descriptions, that can only be resolved by consulting type specimens ("superficial description impediment"). Recently, Sharkey et al. (2021) proposed to address the dark taxon impediment for Costa Rican braconid wasps by describing 403 species based on COI barcode clusters ("BINs") computed by BOLD Systems. More than 99% of the BINs (387 of 390) were converted into species by assigning binominal names (e.g. BIN "BOLD:ACM9419" becomes Bracon federicomatarritai) and adding a minimal diagnosis (consisting only of a consensus barcode for most species). We here show that many of Sharkey et al.'s species are unstable when the underlying data are analyzed using different species delimitation algorithms. Add the insufficiently informative diagnoses, and many of these species will become the next "superficial description impediment" for braconid taxonomy because they will have to be tested and redescribed after obtaining sufficient evidence for confidently delimiting species. We furthermore show that Sharkey et al.'s approach of using consensus barcodes as diagnoses is not functional because it cannot be applied consistently. Lastly, we reiterate that COI alone is not suitable for delimiting and describing species, and voice concerns over Sharkey et al.'s uncritical use of BINs because they are calculated by a proprietary algorithm (RESL) that uses a mixture of public and private data. We urge authors, reviewers and editors to maintain high standards in taxonomy by only publishing new species that are rigorously delimited with open-access tools and supported by publicly available evidence.

Minimalist revision and description of 403 new species in 11 subfamilies of Costa Rican braconid parasitoid wasps, including host records for 219 species

