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In the deep sea, the phylogeny and biogeography of only a few taxa have been well studied. Although more than 200 species in 32 genera have been described for the asellote isopod families Desmosomatidae Sars, 1897 and Nannoniscidae Hansen, 1916 from all ocean basins, their phylogenetic relationships are not completely understood. There is little doubt about the close relationship of these families, but the taxonomic position of a number of genera is so far unknown. Based on a combined morphological phylogeny using the Hennigian method with a dataset of 107 described species and a molecular phylogeny based on three markers (COI, 16S, and 18S) with 75 species (most new to science), we could separate Desmosomatidae and Nannoniscidae as separate families. However, we could not support the concept of the subfamilies Eugerdellatinae Hessler, 1970 and Desmosomatinae Hessler, 1970. Most genera of both families were well supported, but several genera appear as para- or even polyphyletic. Within both families, convergent evolution and analogies caused difficulty in defining apomorphies for phylogenetic reconstructions and this is reflected in the results of the concatenated molecular tree. There is no biogeographic pattern in the distribution as the genera occur over the entire Atlantic and Pacific Ocean, showing no specific phylogeographical pattern. Poor resolution at deep desmosomatid nodes may reflect the long evolutionary history of the family and rapid evolutionary radiations. Supplementary Information The online version contains supplementary material available at 10.1007/s13127-021-00509-9.

Biodiversity assessments are critical for setting conservation priorities, understanding ecosystem function and establishing a baseline to monitor change. Surveys of marine biodiversity that rely almost entirely on sampling adult organisms underestimate diversity because they tend to be limited to habitat types and individuals that can be easily surveyed. Many marine animals have planktonic larvae that can be sampled from the water column at shallow depths. This life stage often is overlooked in surveys but can be used to relatively rapidly document diversity, especially for the many species that are rare or live cryptically as adults. Using DNA barcode data from samples of nemertean worms collected in three biogeographical regions—Northeastern Pacific, the Caribbean Sea and Eastern Tropical Pacific—we found that most species were collected as either benthic adults or planktonic larvae but seldom in both stages. Randomization tests show that this deficit of operational taxonomic units collected as both adults and larvae is extremely unlikely if larvae and adults were drawn from the same pool of species. This effect persists even in well-studied faunas. These results suggest that sampling planktonic larvae offers access to a different subset of species and thus significantly increases estimates of biodiversity compared to sampling adults alone. Spanish abstract is available in the electronic supplementary material.

Peppermint shrimp resembling Lysmata vittataStimpson, 1860, a species native to the Indo-West Pacific, were found in the lower Chesapeake Bay and adjacent coastal embayments in 2013, representing the first recorded introduction of this species in the northwestern Atlantic. Conflicting morphological descriptions, inconsistent morphological terminology, and limited molecular data (i.e., unresolved taxonomy), as well as the destruction of the type material of L. vittata, created uncertainty regarding proper identification. We provide the first phylogeny incorporating individuals from across the presumed native and introduced range of L. vittata. Morphological and phylogenetic analyses clearly indicate L. vittata represents a species complex of two widely divergent groups: 1) “Bruce Type” with a uniramous dorsal antennule that agrees with A.J. Bruce’s 1990 redescription of L. vittata, and 2) “Rauli Type” with a one-article accessory branch on the dorsal antennule that agrees most closely with the junior synonym L. rauliLaubenheimer & Rhyne, 2010. Given the taxonomic ambiguity surrounding L. vittata, we designate the individual used by A.J. Bruce to redescribe L. vittata and incorporated in our analyses as a neotype to fix the identity of this species. We therefore identify introduced North American and New Zealand populations as L. vittata sensu stricto and postulate that the native range spans temperate/subtropical East Asia. These data suggest that L. rauli is a valid species, which includes a possible undescribed sister species. We confirm the presence of L. californicaStimpson, 1866 in New Zealand, the first non-native record for this species. We also provide data suggesting L. disparHayashi, 2007 may be more widespread in the Indo-West Pacific than currently known and consider L. lipkeiOkuno & Fiedler, 2010 to be a likely junior synonym.

Australo-Pacific Petroica robins are known for their striking variability in sexual plumage coloration. Molecular studies in recent years have revised the taxonomy of species and subspecies boundaries across the southwest Pacific and New Guinea. However, these studies have not been able to resolve phylogenetic relationships within Petroica owing to limited sampling of the nuclear genome. Here, we sequence five nuclear introns across all species for which fresh tissue was available. Nuclear loci offer support for major geographic lineages that were first inferred from mtDNA. We find almost no shared nuclear alleles between currently recognized species within the New Zealand and Australian lineages, whereas the Pacific robin radiation has many shared alleles. Multilocus coalescent species trees based on nuclear loci support a sister relationship between the Australian lineage and the Pacific robin radiation-a node that is poorly supported by mtDNA. We also find discordance in support for a sister relationship between the similarly plumaged Rose Robin (P. rosea) and Pink Robin (P. rodinogaster). Our nuclear data complement previous mtDNA studies in suggesting that the phenotypically cryptic eastern and western populations of Australia's Scarlet Robin (P. boodang) are genetically distinct lineages at the early stages of divergence and speciation.

Molecular identification is increasingly used to speed up biodiversity surveys and laboratory experiments. However, many groups of organisms cannot be reliably identified using standard databases such as GenBank or BOLD due to lack of sequenced voucher specimens identified by experts. Sometimes a large number of sequences are available, but with too many errors to allow identification. Here we address this problem for parasitoids of Drosophila by introducing a curated open-access molecular reference database, DROP (Drosophilaparasitoids). Identifying Drosophila parasitoids is challenging and poses a major impediment to realize the full potential of this model system in studies ranging from molecular mechanisms to food webs, and in biological control of Drosophila suzukii. In DROP (http://doi.org/10.5281/zenodo.4519656), genetic data are linked to voucher specimens and, where possible, the voucher specimens are identified by taxonomists and vetted through direct comparison with primary type material. To initiate DROP, we curated 154 laboratory strains, 856 vouchers, 554 DNA sequences, 16 genomes, 14 transcriptomes, and 6 proteomes drawn from a total of 183 operational taxonomic units (OTUs): 114 described Drosophila parasitoid species and 69 provisional species. We found species richness of Drosophila parasitoids to be heavily underestimated and provide an updated taxonomic catalogue for the community. DROP offers accurate molecular identification and improves cross-referencing between individual studies that we hope will catalyze research on this diverse and fascinating model system. Our effort should also serve as an example for researchers facing similar molecular identification problems in other groups of organisms.

