COI Dataset Research Articles

DNA Barcode Libraries Provide Insight into Continental Patterns of Avian Diversification

BackgroundThe causes for the higher biodiversity in the Neotropics as compared to the Nearctic and the factors promoting species diversification in each region have been much debated. The refuge hypothesis posits that high tropical diversity reflects high speciation rates during the Pleistocene, but this conclusion has been challenged. The present study investigates this matter by examining continental patterns of avian diversification through the analysis of large-scale DNA barcode libraries.Methodology and Principal FindingsStandardized COI datasets from the avifaunas of Argentina, the Nearctic, and the Palearctic were analyzed. Average genetic distances between closest congeners and sister species were higher in Argentina than in North America reflecting a much higher percentage of recently diverged species in the latter region. In the Palearctic genetic distances between closely related species appeared to be more similar to those of the southern Neotropics. Average intraspecific variation was similar in Argentina and North America, while the Palearctic fauna had a higher value due to a higher percentage of variable species. Geographic patterning of intraspecific structure was more complex in the southern Neotropics than in the Nearctic, while the Palearctic showed an intermediate level of complexity.Conclusions and SignificanceDNA barcodes can reveal continental patterns of diversification. Our analysis suggests that avian species are older in Argentina than in the Nearctic, supporting the idea that the greater diversity of the Neotropical avifauna is not caused by higher recent speciation rates. Species in the Palearctic also appear to be older than those in the Nearctic. These results, combined with the patterns of geographic structuring found in each region, suggest a major impact of Pleistocene glaciations in the Nearctic, a lesser effect in the Palearctic and a mild effect in the southern Neotropics.

Redescription of Marstonia comalensis (Pilsbry & Ferriss, 1906), a poorly known and possibly threatened freshwater gastropod from the Edwards Plateau region (Texas)

Marstonia comalensis, a poorly known nymphophiline gastropod (originally described from Comal Creek, Texas) that has often been confused with Cincinnatia integra, is re-described and the generic placement of this species, which was recently allocated to Marstonia based on unpublished evidence, is confirmed by anatomical study. Marstonia comalensis is a large congener having an ovate-conic, openly umbilicate shell and penis having a short filament and oblique, squarish lobe bearing a narrow gland along its distal edge. It is well differentiated morphologically from congeners having similar shells and penes and is also genetically divergent relative to those congeners that have been sequenced (mtCOI divergence 3.0–8.5%). A Bayesian analysis of a small COI dataset resolved Marstonia comalensis in a poorly supported sub-clade together with Marstonia hershleri, Marstonia lustrica and Marstonia pachyta. The predominantly new records presented herein indicate that Marstonia comalensis was historically distributed in the upper portions of the Brazos, Colorado, Guadalupe and Nueces River basins, south-central Texas. The species has been live collected at only 12 localities and only two of these have been re-visited since 1993. These data suggest that the conservation status of this snail, which has a critically imperiled (G1) NatureServe ranking and was recently proposed for federal listing, needs to be re-assessed.

Transfer of Cochliopa texana to Pyrgulopsis (Hydrobiidae) and description of a third congener from the lower Pecos River basin

The Phantom Cave snail (Cochliopa texana), a little-studied rissooidean gastropod that is locally endemic within the lower Pecos River basin (Texas) and currently a candidate for addition to the Federal list of threatened and endangered species, is redescribed and transferred to the hydrobiid genus Pyrgulopsis, based on shell and anatomical characters. Specimens from the type locality (Phantom Lake Spring) and San Solomon Spring are larger than those from East Sandia Spring and also differ somewhat in shell shape and shape of the central cusps of the lateral radular teeth. However genetic (mtCOI, NDI) variation within and among these geographically proximal (6– 13 km) populations was slight, providing no basis for the recognition of distinct conservation units of this imperiled species. We also describe Pyrgulopsis ignota n. sp., which was recently discovered in a different part of the lower Pecos River basin and initially confused with the Phantom Cave snail. These two species differ in shell shape, operculum morphology, and form and glandular ornament of the penis. They are also strongly differentiated genetically from each other and from (13) other regional congeners ( pairwise sequence divergence .6.3% for both genes). A Bayesian phylogenetic analysis of the COI and NDI dataset indicated that these two snails are not closely related and that P. ignota occupies a basal position relative to other regional congeners.