Three new genera are described: Michener (Proteropinae), Bioalfa (Rogadinae), and Hermosomastax (Rogadinae). Keys are given for the New World genera of the following braconid subfamilies: Agathidinae, Braconinae, Cheloninae, Homolobinae, Hormiinae, Ichneutinae, Macrocentrinae, Orgilinae, Proteropinae, Rhysipolinae, and Rogadinae. In these subfamilies 416 species are described or redescribed. Most of the species have been reared and all but 13 are new to science. A consensus sequence of the COI barcodes possessed by each species is employed to diagnose the species, and this approach is justified in the introduction. Most descriptions consist of a lateral or dorsal image of the holotype, a diagnostic COI consensus barcode, the Barcode Index Number (BIN) code with a link to the Barcode of Life Database (BOLD), and the holotype specimen information required by the International Code of Zoological Nomenclature. The following species are treated and those lacking authorship are newly described here with authorship attributable to Sharkey except for the new species of Macrocentrinae which are by Sharkey & van Achterberg: AGATHIDINAE: Aerophiluspaulmarshi, Mesocoelusdavidsmithi, Neothlipsisbobkulai, Plesiocoelusvanachterbergi, Pneumagathiserythrogastra (Cameron, 1905), Therophilusbobwhartoni, T.donaldquickei, T.gracewoodae, T.maetoi, T.montywoodi, T.penteadodiasae, Zacremnopsbrianbrowni, Z.coatlicue Sharkey, 1990, Zacremnopscressoni (Cameron, 1887), Z.ekchuah Sharkey, 1990, Z.josefernandezi, Zelomorphasarahmeierottoae. BRACONINAE: Braconalejandromarini, B.alejandromasisi, B.alexamasisae, B.andresmarini, B.andrewwalshi, B.anniapicadoae, B.anniemoriceae, B.barryhammeli, B.bernardoespinozai, B.carlossanabriai, B.chanchini, B.christophervallei, B.erasmocoronadoi, B.eugeniephillipsae, B.federicomatarritai, B.frankjoycei, B.gerardovegai, B.germanvegai, B.isidrochaconi, B.jimlewisi, B.josejaramilloi, B.juanjoseoviedoi, B.juliodiazi, B.luzmariaromeroae, B.manuelzumbadoi, B.marialuisariasae, B.mariamartachavarriae, B.mariorivasi, B.melissaespinozae, B.nelsonzamorai, B.nicklaphami, B.ninamasisae, B.oliverwalshi, B.paulamarinae, B.rafamoralesi, B.robertofernandezi, B.rogerblancoi, B.ronaldzunigai, B.sigifredomarini, B.tihisiaboshartae, B.wilberthbrizuelai, Digonogastramontylloydi, D.montywoodi, D.motohasegawai, D.natwheelwrighti, D.nickgrishini. CHELONINAE: Adeliusadrianguadamuzi, A.gauldi Shimbori & Shaw, 2019, A.janzeni Shimbori & Shaw, 2019, Ascogastergloriasihezarae, A.grettelvegae, A.guillermopereirai, A.gustavoecheverrii, A.katyvandusenae, A.luisdiegogomezi, Chelonusalejandrozaldivari, C.gustavogutierrezi, C.gustavoinduni, C.harryramirezi, C.hartmanguidoi, C.hazelcambroneroae, C.iangauldi, C.isidrochaconi, C.janecheverriae, C.jeffmilleri, C.jennyphillipsae, C.jeremydewaardi, C.jessiehillae, C.jesusugaldei, C.jimlewisi, C.jimmilleri, C.jimwhitfieldi, C.johanvalerioi, C.johnburnsi, C.johnnoyesi, C.jorgebaltodanoi, C.jorgehernandezi, C.josealfredohernandezi, C.josefernandeztrianai, C.josehernandezcortesi, C.josemanuelperezi, C.josephinerodriguezae, C.juanmatai, C.junkoshimurae, C.kateperezae, C.luciariosae, C.luzmariaromeroae, C.manuelpereirai, C.manuelzumbadoi, C.marianopereirai, C.maribellealvarezae, C.markmetzi, C.markshawi, C.martajimenezae, C.mayrabonillae, C.meganmiltonae, C.melaniamunozae, C.michaelstroudi, C.michellevanderbankae, C.mingfangi, C.minorcarmonai, C.monikaspringerae, C.moniquegilbertae, C.motohasegawai, C.nataliaivanovae, C.nelsonzamorai, C.normwoodleyi, C.osvaldoespinozai, C.pamelacastilloae, C.paulgoldsteini, C.paulhansoni, C.paulheberti, C.petronariosae, C.ramyamanjunathae, C.randallgarciai, C.rebeccakittelae, C.robertoespinozai, C.robertofernandezi, C.rocioecheverriae, C.rodrigogamezi, C.ronaldzunigai, C.rosibelelizondoae, C.rostermoragai, C.ruthfrancoae, C.scottmilleri, C.scottshawi, C.sergioriosi, C.sigifredomarini, C.stevearonsoni, C.stevestroudi, C.sujeevanratnasinghami, C.sureshnaiki, C.torbjornekremi, C.yeimycedenoae, Leptodrepanaalexisae, L.erasmocoronadoi, L.felipechavarriai, L.freddyquesadai, L.gilbertfuentesi, L.manuelriosi, Phanerotomaalmasolisae, P.alvaroherrerai, P.anacordobae, P.anamariamongeae, P.andydeansi, P.angelagonzalezae, P.angelsolisi, P.barryhammeli, P.bernardoespinozai, P.calixtomoragai, P.carolinacanoae, P.christerhanssoni, P.christhompsoni, P.davesmithi, P.davidduthiei, P.dirksteinkei, P.donquickei, P.duniagarciae, P.duvalierbricenoi, P.eddysanchezi, P.eldarayae, P.eliethcantillanoae, P.jenopappi, Pseudophanerotomaalanflemingi, Ps.albanjimenezi, Ps.alejandromarini, Ps.alexsmithi, Ps.allisonbrownae, Ps.bobrobbinsi. HOMOLOBINAE: Exasticolusjennyphillipsae, E.randallgarciai, E.robertofernandezi, E.sigifredomarini, E.tomlewinsoni. HORMIINAE: Hormiusanamariamongeae, H.angelsolisi, H.anniapicadoae, H.arthurchapmani, H.barryhammeli, H.carmenretanae, H.carloswalkeri, H.cesarsuarezi, H.danbrooksi, H.eddysanchezi, H.erikframstadi, H.georgedavisi, H.grettelvegae, H.gustavoinduni, H.hartmanguidoi, H.hectoraritai, H.hesiquiobenitezi, H.irenecanasae, H.isidrochaconi, H.jaygallegosi, H.jimbeachi, H.jimlewisi, H.joelcracrafti, H.johanvalerioi, H.johnburleyi, H.joncoddingtoni, H.jorgecarvajali, H.juanmatai, H.manuelzumbadoi, H.mercedesfosterae, H.modonnellyae, H.nelsonzamorai, H.pamelacastilloae, H.raycypessi, H.ritacolwellae, H.robcolwelli, H.rogerblancosegurai, H.ronaldzunigai, H.russchapmani, H.virginiaferrisae, H.warrenbrighami, H.willsflowersi. ICHNEUTINAE: Oligoneuruskriskrishtalkai, O.jorgejimenezi, Paroligoneuruselainehoaglandae, P.julianhumphriesi, P.mikeiviei. MACROCENTRINAE: Austrozelejorgecampabadali, A.jorgesoberoni, Dolichozelegravitarsis (Muesebeck, 1938), D.josefernandeztrianai, D.josephinerodriguezae, Hymenochaoniakalevikulli, H.kateperezae, H.katherinebaillieae, H.katherineellisonae, H.katyvandusenae, H.kazumifukunagae, H.keithlangdoni, H.keithwillmotti, H.kenjinishidai, H.kimberleysheldonae, H.krisnorvigae, H.lilianamadrigalae, H.lizlangleyae, Macrocentrusfredsingeri, M.geoffbarnardi, M.gregburtoni, M.gretchendailyae, M.grettelvegae, M.gustavogutierrezi, M.hannahjamesae, M.harisridhari, M.hillaryrosnerae, M.hiroshikidonoi, M.iangauldi, M.jennyphillipsae, M.jesseausubeli, M.jessemaysharkae, M.jimwhitfieldi, M.johnbrowni, M.johnburnsi, M.jonathanfranzeni, M.jonathanrosenbergi, M.jorgebaltodanoi, M.lucianocapelli. ORGILINAE: Orgilusamyrossmanae, O.carrolyoonae, O.christhompsoni, O.christinemcmahonae, O.dianalipscombae, O.ebbenielsoni, O.elizabethpennisiae, O.evertlindquisti, O.genestoermeri, O.jamesriegeri, O.jeanmillerae, O.jeffmilleri, O.jerrypowelli, O.jimtiedjei, O.johnlundbergi, O.johnpipolyi, O.jorgellorentei, O.larryspearsi, O.marlinricei, O.mellissaespinozae, O.mikesmithi, O.normplatnicki, O.peterrauchi, O.richardprimacki, O.sandraberriosae, O.sarahmirandae, O.scottmilleri, O.scottmorii, Stantoniabillalleni, S.brookejarvisae, S.donwilsoni, S.erikabjorstromae, S.garywolfi, S.henrikekmani, S.luismirandai, S.miriamzunzae, S.quentinwheeleri, S.robinkazmierae, S.ruthtifferae. PROTEROPINAE: Hebichneutestricolor Sharkey & Wharton, 1994, Proteropsiangauldi, P.vickifunkae, Michenercharlesi. RHYSIPOLINAE: Pseudorhysipolisluisfonsecai, P. mailyngonzalezaeRhysipolisjulioquirosi. ROGADINAE: Aleiodesadrianaradulovae, A.adrianforsythi, A.agnespeelleae, A.alaneaglei, A.alanflemingi, A.alanhalevii, A.alejandromasisi, A.alessandracallejae, A.alexsmithi, A.alfonsopescadori, A.alisundermieri, A.almasolisae, A.alvarougaldei, A.alvaroumanai, A.angelsolisi, A.annhowdenae, A.bobandersoni, A.carolinagodoyae, A.charlieobrieni, A.davefurthi, A.donwhiteheadi, A.doylemckeyi, A.frankhovorei, A.henryhowdeni, A.inga Shimbori & Shaw, 2020, A.johnchemsaki, A.johnkingsolveri, A.gonodontovorus Shimbori & Shaw, 2020, A.manuelzumbadoi, A.mayrabonillae, A.michelledsouzae, A.mikeiviei, A.normwoodleyi, A.pammitchellae, A.pauljohnsoni, A.rosewarnerae, A.steveashei, A.terryerwini, A.willsflowersi, Bioalfapedroleoni, B.alvarougaldei, B.rodrigogamezi, Choreborogasandydeansi, C.eladiocastroi, C.felipechavarriai, C.frankjoycei, Clinocentrusandywarreni, Cl.angelsolisi, Cystomastaxalexhausmanni, Cy.angelagonzalezae, Cy.ayaigarashiae, Hermosomastaxclavifemorus Quicke sp. nov., Heterogamusdonstonei, Pseudoyeliconesbernsweeneyi, Stiropiusbencrairi, S.berndkerni, S.edgargutierrezi, S.edwilsoni, S.ehakernae, Triraphisbillfreelandi, T.billmclarneyi, T.billripplei, T.bobandersoni, T.bobrobbinsi, T.bradzlotnicki, T.brianbrowni, T.brianlaueri, T.briannestjacquesae, T.camilocamargoi, T.carlosherrerai, T.carolinepalmerae, T.charlesmorrisi, T.chigiybinellae, T.christerhanssoni, T.christhompsoni, T.conniebarlowae, T.craigsimonsi, T.defectus Valerio, 2015, T.danielhubi, T.davidduthiei, T.davidwahli, T.federicomatarritai, T.ferrisjabri, T.mariobozai, T.martindohrni, T.matssegnestami, T.mehrdadhajibabaei, T.ollieflinti, T.tildalauerae, Yeliconesdirksteinkei, Y.markmetzi, Y.monserrathvargasae, Y.tricolor Quicke, 1996. Y.woldai Quicke, 1996.