A novel trap designed for monitoring parasitoids of spotted-wing Drosophila (SWD) is described. This new trap utilizes host fruits that are known host substrates for SWD and chocolate or vanilla baits, yielding a more accurate measure of SWD-parasitoids populations than banana traps. Fieldwork was carried out in Michoacan, Mexico, and the dominant parasitoids captured were all Figitidae: Leptopilina boulardi Barbotin, Carton and Kelner-Pillault and Ganaspis brasiliensis Ihering. The capture of Ganaspis brasiliensis is the first record of this species in Michoacan, and using DNA ‘COI barcode’ data, this Mexican population is consistent with the G5 population. We conclude that it is possible to promote this species as a biological control agent through inoculation and conservation in organic production of blackberry against D. suzukii, through an “Augmentoria” strategy using our sentinel trap with chocolate baits and preferred host of SWD to attract more SWD-parasitoids.

The checklist by Robertson et al. (2017) of fishes from the tropical eastern Pacific included information on three members of the family Triglidae: Bellator loxias (Jordan, 1897), Prionotus ruscarius and P. stephanophrys Lockington, 1881. Unfortunately, the identification of four specimens as P. ruscarius is incorrect, as they are Bellator gymnostethus. We thank Benjamin Victor for bringing these misidentifications to our notice through his work with mtDNA sequence data from the Barcode of Life Database (BOLD: http://www.boldsystems.org). The photographs of the four specimens on the BOLD website clearly depict a Bellator species rather than a Prionotus. However, the photograph in the 2017 paper (Figure 75, page 78), is correctly identified and labelled as P. ruscarius, and this species was collected on the cruise of the Miguel Oliver discussed in Robertson et al. (2017), see Benavides Moreno et al. (2019). This correction brings the number of triglids collected on that cruise to four species.

Pacific robins exhibit one of the most complex range‐wide mosaics of sexual dichromatism and monochromatism. The evolutionary origins of this geographic mosaic remain poorly understood despite long‐standing interest from ornithologists, and its influential role in the development of Ernst Mayr's theories on speciation and the 'Biological Species Concept'. One factor limiting our understanding of the evolution of sexual plumage variation in Pacific robins is a lack of well‐resolved taxon boundaries and phylogenetic relationships in the group. Here, we use primarily historical museum specimens to obtain dense sampling of mtDNA, nuclear DNA, plumage color and morphometrics from all named taxa in the radiation in order to infer taxon boundaries and relationships. We use these data to test hypotheses about colonization history, plumage evolution and reduced island dichromatism. Our data show that the Pacific robin radiation comprises four distinct lineages, which warrant recognition as separate species – the previously recognized Norfolk robin P. multicolor and red‐capped robin P. goodenovii, and two new species we propose to name: ‘Solomon robin’ P. polymorpha Mayr, 1934 for the populations on Solomon and Bougainville Islands, and ‘Mayr's robin’ P. pusilla Peale, 1848 (in honor of Ernst Mayr's detailed work on the southwest Pacific robins) for the populations on Vanuatu, Fiji and Samoa. Our data suggest that the common ancestor of the entire Pacific robin radiation was most likely sexually dichromatic and that the radiation‐wide mosaic of sexual plumage color arose via repeated losses of elaborate plumage in males and gains of elaborate plumage in females on separate islands.

Eurycope producta Sars, 1868 and Eurycope inermis Hansen, 1916 are two widely distributed and highly abundant isopod species complexes within Icelandic waters, a region known for its highly variable environment. The two species complexes have bathymetric depth ranges from 103 to 2029 m (E. producta) and from 302 to 2113 m (E. inermis). Molecular evidence was used for species delimitation within these species complexes by analyzing nuclear (18S rDNA, H3) and mitochondrial (16S rDNA, COI) sequence data. Tree-based methods (BI and ML) and four species delimitation methods (ABGD, GMYC, NDT, PTP) were applied, in order to disentangle the two species complexes. A total of eight and four species clades could be identified within samples of the E. producta and E. inermis complexes and respectively included the closely related species E. dahli Svavarsson, 1987; E. hanseni Ohlin, 1901; and E. cornuta Sars, 1864. The morphological findings coincide with the observed molecular species clades. The elucidated species clades were geographically and bathymetrically much more restricted than previously assumed. Eight species clades featured depth spans of less than 400 m and only four species clades featured depth spans of 1000 to 1500 m. Only two species clades (E. producta sensu stricto and E. inermis sensu stricto) were found on both sides of the Greenland-Scotland Ridge. Further, species distribution maps were generated using random forest, to predict potential distributional patterns for the resolved species clades of the two species complexes. We present the first attempt of combining morphological, molecular, and species distribution models in marine isopods thus far.

Oecidiobranchus (Isopoda, Asellota) is distinctive among asellote isopod genera in that most of its known species occur in the Nordic Seas and the Arctic Ocean. Some of these species are known only from a few specimens (i.e., poorly known). We used a combined morphological and genetic approach to evaluate the diversity of Oecidiobranchus species in this region. On the basis of genetics, at least three species were recognized, representing Oecidiobranchus cf. nanseni, Oecidiobranchus cf. plebejum, and a third, probably undescribed species. Oecidiobranchus cf. plebejum was found at several locations to the north of the large Greenland-Iceland-Faeroe Ridge, while O. cf. nanseni occurred on both sides of the ridge; temporal or spatial changes during and after the last ice age may have contributed to the genetic differences of populations on each side of the ridge. The wide distribution of the genus in the Nordic Seas and the Arctic Ocean suggests that the genus has been present there for an extensive period.