The actinopterygian diversity of the CEAMARC cruises: Barcoding and molecular taxonomy as a multi-level tool for new findings

In the winter 2007–2008, the CAML-CEAMARC cruises prospected in the Eastern part of the Antarctic continental shelf (Dumont d'Urville Sea, off Terre Adélie). The Australian R/V “Aurora Australis” and the Japanese R/V “Umitaka Maru” sampled in locations and at depths previously uninvestigated in this region. In total, 538 teleost specimens collected during these cruises were sequenced for the mitochondrial cytochrome oxidase I gene (COI), with the goal of barcoding a representative sampling from the campaign. The efficiency of barcoding for identification has been questioned for some taxonomic groups, thus we compared the COI results for a few of the families and genera included here (genus Trematomus, Artedidraconidae, Liparidae) to results for other markers for the same specimens. To better explore intra- and interspecific variability, sequences from previous campaigns and public databases were added to the analysis for these groups. The congruence among the results for different genes (COI, cytochrome b, D-loop and the nuclear rhodopsin retrogene) and morphological identification was used to assess the efficiency of the COI dataset at recovering species delimited using other data. Where discrepancies were present among the different data sources, a morphological re-identification was performed. The partial COI sequence yields reliable identification in most Antarctic teleost families when using their position in the clusters on a NJ tree. However, for several groups of species neither COI nor the other molecular markers investigated nor morphology recover unambiguously the currently accepted species. The taxonomy of these groups needs to be reconsidered. Identification through sequence similarity using the Barcode of Life Data System (BOLD) works for some groups, but is hampered by the incompleteness of the taxonomic coverage for antarctic teleosts. For four families (Artedidraconidae, Zoarcidae, Liparidae and Channichthyidae), several interspecific divergences were very small, and of the same magnitude as intraspecific divergences for other antarctic species. Despite these small divergences, almost all the species investigated in artedidraconids have molecular synapomorphies in the COI sequences, and a barcoding gap from the closest species. In the genus Trematomus, almost all species are well separated except for two pairs of closely related species that could not be distinguished by the other molecular markers either. For the typically hard to identify zoarcids and liparids, the results of barcoding are in agreement with in-depth morphological study. Once a reasonably complete reference dataset is available, barcoding will be invaluable to discriminate species from one another in these families. A careful comparison of the morphological and molecular results for our specimens allowed us to add numerous well-identified specimens (including some rare species) and sequences to BOLD. It helped to pinpoint the specimens that needed to be re-identified morphologically, and highlighted groups where barcoding is most helpful for specimen identification ( Chionodraco species). This large-scale project underlines the need for further taxonomic work in antarctic actinopterygians.

The cereal rust miteAbacarus hystrix(Acari: Eriophyoidea) is a complex of species: evidence from mitochondrial and nuclear DNA sequences

The cereal rust mite Abacarus hystrix (Nalepa), a significant pest of grasses, has been regarded as one of a few exceptions among eriophyoid mites with reference to the pattern of host plant utilization. At least 60 grass species have been recorded as its hosts. Thus, the mite has long been considered as a host generalist in which host specialization would not be likely to evolve. However, recent studies have revealed that host-associated specialization is possible in A. hystrix. Here, we aimed to discriminate between the three populations of A. hystrix associated with the different hosts (namely quackgrass, ryegrass and smooth brome) on the basis of mitochondrial (COI) and nuclear (D2 region of 28S rDNA) DNA sequences. The phylogenetic trees obtained with the maximum likelihood analysis of both COI and D2 region data sets showed that host-adapted strains of A. hystrix form distinct clades. Furthermore, on the COI nucleotide tree, the quackgrass- and brome-associated strains were internally divided each into two well-supported monophyletic clusters. The nucleotide D2 region data set tree showed that brome-associated strain is polyphyletic in origin. There is clear co-variation of DNA results with earlier morphological and ecological traits, as well as the results of crossing experiments. We showed that reproductively incompatible strains of A. hystrix exhibit more than 20% sequence divergence in the COI gene and 0.2% sequence divergence in the D2 28S rDNA. Our results did not confirm the placement of three host-associated strains of A. hystrix within one, ostensibly generalist, species.