The following new combinations are proposed: Neothlipsissmithi (Ashmead), new combination for Microdussmithi Ashmead, 1894; Neothlipsispygmaeus (Enderlein), new combination for Microduspygmaeus Enderlein, 1920; Neothlipsisunicinctus (Ashmead), new combination for Microdusunicinctus Ashmead, 1894; Therophilusanomalus (Bortoni and Penteado-Dias) new combination for Plesiocoelusanomalus Bortoni and Penteado-Dias, 2015; Aerophilusareolatus (Bortoni and Penteado-Dias) new combination for Plesiocoelusareolatus Bortoni and Penteado-Dias, 2015; Pneumagathiserythrogastra (Cameron) new combination for Agathiserythrogastra Cameron, 1905. Dolichozelecitreitarsis (Enderlein), new combination for Paniscozelecitreitarsis Enderlein, 1920. Dolichozelefuscivertex (Enderlein) new combination for Paniscozelefuscivertex Enderlein, 1920. Finally, Bassusbrooksi Sharkey, 1998 is synonymized with Agathiserythrogastra Cameron, 1905; Paniscozelegriseipes Enderlein, 1920 is synonymized with Dolichozelekoebelei Viereck, 1911; Paniscozelecarinifrons Enderlein, 1920 is synonymized with Dolichozelefuscivertex (Enderlein, 1920); and Paniscozelenigricauda Enderlein,1920 is synonymized with Dolichozelequaestor (Fabricius, 1804). (originally described as Ophionquaestor Fabricius, 1804).