We found 72 species for COI and 45 for 16 S by species delimitation among 186 (from 195 extracted) desmosomatid (144) and nannoniscid (42) sequenced specimens of a total of > 400 specimens for both families. Multiple “discovery”-type species delimitation methods were used, so that consistency across methods could be assessed: The ABGD analysis detected a barcode gap of 3–6% for COI and 4–6% for 16 S, in the whole dataset. Most putative species have a horizontally limited distribution along the Vema fracture zone, although the details depend in part on the interpretation of species delimitation analyses. Putative species were mostly restricted to the eastern or western Vema fracture zone, with only eight crossing the complete Vema fracture zone. Our data suggest that even robustly-sampled species exhibited small ranges; the range estimates calculable from present data were around 500 km, and three were on the order of 1000–2500 km. We chose an abundant, but geographically restricted species (Eugerdella egoni Tschesche and Brix sp. nov.) collected at a single site in the Vema transform fault, and two species (Prochelator barnacki Bober and Brix sp. nov. and Whoia sockei Brix and Kihara sp. nov.) with a broad, but disjunct distribution in the Vema fracture zone for taxonomic description.

Source at https://doi.org/10.3897/zookeys.731.19931. Amphipods constitute an abundant part of Icelandic deep-sea zoobenthos yet knowledge of the diversity of this fauna, particularly at the molecular level, is scarce. The present work aims to use molecular methods to investigate genetic variation of the Amphipoda sampled during two IceAGE collecting expeditions. The mitochondrial cytochrome oxidase subunit 1 (COI) of 167 individuals originally assigned to 75 morphospecies was analysed. These targeted morhospecies were readily identifiable by experts using light microscopy and representative of families where there is current ongoing taxonomic research. The study resulted in 81 Barcode Identity Numbers (BINs) (of which >90% were published for the first time), while Automatic Barcode Gap Discovery revealed the existence of 78 to 83 Molecular Operational Taxonomic Units (MOTUs). Six nominal species (Rhachotropis helleri, Arrhis phyllonyx, Deflexilodes tenuirostratus, Paroediceros propinquus, Metopa boeckii, Astyra abyssi) appeared to have a molecular variation higher than the 0.03 threshold of both p-distance and K2P usually used for amphipod species delineation. Conversely, two Oedicerotidae regarded as separate morphospecies clustered together with divergences in the order of intraspecific variation. The incongruence between the BINs associated with presently identified species and the publicly available data of the same taxa was observed in case of Paramphithoe hystrix and Amphilochus manudens. The findings from this research project highlight the necessity of supporting molecular studies with thorough morphology species analyses.

DNA barcoding is a useful tool to identify the components of mixed or bulk samples, as well as to determine individuals that lack morphologically diagnostic features. However, the reference database of DNA barcode sequences is particularly sparsely populated for marine invertebrates and for tropical taxa. We used samples collected as part of two field courses, focused on graduate training in taxonomy and systematics, to generate DNA sequences of the barcode fragments of cytochrome c oxidase subunit I (COI) and mitochondrial ribosomal 16S genes for 447 individuals, representing at least 129 morphospecies of decapod crustaceans. COI sequences for 36% (51/140) of the species and 16S sequences for 26% (37/140) of the species were new to GenBank. Automatic Barcode Gap Discovery identified 140 operational taxonomic units (OTUs) which largely coincided with the morphospecies delimitations. Barcode identifications (i.e. matches to identified sequences) were especially useful for OTUs within Synalpheus, a group that is notoriously difficult to identify and rife with cryptic species, a number of which we could not identify to species, based on morphology. Non-concordance between morphospecies and barcode OTUs also occurred in a few cases of suspected cryptic species. As mitochondrial pseudogenes are particularly common in decapods, we investigate the potential for this dataset to include pseudogenes and discuss the utility of these sequences as species identifiers (i.e. barcodes). These results demonstrate that material collected and identified during training activities can provide useful incidental barcode reference samples for under-studied taxa.

In the search for native Asian parasitoids of Drosophila suzukii, the notorious spotted-wing Drosophila (SWD), an odd new species of Eucoilinae was discovered. Leptopilina lasalleisp. nov. is herein described and diagnosed relative to other eucoilines associated with drosophilid hosts. Morphologically, L. lasallei is somewhat aberrant within Leptopilina; phylogenetically, L. lasallei is sister group to the core Leptopilina. In the process of investigating L. lasallei, a de novo molecular phylogeny of Leptopilina was generated and is included here. The integrated approach used for the characterisation of L. lasallei, and the resulting phylogeny of Leptopilina, produced data useful to select parasitoid species for SWD biological control.http://www.zoobank.org/urn:lsid:zoobank.org:act:402D504A-4616-4524-85D7-1C13A6276F06http://www.zoobank.org/urn:lsid:zoobank.org:act:402D504A-4616-4524-85D7-1C13A6276F06.