DNA barcoding demystified

Only 10% of the earth’s biota has been described despite250 yearsoftaxonomicresearch(Wilson2000).Thisisinlargepart a reflection of the extent and complexity of biologicaldiversity,butitisalsotruethattraditionaltaxonomictechniquesare labourious and highly specialised, and taxonomic expertiseis very thinly spread across the myriad groups of life (Scotland

Phylogeny of Apaturinae Butterflies (Lepidoptera: Nymphalidae) Based on Mitochondrial Cytochrome Oxidase? Gene

The phylogenetic relationships of genera in the subfamily Apaturinae were examined using mtDNA sequence data from 1,471 bp of cytochrome oxidase subunit?( COI). The mitochondrial COI gene from a total of 16 species in 11 genera were sequenced to obtain mtDNA data, along with those of 4 species obtained from GenBank, to construct the MP and the NJ trees using Athyma jina, Penthema adelma, Polyura nepenthes, and Charaxes bernardus as outgroups. The transitions at the third codon positions of the COI data set were found saturated, but they were retained for analysis, because they contain the majority of the phylogenetic information. The impacts of equal weight assumptions for all characters in the parsimonious analysis were assessed by potential alternations in clades in response to different transition/transversion weighting schemes. The results indicated four distinct major groups in Apaturinae. Moreover, several well supported and stable clades were found in the Apaturinae. The study also identified undetermined taxon groups whose positions were weakly supported and were subject to changes under different weighting schemes. Within the Apaturinae, the clustering results are approximately identical to the classical morphological classification. The mtDNA data suggest the genus Mimathyma as a monophyletic group. Lelecella limenitoides and Dilipa fenestra have close relationship with very strong support in all phylogenetic trees. It also supports the taxonomic revision of removing several species from Apatura to other genera, namely Mimathyma schrenckii, M. chevana, M. nycteis, Chitoria subcaerulea, C. fasciola, C. pallas, and Helcyra subalba.

Molecular phylogeny in mytilids supports the wooden steps to deep-sea vents hypothesis

Molecular data were used to study the diversity of mytilids associated with sunken-woods sampled in the Solomon Islands and discuss the ‘wooden steps to deep-sea vent’ hypothesis proposed by Distel et al. First, COI data used in a barcoding approach confirm the presence of four distinct species. Analyses of the 18S rDNA and COI dataset then confirmed that these sunken-wood mytilids belonged to a monophyletic group including all species from deep-sea reducing environments. Finally, we analyzed the relationships within this monophyletic group that include the Bathymodiolinae using a COI dataset and a combined analysis of mitochondrial COI and ND4 genes and nuclear rDNA 18S and 28S. Our study supported the ‘wooden steps to deep-sea vent’ hypothesis: one of the sunken-wood species had a basal position within the Bathymodiolionae, and all described vent and seep mussels included in our analyses were derived taxa within Bathymodiolinae. To cite this article: S. Samadi et al., C. R. Biologies 330 (2007).