DNA barcoding the Lepidoptera inventory of a large complex tropical conserved wildland, Area de Conservacion Guanacaste, northwestern Costa Rica

The 37-year ongoing inventory of the estimated 15 000 species of Lepidoptera living in the 125 000 terrestrial hectares of Area de Conservacion Guanacaste, northwestern Costa Rica, has DNA barcode documented 11 000+ species, and the simultaneous inventory of at least 6000+ species of wild-caught caterpillars, plus 2700+ species of parasitoids. The inventory began with Victorian methodologies and species-level perceptions, but it was transformed in 2004 by the full application of DNA barcoding for specimen identification and species discovery. This tropical inventory of an extraordinarily species-rich and complex multidimensional trophic web has relied upon the sequencing services provided by the Canadian Centre for DNA Barcoding, and the informatics support from BOLD, the Barcode of Life Data Systems, major tools developed by the Centre for Biodiversity Genomics at the Biodiversity Institute of Ontario, and available to all through couriers and the internet. As biodiversity information flows from these many thousands of undescribed and often look-alike species through their transformations to usable product, we see that DNA barcoding, firmly married to our centuries-old morphology-, ecology-, microgeography-, and behavior-based ways of taxonomizing the wild world, has made possible what was impossible before 2004. We can now work with all the species that we find, as recognizable species-level units of biology. In this essay, we touch on some of the details of the mechanics of actually using DNA barcoding in an inventory.

Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform

Genetic information is a valuable component of biosystematics, especially specimen identification through the use of species-specific DNA barcodes. Although many genomics applications have shifted to High-Throughput Sequencing (HTS) or Next-Generation Sequencing (NGS) technologies, sample identification (e.g., via DNA barcoding) is still most often done with Sanger sequencing. Here, we present a scalable double dual-indexing approach using an Illumina Miseq platform to sequence DNA barcode markers. We achieved 97.3% success by using half of an Illumina Miseq flowcell to obtain 658 base pairs of the cytochrome c oxidase I DNA barcode in 1,010 specimens from eleven orders of arthropods. Our approach recovers a greater proportion of DNA barcode sequences from individuals than does conventional Sanger sequencing, while at the same time reducing both per specimen costs and labor time by nearly 80%. In addition, the use of HTS allows the recovery of multiple sequences per specimen, for deeper analysis of genetic variation in target gene regions.

Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens

DNA barcoding is an efficient method to identify specimens and to detect undescribed/cryptic species. Sanger sequencing of individual specimens is the standard approach in generating large-scale DNA barcode libraries and identifying unknowns. However, the Sanger sequencing technology is, in some respects, inferior to next-generation sequencers, which are capable of producing millions of sequence reads simultaneously. Additionally, direct Sanger sequencing of DNA barcode amplicons, as practiced in most DNA barcoding procedures, is hampered by the need for relatively high-target amplicon yield, coamplification of nuclear mitochondrial pseudogenes, confusion with sequences from intracellular endosymbiotic bacteria (e.g. Wolbachia) and instances of intraindividual variability (i.e. heteroplasmy). Any of these situations can lead to failed Sanger sequencing attempts or ambiguity of the generated DNA barcodes. Here, we demonstrate the potential application of next-generation sequencing platforms for parallel acquisition of DNA barcode sequences from hundreds of specimens simultaneously. To facilitate retrieval of sequences obtained from individual specimens, we tag individual specimens during PCR amplification using unique 10-mer oligonucleotides attached to DNA barcoding PCR primers. We employ 454 pyrosequencing to recover full-length DNA barcodes of 190 specimens using 12.5% capacity of a 454 sequencing run (i.e. two lanes of a 16 lane run). We obtained an average of 143 sequence reads for each individual specimen. The sequences produced are full-length DNA barcodes for all but one of the included specimens. In a subset of samples, we also detected Wolbachia, nontarget species, and heteroplasmic sequences. Next-generation sequencing is of great value because of its protocol simplicity, greatly reduced cost per barcode read, faster throughout and added information content.