Aim: We investigate the spatiotemporal context of the diversification of Allobates, a widespread genus of Amazonian frogs with high species diversity particularly in western Amazonia. We tested if that diversity originated in situ or through repeated dispersals from other Amazonian areas and if this diversification took place during or after the Pebas system, a vast lacustrine system occupying most western Amazonia between 23 and 10 million years ago (Mya). Location: Amazonia. Taxon: Allobates (Anura: Aromobatidae). Methods: We gathered a spatially and taxonomically extensive sampling of mitochondrial DNA sequences from 932 Allobates specimens to delimit Operational Taxonomic Units (OTUs). Complete mitogenomes of these OTUs were assembled to reconstruct a time-calibrated phylogeny used to infer the historical and spatial origin of the Amazonian Allobates lineages. Results: Phylogenetic analyses and ancestral area reconstruction suggested that most of the western Amazonian lineages resulted from in situ diversification and that these events occurred between the inferred origin of the genus (25 Mya) and 10 Mya, with a possible peak between 14 and 10 Mya. Dispersal among areas mostly occurred from western Amazonia towards the Brazilian and the Guiana Shields. Closely related Allobates OTUs display an allopatric pattern of distribution, matching interfluves delimited by modern Amazonian rivers. Main Conclusions: In western Amazonia, diversification of Allobates appears to have been simultaneous with the last stages of the Pebas system (14–10 Mya). Subsequently (within the last 10 Mya), modern Amazonian river courses shaped the distribution pattern of Allobates species and possibly promoted allopatric speciation., This study benefited from an “Investissement d’Avenir” grant managed by the Agence Nationale de la Recherche (CEBA, ref. ANR-10-LABX-25-01; TULIP, ref. ANR-10-LABX-0041; ANAEE-France: ANR-11-INBS-0001). AF and FPW acknowledge the French/Brazilian GUYAMAZON program action (IRD, CNRS, CTG, CIRAD and Brazilian Fundação de Amparo à Pesquisa do Estado do Amazonas-FAPEAM 062.00962/2018) and co-coordinated by A. Fouquet and F. P. Werneck. MTR thanks Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP grant numbers: 2003/10335-8, 2011/50146-6 and NSF-FAPESP Dimensions of Biodiversity Program [grant numbers: BIOTA 2013/50297-0, NSF-DEB 1343578]) and NASA. SRR acknowledges a grant from SENESCYT (Arca de Noé Initiative). FPW thanks CNPq (Productivity Fellowship), FAPEAM, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-CAPES (Visiting Professor Fellowship) and the L’Oréal-UNESCO For Women In Science Program. AFJ is supported by the Coordenação de Aperfeiçoamento de Pessoal de Nivel Superior-Brasil (CAPES Finance Code: 88882.462010/2019-01). JM is supported by the Ministry of Culture of the Czech Republic (DKRVO 2019-20023/6.VI.b, National Museum Prague, 00023272). PJRK was supported by research grants from the Fonds voor Wetenschappelijk Onderzoek (FWO12A7614N and FWO12A7617N). AJC was supported by Research Program INV-2017-51-1432 from the School of Sciences, Universidad de los Andes. RE was supported by research grants from the Deutsche Forschungsgemeinschaft (DFG ER 589/1-1 & ER 589/2-1).

The emergence of DNA barcoding and metabarcoding opened new ways to study biological diversity, however, the completion of DNA barcode libraries is fundamental for such approaches to succeed. This dataset is a DNA barcode reference library (fragment of Cytochrome Oxydase I gene) for 2,190 specimens representing at least 540 species of shore fishes collected over 10 years at 154 sites across the four volcanic archipelagos of French Polynesia; the Austral, Gambier, Marquesas and Society Islands, a 5,000,000 km2 area. At present, 65% of the known shore fish species of these archipelagoes possess a DNA barcode associated with preserved, photographed, tissue sampled and cataloged specimens, and extensive collection locality data. This dataset represents one of the most comprehensive DNA barcoding efforts for a vertebrate fauna to date. Considering the challenges associated with the conservation of coral reef fishes and the difficulties of accurately identifying species using morphological characters, this publicly available library is expected to be helpful for both authorities and academics in various fields., Design Type(s)population data analysis objective • biodiversity assessment objectiveMeasurement Type(s)fishTechnology Type(s)taxonomic diversity assessment by targeted gene surveyFactor Type(s)Species • geographic locationSample Characteristic(s)Actinopterygii • French Polynesia • ocean biome Machine-accessible metadata file describing the reported data (ISA-Tab format)

The diversity of tropical marine invertebrates is poorly documented, especially those groups for which collecting adults is difficult. We collected the planktonic tornaria larvae of hemichordates (acorn worms) to assess their hidden diversity in the Neotropics. Larvae were retrieved in plankton tows from waters of the Pacific and Caribbean coasts of Panama, followed by DNA barcoding of mitochondrial cytochrome c oxidase subunit I (COI) and 16S ribosomal DNA to estimate their diversity in the region. With moderate sampling efforts, we discovered six operational taxonomic units (OTUs) in the Bay of Panama on the Pacific coast, in contrast to the single species previously recorded for the entire Tropical Eastern Pacific. We found eight OTUs in Bocas del Toro province on the Caribbean coast, compared to seven species documented from adults in the entire Caribbean. All OTUs differed from each other and from named acorn worm sequences in GenBank by >10% pairwise distance in COI and >2% in 16S. Two of our OTUs matched 16S hemichordate sequences in GenBank: one was an unidentified or unnamed Balanoglossus from the Caribbean of Panama, and the other was an unidentified ptychoderid larva from the Bahamas. The species accumulation curves suggest that nearly all the species have been collected and only one more species might still remain undetected in the Pacific. In contrast, the Caribbean species accumulation curve suggests that further sampling could yield more than 10 additional OTUs. Tornaria from the 14 OTUs exhibited typical planktotrophic morphologies, and, in some cases, may be distinguished by differences in pigmentation and by the number of telotrochal ciliary bands, but in general, few diagnostic differences were detected.

The emergence of DNA barcoding and metabarcoding opened new ways to study biological diversity, however, the completion of DNA barcode libraries is fundamental for such approaches to succeed. This dataset is a DNA barcode reference library (fragment of Cytochrome Oxydase I gene) for 2,190 specimens representing at least 540 species of shore fishes collected over 10 years at 154 sites across the four volcanic archipelagos of French Polynesia; the Austral, Gambier, Marquesas and Society Islands, a 5,000,000 km2area. At present, 65% of the known shore fish species of these archipelagoes possess a DNA barcode associated with preserved, photographed, tissue sampled and cataloged specimens, and extensive collection locality data. This dataset represents one of the most comprehensive DNA barcoding efforts for a vertebrate fauna to date. Considering the challenges associated with the conservation of coral reef fishes and the difficulties of accurately identifying species using morphological characters, this publicly available library is expected to be helpful for both authorities and academics in various fields.