Phylogeny of Eunicida (Annelida) and Exploring Data Congruence Using a Partition Addition Bootstrap Alteration (PABA) Approach

Even though relationships within Annelida are poorly understood, Eunicida is one of only a few major annelid lineages well supported by morphology. The seven recognized eunicid families possess sclerotized jaws that include mandibles and a maxillary apparatus. The maxillary apparatuses vary in shape and number of elements, and three main types are recognized in extant taxa: ctenognath, labidognath, and prionognath. Ctenognath jaws are usually considered to represent the plesiomorphic state of Eunicida, whereas taxa with labidognath and prionognath are thought to form a derived monophyletic assemblage. However, this hypothesis has never been tested in a statistical framework even though it holds considerable importance for understanding annelid phylogeny and possibly lophotrochozoan evolution because Eunicida has the best annelid fossil record. Therefore, we used maximum likelihood and Bayesian inference approaches to reconstruct Eunicida phylogeny using sequence data from nuclear 18S and 28S rDNA genes and mitochondrial 16S rDNA and cytochrome c oxidase subunit I genes. Additionally, we conducted three different tests to investigate suitability of combining data sets. Incongruence length difference (ILD) and Shimodaira-Hasegawa (SH) test comparisons of resultant trees under different data partitions have been widely used previously but do not give a good indication as to which nodes may be causing the conflict. Thus, we developed a partition addition bootstrap alteration (PABA) approach that evaluates congruence or conflict for any given node by determining how bootstrap scores are altered when different data partitions are added. PABA shows the contribution of each partition to the phylogeny obtained in the combined analysis. Generally, the ILD test performed worse than the other approaches in detecting incongruence. Both PABA and the SH approach indicated the 28S and COI data sets add conflicting signal, but PABA is more informative for elucidating which data partition may be misleading at a given node. All our analyses indicate that the monophyly of the labidognath/prionognath taxa and even a labidognath clade (i.e., a "Eunicidae"/Onuphidae/Lumbrineridae clade) is significantly rejected. We show that the definition of both the labidognath and ctenognath jaw type does not address adequately the variation within Eunicida and thus misleads our current evolutionary understanding. Based on the presented results a symmetric maxillary apparatus with a carrier and four to six maxillae is most likely the plesiomorphic condition for Eunicida. [COI; conflicting data; fossil record; ILD; Jaw Evolution; molecular phylogeny; rDNA; SH test.].

Towards a better understanding of the higher systematics of Nymphalidae (Lepidoptera: Papilionoidea)

Research on the molecular systematics of higher taxa in the butterfly family Nymphalidae (Lepidoptera) is only just beginning. Outgroup selection is difficult at the moment due to the lack of consensus on the basal relationships of the major groups in Nymphalidae. We identify four major clades in the Nymphalidae based on a cladistic analysis of one mitochondrial gene sequence (COI, 1450 bp) and two nuclear gene sequences (EF-1α, 1064 bp, and wingless, 412–415 bp) from 54 exemplar species sampled from all currently recognized subfamilies. The COI data set was found to be highly incongruent with the nuclear data sets and a Partitioned Bremer Support analysis shows that the COI data set largely undermines support for most clades. Transitions at the third codon positions of the COI data set were highly saturated, but analyzing the combined data set with the COI third positions removed did not change the results. The major clades we found are termed the danaine clade (including Danainae), the satyrine clade (including Charaxinae, Satyrinae, Calinaginae, and Morphinae), the heliconiine clade (including Heliconiinae and Limenitidinae excluding Biblidini, Cyrestini, Pseudergolini, and Coeini) and the nymphaline clade (including Nymphalinae, Apaturinae, and Coeini, Cyrestini, Pseudergolini, and Biblidini from Limenitidinae). The heliconiine and nymphaline clades are sister groups, while the most parsimonious explanation for the combined data set places the danaine clade as the most basal large group of Nymphalidae. Our results give one of the strongest hypotheses for the subfamilial relationships within Nymphalidae. We were able to resolve the polyphyletic nature of Limenitidinae, which we recommend to be split into three subfamilies: Limenitidinae, Biblidinae, and Cyrestinae. The tribe Coeini belongs in Nymphalinae.