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- Partial Mitochondrial Genome Sequences of Two Abyssal Sponges (Porifera Hexactinellida), Bathydorus laniger and Docosaccus maculatus
- We announce the nearly complete mitochondrial genome sequences of two hexactinellid sponges, Bathydorus laniger and Docosaccus maculatus. A contiguous region of over 15,000 bp was sequenced from each genome. An uncommon structural element was identified as a series of repetitive elements with sequences matching cob in the genome of D. maculatus.
- Kahn, Geller
- Porifera (Sponges) from Japanese Tsunami Marine Debris arriving in the Hawaiian Islands and on the Pacific coast of North America
- Twelve species of sponges (Calcarea and Demospongiae) were found on Japanese Tsunami Marine Debris (JTMD) that washed ashore in Oregon, Washington, and Hawai‘i. All taxa but one determined to species level are amphi-Pacific, with three having type localities in California (Leucosolenia eleanor Urban, 1906, Hymeniacidon sinapium de Laubenfels, 1930, and Mycale macginitei de Laubenfels, 1930). Haliclona xena de Weerdt, 1986, known previously only from western Europe (and where it is regarded as introduced from an unknown region) is here newly reported from the Tohoku coast of Honshu, as is Halisarca “dujardini Johnston, 1842”. Five species (Mycale macginitei, Hymeniacidon sinapium, Ute sp., Haliclona xena and Halisarca “dujardini”) were observed only once. Multiple lines of evidence (including lack of colonization by uniquely Eastern Pacific sponge species, the arrival in Hawai‘i of some of the same species whose only possible origin was Japan, and the low probability of coastal sponge larvae colonizing JTMD in the open ocean) indicate that the sponges on JTMD originate from the Western Pacific. Several species of sponges may have completed multiple generations on these long-distance rafts.
- Elvin, Carlton, Geller, Chapman, Miller
- The importance of standardization for biodiversity comparisons: A case study using autonomous reef monitoring structures (ARMS) and metabarcoding to measure cryptic diversity on coral reefs
- Export Date: 15 May 2017, subtitle needed to be truncated, The advancement of metabarcoding techniques, declining costs of high-Throughput sequencing and development of systematic sampling devices, such as autonomous reef monitoring structures (ARMS), have provided the means to gather a vast amount of diversity data from cryptic marine communities. However, such increased capability could also lead to analytical challenges if the methods used to examine these communities across local and global scales are not standardized. Here we compare and assess the underlying biases of four ARMS field processing methods, preservation media, and current bioinformatic pipelines in evaluating diversity from cytochrome c oxidase I metabarcoding data. Illustrating the ability of ARMS-based metabarcoding to capture a wide spectrum of biodiversity, 3,372 OTUs and twenty-eight phyla, including 17 of 33 marine metazoan phyla, were detected from 3 ARMS (2.607 m2 area) collected on coral reefs in Mo'orea, French Polynesia. Significant differences were found between processing and preservation methods, demonstrating the need to standardize methods for biodiversity comparisons. We recommend the use of a standardized protocol (NOAA method) combined with DMSO preservation of tissues for sessile macroorganisms because it gave a more accurate representation of the underlying communities, is cost effective and removes chemical restrictions associated with sample transportation. We found that sequences identified at 97% similarity increased more than 7-fold (5.1% to 38.6%) using a geographically local barcode inventory, highlighting the importance of local species inventories. Phylogenetic approaches that assign higher taxonomic ranks accrued phylum identification errors (9.7%) due to sparse taxonomic coverage of the understudied cryptic coral reef community in public databases. However, a 85% sequence identity cut-off provided more accurate results (0.7% errors) and enabled phylum level identifications of 86.3% of the sequence reads. With over 1600 ARMS deployed, standardizing methods and improving databases are imperative to provide unprecedented global baseline assessments of understudied cryptic marine species in a rapidly changing world., published
- Ransome, Geller, Timmers, Leray, Mahardini, Sembiring, Collins, Meyer