DNA barcoding is a useful tool for documenting the diversity of metazoans. The most commonly used barcode markers, 16S and COI, are not considered suitable for species identification within some "basal" phyla of metazoans. Nevertheless metabarcoding studies of bulk mixed samples commonly use these markers and may obtain sequences for "basal" phyla. We sequenced mitochondrial DNA fragments of cytochrome oxidase c subunit I (COI), 16S ribosomal RNA (16S), NADH dehydrogenase subunits 2 (16S-ND2), 6 (ND6-ND3) and 4L (ND4L-MSH) for 27 species of Caribbean octocorals to create a reference barcode dataset and to compare the utility of COI and 16S to other markers more typically used for octocorals. The most common genera (Erythropodium, Ellisella, Briareum, Plexaurella, Muriceopsis and Pterogorgia) were effectively distinguished by small differences (5 or more substitutions or indels) in COI and 16S sequences. Gorgonia and Antillogorgia were effectively distinguished from each other by unique haplotypes, but the small genetic differences make distance approaches ineffective for these taxa. Plexaura, Pseudoplexaura and Eunicea were indistinguishable from each other but were generally effectively distinguished from other genera, further supporting the idea that these genera have undergone a rapid endemic radiation in the Caribbean.

The genus Leptopilina has historically been a poorly understood group. However, some species of Leptopilina are among the best-known model organisms for studying host-parasitoid interactions. As there is no identification system for Leptopilina in any part of the United States, we review species that were collected throughout their range in Eastern North America and those commonly used in laboratories. We provide a key for seven species, L. boulardi, L. heterotoma, L. clavipes, L. victoriae, L. decemflagella sp. n., L. maia sp. n. and L. leipsi sp. n., the last three of which are newly described here. This study is the first of its kind for Leptopilina species in North America, as our review and key were developed by examining a large number of specimens collected across broad chronological and geographic scales. This allowed us to account for the phenotypic variation within species, and helped us discover diagnostic characters. The geographic distribution and taxonomic information from this review provides a solid foundation for future research on Leptopilina.

A major focus of ecology is understanding trophic relationships and energy flows in natural systems, associated food web dynamics and changes in food webs due to introduced species. Predator-prey interactions are often assessed by examining stomach contents. However, partially digested remains may be difficult to accurately identify by traditional visual analysis. Here we evaluate the effectiveness of DNA barcoding to identify digested piscine prey remains in invasive Blue Catfish Ictalurus furcatus, non-native, but established Channel Catfish Ictalurus punctatus and native White Catfish Ameiurus catus from Chesapeake Bay, USA. Stomach contents were examined and piscine prey items were scored as lightly digested, moderately digested or severely digested. A 652 base pair region of the cytochrome c oxidase subunit I (COI-5P) mitochondrial DNA gene was sequenced for each prey item. Edited barcode sequences were compared to locally-caught and validated reference sequences in BOLD (Barcode of Life Database). A large majority of prey items were sufficiently digested to limit morphological identification (9.4 % to species and an additional 12.1 % to family). However, overall barcoding success was high (90.3 %) with little difference among the digestion classifications. Combining morphological and genetic identifications, we classified 91.6 % of fish prey items to species. Twenty-three fish species were identified, including species undergoing active restoration efforts (e.g., Alosa spp.) and commercially important species, e.g., Striped Bass Morone saxatilis, White Perch Morone americana, American Eel Anguilla rostrata and Menhaden Brevoortia tyrannus. We found DNA barcoding highly successful at identifying all but the most heavily degraded prey items and to be an efficient and effective method for obtaining diet information to strengthen the resolution of trophic analyses including diet comparisons among sympatric native and non-native predators.

Uncertain taxonomy hinders the effective prioritization of taxa for conservation. This problem is acute for understudied island populations in the southwest Pacific Ocean, which are increasingly threatened by habitat loss, predation and climate change. Here, we offer the first test of taxonomic limits and phylogenetic affinities of the iconic Pacific Robin radiation (Petroica multicolor) in order to prioritize the conservation of its nominotypical subspecies, the endangered Norfolk Island Robin (P. m. multicolor). We integrate phylogenetic analyses of ancient DNA and quantitative measures of plumage and morphometric variation to show that the Norfolk Island Robin should be recognized as a distinct species. Phenotypic and genetic datasets contradict the longstanding treatment of Pacific Robins (including Norfolk Island Robins) and Scarlet Robins (P. boodang) as a single species. Instead, we show that Norfolk Island Robins are deeply divergent from Scarlet Robins and have more genetic similarity to Red-capped Robins (P. goodenovii) than to other Pacific Robins. This finding is unrepresentative of the current taxonomic and conservation status of the Norfolk Island Robin, which we propose should be recognised as an endemic endangered species. Our study clearly shows that in the absence of contemporary tissues, ancient DNA approaches using historical museum specimens can address taxonomic questions that morphological traits are unable to resolve. Further, it highlights the need for similar studies of other threatened Norfolk fauna with uncertain taxonomic status in order to ensure appropriate conservation prioritization.

