Reference DNA barcodes and other mitochondrial markers for identifying Caribbean Octocorals

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

A genetic fingerprint of Amphipoda from Icelandic waters – the baseline for further biodiversity and biogeography studies

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

Pandora’s box in the deep sea –intraspecific diversity patterns and distribution of two congeneric scavenging amphipods

Paralicella tenuipes Chevreux, 1908 and Paralicella Shulenberger and Barnard, 1976 are known as widely distributed deep-sea scavenging amphipods. Some recent studies based on genetic data indicated the presence of high intraspecificvariationofP.caperescasuggestingitisaspeciescomplex.Basedon published molecular data from the Pacific and Indian oceans and new material obtained from the North and South Atlantic, we integrated the knowledge on the intraspecific variation and species distribution of the two nominal taxa. The study included analysis of three genes (COI, 16S rRNA, 28S rRNA) and revealed the existence of a single Molecular Operational Taxonomic Unit (MOTU) within P. tenuipes and six different MOTUs forming P. caperesca. The distribution pattern of the recognized lineages varied with three (P. tenuipes, MOTU 1 and MOTU 5 of P. caperesca) being widely distributed. There was evidence of contemporary population connectivity expressed by the share of the same COI haplotypes by individuals from very distant localities. At the same time no signal of recent demographic changes was observed within the studied taxa. The time-calibrated phylogeny suggested the emergence of species to be at the time of Mesozoic/Cenozoic transition that may be associated with global changes of the ocean circulation and deep sea water cooling

Sampling multiple life stages significantly increases estimates of marine biodiversity

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.Fil: Maslakova, Svetlana A.. University of Oregon; Estados UnidosFil: Ellison, Christina I.. University of Oregon; Estados UnidosFil: Hiebert, Terra C.. University of Oregon; Estados UnidosFil: Conable, Frances. University of Oregon; Estados UnidosFil: Heapy, Maureen C.. University of Oregon; Estados UnidosFil: Venera Pontón, Dagoberto E.. Smithsonian Tropical Research Institute; PanamáFil: Norenburg, Jon L.. National Museum Of Natural History. Departamento de Zoología. Area de Invertebrados; Estados UnidosFil: Schwartz, Megan L.. University of Washington; Estados UnidosFil: Boyle, Michael J.. Smithsonian Tropical Research Institute; PanamáFil: Driskell, Amy C.. National Museum Of Natural History. Departamento de Zoología. Area de Invertebrados; Estados UnidosFil: Macdonald, Kenneth S.. National Museum Of Natural History. Departamento de Zoología. Area de Invertebrados; Estados UnidosFil: Zattara, Eduardo Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; ArgentinaFil: Collin, Rachel. Smithsonian Tropical Research Institute; Panam

Building a transdisciplinary expert consensus on the cognitive drivers of performance under pressure: An international multi-panel Delphi study

IntroductionThe ability to perform optimally under pressure is critical across many occupations, including the military, first responders, and competitive sport. Despite recognition that such performance depends on a range of cognitive factors, how common these factors are across performance domains remains unclear. The current study sought to integrate existing knowledge in the performance field in the form of a transdisciplinary expert consensus on the cognitive mechanisms that underlie performance under pressure.MethodsInternational experts were recruited from four performance domains [(i) Defense; (ii) Competitive Sport; (iii) Civilian High-stakes; and (iv) Performance Neuroscience]. Experts rated constructs from the Research Domain Criteria (RDoC) framework (and several expert-suggested constructs) across successive rounds, until all constructs reached consensus for inclusion or were eliminated. Finally, included constructs were ranked for their relative importance.ResultsSixty-eight experts completed the first Delphi round, with 94% of experts retained by the end of the Delphi process. The following 10 constructs reached consensus across all four panels (in order of overall ranking): (1) Attention; (2) Cognitive Control—Performance Monitoring; (3) Arousal and Regulatory Systems—Arousal; (4) Cognitive Control—Goal Selection, Updating, Representation, and Maintenance; (5) Cognitive Control—Response Selection and Inhibition/Suppression; (6) Working memory—Flexible Updating; (7) Working memory—Active Maintenance; (8) Perception and Understanding of Self—Self-knowledge; (9) Working memory—Interference Control, and (10) Expert-suggested—Shifting.DiscussionOur results identify a set of transdisciplinary neuroscience-informed constructs, validated through expert consensus. This expert consensus is critical to standardizing cognitive assessment and informing mechanism-targeted interventions in the broader field of human performance optimization

The challenge of constructing large phylogenetic trees

The amount of sequence data available to reconstruct the evolutionary history of genes and species has increased 20-fold in the past decade. Consequently the size of phylogenetic analyses has grown as well, and phylogenetic methods, algorithms and their implementations have struggled to keep pace. Computational and other challenges raised by this burgeoning database emerge at several stages of analysis, from the optimal assembly of large data matrices from sequence databases, to the efficient construction of trees from these large matrices and the piece-wise assembly of ‘supertrees ’ from those trees in turn. A final challenge is posed by the difficulty of visualizing and making inferences from trees that might soon routinely contain thousands of species

Review of the genus Leptopilina (Hymenoptera, Cynipoidea, Figitidae, Eucoilinae) from the Eastern United States, including three newly described species

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

Review of the genus Leptopilina (Hymenoptera, Cynipoidea, Figitidae, Eucoilinae) from the Eastern United States, including three newly described species

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

Rhachotropis (Eusiroidea, Amphipoda) from the North East Atlantic

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