Four new species of Symmerista Hübner, 1816 (Notodontidae, Nystaleinae) from Costa Rica

The genus Symmerista Hübner (Notodontidae, Nystaleinae) is reviewed for Costa Rica, based on 49 wild-caught specimens. Four species are newly described: Symmerista luisdiegogomezi Chacón, Symmerista inbioi Chacón, Symmerista minaei Chacón and Symmerista aura Chacón. All are from the cloud forests of the Talamanca moutain range, southern Costa Rica. Photographs of the adults, male and female genitalia, and barcodes are also provided. The species Symmerista tlotzin Schaus (1892) is removed from Symmerista and assigned to the genus Elymiotis Walker as a new combination.

Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics

Conventional assessments of ecosystem sample composition are based on morphology-based or DNA barcode identification of individuals. Both approaches are costly and time-consuming, especially when applied to the large number of specimens and taxa commonly included in ecological investigations. Next-generation sequencing approaches can overcome the bottleneck of individual specimen isolation and identification by simultaneously sequencing specimens of all taxa in a bulk mixture. Here we apply multiple parallel amplification primers, multiple DNA barcode markers, 454-pyrosequencing, and Illumina MiSeq sequencing to the same sample to maximize recovery of the arthropod macrobiome and the bacterial and other microbial microbiome of a bulk arthropod sample. We validate this method with a complex sample containing 1,066 morphologically distinguishable arthropods from a tropical terrestrial ecosystem with high taxonomic diversity. Multiamplicon next-generation DNA barcoding was able to recover sequences corresponding to 91% of the distinguishable individuals in a bulk environmental sample, as well as many species present as undistinguishable tissue. 454-pyrosequencing was able to recover 10 more families of arthropods and 30 more species than did conventional Sanger sequencing of each individual specimen. The use of other loci (16S and 18S ribosomal DNA gene regions) also added the detection of species of microbes associated with these terrestrial arthropods. This method greatly decreases the time and money necessary to perform DNA-based comparisons of biodiversity among ecosystem samples. This methodology opens the door to much cheaper and increased capacity for ecological and evolutionary studies applicable to a wide range of socio-economic issues, as well as a basic understanding of how the world works.

Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens

DNA barcoding is an efficient method to identify specimens and to detect undescribed/cryptic species. Sanger sequencing of individual specimens is the standard approach in generating large-scale DNA barcode libraries and identifying unknowns. However, the Sanger sequencing technology is, in some respects, inferior to next-generation sequencers, which are capable of producing millions of sequence reads simultaneously. Additionally, direct Sanger sequencing of DNA barcode amplicons, as practiced in most DNA barcoding procedures, is hampered by the need for relatively high-target amplicon yield, coamplification of nuclear mitochondrial pseudogenes, confusion with sequences from intracellular endosymbiotic bacteria (e.g. Wolbachia) and instances of intraindividual variability (i.e. heteroplasmy). Any of these situations can lead to failed Sanger sequencing attempts or ambiguity of the generated DNA barcodes. Here, we demonstrate the potential application of next-generation sequencing platforms for parallel acquisition of DNA barcode sequences from hundreds of specimens simultaneously. To facilitate retrieval of sequences obtained from individual specimens, we tag individual specimens during PCR amplification using unique 10-mer oligonucleotides attached to DNA barcoding PCR primers. We employ 454 pyrosequencing to recover full-length DNA barcodes of 190 specimens using 12.5% capacity of a 454 sequencing run (i.e. two lanes of a 16 lane run). We obtained an average of 143 sequence reads for each individual specimen. The sequences produced are full-length DNA barcodes for all but one of the included specimens. In a subset of samples, we also detected Wolbachia, nontarget species, and heteroplasmic sequences. Next-generation sequencing is of great value because of its protocol simplicity, greatly reduced cost per barcode read, faster throughout and added information content.