The genus Rhachotropis has the widest geographic and bathymetric distribution of all amphipod genera worldwide. Molecular and morphological investigations of specimens sampled around Iceland and off the Norwegian coast allow the first insights into the relationships of North East Atlantic Rhachotropis. The 31 cytochrome oxidase subunit I (COI) sequences generated for this study were assigned 13 Barcode Index Numbers (BINs) in the Barcode of Life database (BOLD), of which 12 are new to the database. Molecular analyses of COI and 16S sequences could not confirm a theory that depth has a greater influence on the phylogeny of Rhachotropis than geographic distance. Although the North East Atlantic is a well-studied area, our molecular investigations revealed the genus Rhachotropis may contain cryptic species, which indicates a higher biodiversity than currently known. For example, the specimens which key to Rhachotropis helleri is a complex of three COI clades, two of which cannot be identified with morphological traits. One specimen of each of the clades in the cladogram was documented by high definition photographs. A special focus was on the visual morphology of the eyes, as this character shows interspecific differences within the genus Rhachotropis in response to fixation in ethanol. Detailed morphological investigation showed that some clades thought to be indistinguishable can be separated by minute but consistent morphological characters. Datamining Genbank to examine all registered COI-sequences of R. aculeata, the only previously known Rhachotropis BIN in the North Atlantic and sub-Arctic, showed R. aculeata to be subdivided by an Arctic and a North Atlantic population. publishedVersion

International audience; To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

Field and laboratory protocols that originally led to the success of published stud− ies have previously been only briefly laid out in the methods sections of scientific publica− tions. For the sake of repeatability, we regard the details of the methodology that allowed broad−range DNA studies on deep−sea isopods too valuable to be neglected. Here, a com− prehensive summary of protocols for the retrieval of the samples, fixation on board research vessels, PCR amplification and cycle sequencing of altogether six loci (three mitochondrial and three nuclear) is provided. These were adapted from previous protocols and developed especially for asellote Isopoda from deep−sea samples but have been successfully used in some other peracarids as well. In total, about 2300 specimens of isopods, 100 amphipods and 300 tanaids were sequenced mainly for COI and 16S and partly for the other markers. Although we did not set up an experimental design, we were able to analyze amplification and sequencing success of different methods on 16S and compare success rates for COI and 16S. The primer pair 16S SF/SR was generally reliable and led to better results than univer− sal primers in all studied Janiroidea, except Munnopsidae and Dendrotionidae. The widely applied universal primers for the barcoding region of COI are problematic to use in deep−sea isopods with a success rate of 45-79% varying with family. To improve this, we recommend the development of taxon−specific primers. Key wor ds: Icelandic waters, PCR, DNA sequencing, barcoding, Janiroidea, benthos, bathyal, abyssal.

The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75–100%). Accurate assignment of higher taxa (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values >95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of the underlying database impacts accuracy of results; many outliers in our dataset could be attributed to taxonomic and/or sequencing errors in BOLD and GenBank. It seems that an accurate and complete reference library of families and genera of lifecouldprovide accurate higher level taxonomic identifications cheaply and accessibly, within years rather than decades.

Species complexes that have undergone recent radiations are often characterized by extensive allele sharing due to recent ancestry and (or) introgressive hybridization. This can result in discordant evolutionary histories of genes and heterogeneous genomes, making delineating species limits difficult. Here we examine the phylogenetic relationships among a complex group of birds, the white-headed gulls (Aves: Laridae), which offer a unique window into the speciation process due to their recent evolutionary history and propensity to hybridize. Relationships were examined among 17 species (61 populations) using a multilocus approach, including mitochondrial and nuclear intron DNA sequences and microsatellite genotype information. Analyses of microsatellite and intron data resulted in some species-based groupings, although most species were not represented by a single cluster. Considerable allele and haplotype sharing among white-headed gull species was observed; no locus contained a species-specific clade. Despite this, our multilocus approach provided better resolution among some species than previous studies. Interestingly, most clades appear to correspond to geographic locality: our BEAST analysis recovered strong support for a northern European/Icelandic clade, a southern European/Russian clade, and a western North American/canus clade, with weak evidence for a high latitude clade spanning North America and northwestern Europe. This geographical structuring is concordant with behavioral observations of pervasive hybridization in areas of secondary contact. The extent of allele and haplotype sharing indicates that ecological and sexual selection are likely not strong enough to complete reproductive isolation within several species in the white-headed gull complex. This suggests that just a few genes are driving the speciation process.

The vangas of Madagascar exhibit extreme diversity in morphology and ecology. Recent studies have shown that several other Malagasy species also are part of this endemic radiation, even as the monophyly of the clade remains in question. Using DNA sequences from 13 genes and representatives of all 15 vanga genera, we find strong support for the monophyly of the Malagasy vangids and their inclusion in a family along with six aberrant genera of shrike-like corvoids distributed in Asia and Africa. Biogeographic reconstructions of these lineages include both Asia and Africa as possible dispersal routes to Madagascar. To study patterns of speciation through time, we introduce a method that can accommodate phylogenetically non-random patterns of incomplete taxon sampling in diversification studies. We demonstrate that speciation rates in vangas decreased dramatically through time following the colonization of Madagascar. Foraging strategies of these birds show remarkable congruence with phylogenetic relationships, indicating that adaptations to feeding specializations played a role in the diversification of these birds. Vangas fit the model of an ‘adaptive radiation’ in that they show an explosive burst of speciation soon after colonization, increased diversification into novel niches and extraordinary ecomorphological diversity.

Lingulids and discinids are the only brachiopods that exhibit life histories that include a feeding planktonic stage usually referred to as a &ldquo, larva&rdquo, We collected planktotrophic brachiopod larvae from the Pacific and Caribbean coasts of Panama and took a DNA barcoding approach with mitochondrial cytochrome c oxidase subunit I (COI), mitochondrial ribosomal 16S, and nuclear ribosomal 18S genes to identify those larvae and to estimate their diversity in the region. We observed specimens from both coasts with distinct morphologies typical of lingulid and discinid larvae. COI and 16S were sequenced successfully for the lingulid larvae but failed consistently for all discinid larvae. 18S was sequenced successfully for larvae from both families. Sequence data from each gene revealed one lingulid operational taxonomic unit (OTU) from Bocas del Toro on the Caribbean coast, and one lingulid OTU from the Bay of Panama on the Pacific coast. These OTUs differed by &gt, 20% for COI, &gt, 10% for 16S and ~0.5% for 18S. Both OTUs clustered with GenBank sequences of Glottidia species, the only genus of lingulids in the Americas, but were distinct from G. pyramidata the only species reported for the Caribbean. Analysis of 18S sequence data for discinid larvae recovered 2 OTUs, one exclusively from the Pacific and one with a mixture of Pacific and Caribbean larvae. The 18S marker does not provide enough resolution to distinguish between species, and comparisons with GenBank sequences suggest that one OTU includes Pelagodiscus species, while the other may include Discradisca species. When compared with other marine invertebrates, our surveys of brachiopod larvae through DNA barcoding show relatively low levels of diversity for Panama.

