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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.

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Peppermint shrimp resembling Lysmata vittata Stimpson, 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. rauli Laubenheimer & 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. californica Stimpson, 1866 in New Zealand, the first non-native record for this species. We also provide data suggesting L. dispar Hayashi, 2007 may be more widespread in the Indo-West Pacific than currently known and consider L. lipkei Okuno & Fiedler, 2010 to be a likely junior synonym. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 (mt DNA) 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 mt DNA 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. [ABSTRACT FROM AUTHOR]

Lingulids and discinids are the only brachiopods that exhibit life histories that include a feeding planktonic stage usually referred to as a "larva". 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 >20% for COI, >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. [ABSTRACT FROM AUTHOR]