Genetic variation in the melanocortin-1 receptor (MC1R) locus is responsible for color variation, particularly melanism, in many groups of vertebrates. Fairy-wrens, Maluridae, are a family of Australian and New Guinean passerines with several instances of dramatic shifts in plumage coloration, both intra- and inter-specifically. A number of these color changes are from bright blue to black plumage. In this study, we examined sequence variation at the MC1R locus in most genera and species of fairy-wrens. Our primary focus was subspecies of the white-winged fairy-wren Malurus leucopterus in which two subspecies, each endemic to islands off the western Australian coast, are black while the mainland subspecies is blue. We found fourteen variable amino acid residues within M. leucopterus, but at only one position were alleles perfectly correlated with plumage color. Comparison with other fairy-wren species showed that the blue mainland subspecies, not the black island subspecies, had a unique genotype. Examination of MC1R protein sequence variation across our sample of fairy-wrens revealed no correlation between plumage color and sequence in this group. We thus conclude that amino acid changes in the MC1R locus are not directly responsible for the black plumage of the island subspecies of M. leucopterus. Our examination of the nanostructure of feathers from both black and blue subspecies of M. leucopterus and other black and blue fairy-wren species clarifies the evolution of black plumage in this family. Our data indicate that the black white-winged fairy-wrens evolved from blue ancestors because vestiges of the nanostructure required for the production of blue coloration exist within their black feathers. Based on our phylogeographic analysis of M. leucopterus, in which the two black subspecies do not appear to be each other's closest relatives, we infer that there have been two independent evolutionary transitions from blue to black plumage. A third potential transition from blue to black appears to have occurred in a sister clade.

The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level identifications. We used BLAST queries of each sequence against the entire library and got the top ten hits resulting in 8160 hits. The percent sequence identity was reported from these hits (PIdent, range 75-100%). Accurate identification (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values > 95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all identifications were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of the underlying database impacts accuracy of results; many outliers in our dataset could be attributed to taxonomic and/or sequencing errors in BOLD and GenBank. It seems that an accurate and complete reference library of families and genera of life could provide accurate higher level taxonomic identifications cheaply and accessibly, within years rather than decades.

We analyzed nucleotide variation at four loci for 75 species to produce a phylogenetic hypothesis for the Meliphagidae, and to examine the evolution and biogeographic history of the Meliphagidae. Both maximum parsimony and Bayesian methods of phylogenetic analysis were employed. The family was found to be monophyletic, though the genera Certhionyx, Anthochaera, and Phylidonyris were not. Four major clades were recovered and the spinebills (Acanthorhynchus) formed the sister clade to the remainder of the family in most analyses. The Australian endemic arid-adapted chats (Epthianura, Ashbyia) were found to be nested deeply within the family Meliphagidae. No evidence was found to support the hypothesis of separate New Guinean and Australian endemic radiations, nor of a close phylogenetic relationship between taxa from the New Guinea highlands and those from Australian northern rainforests.

The amount of sequence data available to reconstructthe evolutionary history of genes and species hasincreased 20-fold in the past decade. Consequently thesize of phylogenetic analyses has grown as well, andphylogenetic methods, algorithms and their implemen-tations have struggled to keep pace. Computationaland other challenges raised by this burgeoning data-base emerge at several stages of analysis, from the opti-mal assembly of large data matrices from sequencedatabases, to the efficient construction of trees fromthese large matrices and the piece-wise assembly of‘supertrees’ from those trees in turn. A final challenge isposed by the difficulty of visualizing and making infer-ences from trees that might soon routinely containthousands of species.Much, if not all, of the evolutionary history of genes andspecies can be described by a phylogenetic tree [1,2].Aphylogenetic tree consists of a set of monophyletic groups,or ‘clades’. All members of a clade share a more-recentcommon ancestor with each other than with any speciesoutside of that clade. Rapid accumulation of molecularsequencedatahasspurredincreasinglylargephylogeneticanalyses across the tree of life. Nowhere is this moreevident than in plants. At one extreme, intensivecollaboration by molecular systematists has generatedlarge datasets of a few genes sampled from hundreds tothousands of species [3–5]. The plastid gene rbcL is themost notable example: it has been sequenced in .5000species and is included in one of the largest singlephylogenetic analyses to date, containing .2500 species[6]. Plant phylogenetic analyses have also become large inthe genome ‘direction’. The large number of plant modelsystems has spawned numerous EST (expressed sequencetag) projects, which are now bearing fruit as comparativephylogenetic data. One recent study [7] combinedsequences from 236 ESTs (123 000 nt) for ten angio-sperms. Both of these types of ‘extreme’ datasets poseserious challenges for the available phylogenetic methods.At the moment – perhaps fortunately – no datasets areextreme in both directions, but as genomics technologybecomes more commonplace, the size of these datasets islikely to continue to grow in numbers of species andnucleotide sites. Here, we outline some of the methodo-logical challenges associated with the trend towardincreasingly comprehensive phylogenetic analyses. Weemphasize issues arising in tree building per se, at theexpense of the crucially important and, in some respectsequally challenging, problem of multiple sequence align-ment (see Ref. [8] for an algorithmic treatment).The sparse and uneven distribution of sequence dataamong species places limits on the kinds of strategies thatare useful for constructing large phylogenetic trees. Fig. 1providesaglimpseofthisdistributionforallplantproteinsin a recent release of GenBank. A few species have beensequenced for many genes; a few genes have beensequenced for many species; but most of the potentialdata available for phylogenetic purposes is still missing.

An annotated and photographically illustrated checklist with DNA barcodes of the species of bony fishes collected during a month-long research cruise of the Spanish Research vessel B/O Miguel Oliver is presented. The vessel made trawls on the continental shelf of the Pacific coast of Central America, in November-December 2010, at depths of 108–1625 m. This list, based on 707 specimens (of a total of 876 specimens collected during the whole expedition), includes 129 species belonging to 15 orders, 61 families, and 97 genera. New information is presented on the geographical distributions of more than a third of those species, with 29 species (22.4%) representing new records from Central American waters and 17 species (13.2%) having expanded latitudinal ranges. Data on capture depths demonstrate increased depth ranges due to new minimum and/or maximum known depths for 31 species, i.e. 24% of those captured. Tissue samples from frozen specimens were used to obtain DNA barcodes of 682 (96.5%) individuals belonging to 118 species (91.4% of those recorded here), which have been made publically available in Genbank. Those data include barcodes for 84 species (65.1% of the total collected, and 77.1% of those for which barcodes were obtained) and 30 genera (30.9% of those collected) for which no species barcodes have been previously published. Barcodes of 54 species represent the first genetic sequences of any type published for those species. The abundance of new data indicate that there is still much to learn about the composition and geographical and depth distributions of the fish fauna of the shelf edge and continental slope of this region.

We assess the phylogenetic potential of ∼300,000 protein sequences sampled from Swiss-Prot and GenBank. Although only a small subset of these data was potentially phylogenetically informative, this subset retained a substantial fraction of the original taxonomic diversity. Sampling biases in the databases necessitate building phylogenetic data sets that have large numbers of missing entries. However, an analysis of two “supermatrices” suggests that even data sets with as much as 92% missing data can provide insights into broad sections of the tree of life.

Amphibians constitute a diverse yet still incompletely characterized clade of vertebrates, in which new species are still being discovered and described at a high rate. Amphibians are also increasingly endangered, due in part to disease-driven threats of extinctions. As an emergency response, conservationists have begun ex situ assurance colonies for priority species. The abundance of cryptic amphibian diversity, however, may cause problems for ex situ conservation. In this study we used a DNA barcoding approach to survey mitochondrial DNA (mtDNA) variation in captive populations of 10 species of Neotropical amphibians maintained in an ex situ assurance programme at El Valle Amphibian Conservation Center (EVACC) in the Republic of Panama. We combined these mtDNA sequences with genetic data from presumably conspecific wild populations sampled from across Panama, and applied genetic distance-based and character-based analyses to identify cryptic lineages. We found that three of ten species harboured substantial cryptic genetic diversity within EVACC, and an additional three species harboured cryptic diversity among wild populations, but not in captivity. Ex situ conservation efforts focused on amphibians are therefore vulnerable to an incomplete taxonomy leading to misidentification among cryptic species. DNA barcoding may therefore provide a simple, standardized protocol to identify cryptic diversity readily applicable to any amphibian community.

This chapter is an overview of the techniques for DNA barcoding of fishes from field collection to DNA sequence analysis. Recommendations for modifications of field protocols and best tissue sampling practices are made. A variety of DNA extraction protocols is provided, including high-throughput robot-assisted methods. A pair of well-tested forward and reverse primers for PCR amplification and sequencing are presented. These primers have been successfully used for DNA barcode on a wide array of marine fish taxa and also work well in most freshwater and cartilaginous fishes. Recipes and cycling protocols for both PCR amplification and sequencing and cleanup methods for the reaction products are provided. A method for the consistent production of high-quality DNA barcodes from DNA sequence data is given and stringent guidelines for judging the quality of raw sequence data are laid out.

Procedures and protocols common to many DNA barcoding projects are summarized. Planning for any project should emphasize front-end procedures, especially the "genetic lockdown" of collected materials for downstream genetic procedures. Steps further into the DNA barcoding process chain, such as sequencing, data processing, and other back-end functions vary slightly, if at all, among projects and are presented elsewhere in the volume. Point-of-collection sample and tissue handling and data/metadata handling are stressed. Specific predictions of the future workflows and mechanics of DNA barcoding are difficult, so focus is on that which most or all future methods and technologies will surely share.

The assembly of sequence data obtained from DNA barcodes into phylogenies or NJ trees has proven highly useful in estimating relatedness among species as well as providing a framework in which hypotheses regarding the evolution of traits or species distributions may be investigated. In this chapter, we outline the process by which DNA sequence data is assembled into a phylogenetically informative matrix, and then provide details on the methods to reconstruct NJ or phylogenetic trees that employ DNA barcode data, using only barcode data or combining barcodes with other data.

Procedures and protocols common to many DNA barcoding projects are summarized. Planning for any project should emphasize front-end procedures, especially the "genetic lockdown" of collected materials for downstream genetic procedures. Steps further into the DNA barcoding process chain, such as sequencing, data processing, and other back-end functions vary slightly, if at all, among projects and are presented elsewhere in the volume. Point-of-collection sample and tissue handling and data/metadata handling are stressed. Specific predictions of the future workflows and mechanics of DNA barcoding are difficult, so focus is on that which most or all future methods and technologies will surely share.

The assembly of sequence data obtained from DNA barcodes into phylogenies or NJ trees has proven highly useful in estimating relatedness among species as well as providing a framework in which hypotheses regarding the evolution of traits or species distributions may be investigated. In this chapter, we outline the process by which DNA sequence data is assembled into a phylogenetically informative matrix, and then provide details on the methods to reconstruct NJ or phylogenetic trees that employ DNA barcode data, using only barcode data or combining barcodes with other data.