‘Pliocardia' krylovata, a new species of vesicomyid clam from cold seeps along the Costa Rica Margin

2011 ◽  
Vol 92 (5) ◽  
pp. 1127-1137 ◽  
Author(s):  
Alanna M. Martin ◽  
Shana K. Goffredi
Keyword(s):  
Costa Rica ◽  
Phylogenetic Position ◽  
Cold Seeps ◽  
Thick Shell ◽  
Cytochrome C Oxidase I ◽  
Nucleotide Data ◽  
Costa Rica Margin ◽  
Vesicomyid Clam ◽  
A New Species ◽  
I Gene

‘Pliocardia' krylovata, sp. nov. (Bivalvia: Vesicomyidae: Pliocardiinae) is described from cold seeps off the coast of the Nicoya Peninsula, Costa Rica (700–1000 m depth). The phylogenetic position of‘P.' krylovatawas assessed by both morphological comparisons as well as nucleotide data from the cytochrome c oxidase I gene. Within the vesicomyids,‘P.' krylovatabelongs to the Pliocardiinae and its closest relative is‘Calyptogena' ponderosa, which also bears some morphological resemblance to the genusPliocardia, perhaps suggesting a need for reanalysis of not only its generic designation, but also the entire Pliocardiinae subfamily.‘P.' krylovatahas morphological similarities to‘Pliocardia' bowdenianaand‘Vesicomya' crenulomarginata, recently reassigned to the genusPliocardia, including a thick shell, obvious rostrum, pointed posterior end, and a sculptured shell with concentric ribs on the outer surface, to name a few. It is morphologically distinguished, however, by having a complex pallial sinus and remarkably deep escutcheon.

scholarly journals Using a Ladder of Seeps With Computer Decision Processes to Explore for and Evaluate Cold Seeps on the Costa Rica Active Margin

2021 ◽  
Vol 9 ◽  
Author(s):  
Peter Vrolijk ◽  
Lori Summa ◽  
Benjamin Ayton ◽  
Paraskevi Nomikou ◽  
Andre Hüpers ◽  
...  
Keyword(s):  
Costa Rica ◽  
Chemical Compounds ◽  
Decision Processes ◽  
Mission Planning ◽  
Cold Seeps ◽  
Fluid Sample ◽  
Deep Subsurface ◽  
Costa Rica Margin ◽  
Query Structure ◽  
Scientific Questions

Natural seeps occur at the seafloor as loci of fluid flow where the flux of chemical compounds into the ocean supports unique biologic communities and provides access to proxy samples of deep subsurface processes. Cold seeps accomplish this with minimal heat flux. While individual expertize is applied to locate seeps, such knowledge is nowhere consolidated in the literature, nor are there explicit approaches for identifying specific seep types to address discrete scientific questions. Moreover, autonomous exploration for seeps lacks any clear framework for efficient seep identification and classification. To address these shortcomings, we developed a Ladder of Seeps applied within new decision-assistance algorithms (Spock) to assist in seep exploration on the Costa Rica margin during the R/V Falkor 181210 cruise in December, 2018. This Ladder of Seeps [derived from analogous astrobiology criteria proposed by Neveu et al. (2018)] was used to help guide human and computer decision processes for ROV mission planning. The Ladder of Seeps provides a methodical query structure to identify what information is required to confirm a seep either: 1) supports seafloor life under extreme conditions, 2) supports that community with active seepage (possible fluid sample), or 3) taps fluids that reflect deep, subsurface geologic processes, but the top rung may be modified to address other scientific questions. Moreover, this framework allows us to identify higher likelihood seep targets based on existing incomplete or easily acquired data, including MBES (Multi-beam echo sounder) water column data. The Ladder of Seeps framework is based on information about the instruments used to collect seep information (e.g., are seeps detectable by the instrument with little chance of false positives?) and contextual criteria about the environment in which the data are collected (e.g., temporal variability of seep flux). Finally, the assembled data are considered in light of a Last-Resort interpretation, which is only satisfied once all other plausible data interpretations are excluded by observation. When coupled with decision-making algorithms that incorporate expert opinion with data acquired during the Costa Rica experiment, the Ladder of Seeps proved useful for identifying seeps with deep-sourced fluids, as evidenced by results of geochemistry analyses performed following the expedition.

A new species of sponge-inhabiting barnacle Neoacasta (Archaeobalanidae, Acastinae) in Kyushu, Japan

Crustaceana ◽  
2020 ◽  
Vol 93 (11-12) ◽  
pp. 1515-1532
Author(s):  
Meng-Chen Yu ◽  
Takefumi Yorisue ◽  
Gregory A. Kolbasov ◽  
Benny K. K. Chan
Keyword(s):  
New Species ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Dna Barcode ◽  
Shell Morphology ◽  
Coi Gene ◽  
Cytochrome C Oxidase I ◽  
Morphological Examination ◽  
A New Species ◽  
I Gene

Abstract This paper describes a new species of sponge-inhabiting barnacle, Neoacasta liui sp. nov., collected in Fukuoka, Kyushu, Japan. In the present study we used both the morphological examination and DNA barcode (cytochrome c oxidase I gene) to distinguish this new species from acastine species including its congeners from Neoacasta Kolbasov, 1993. Neoacasta liui sp. nov. is similar to Neoacasta glans (Lamarck, 1818) in shell morphology, but the divergence in COI gene between them reached inter-specific differences. N. liui sp. nov. is characterized by externally latticed, narrow scutum, beak-shaped tergum with wider spur, and lack of six inwardly prominent teeth on margin of basis. N. glans having an Indo-West Pacific distribution may represent a complex of cryptic species.

scholarly journals Review of Caryocolum (Lepidoptera: Gelechiidae) from the Russian Altai with description of two new species

2020 ◽  
Vol 60 (1) ◽  
pp. 65-76
Author(s):  
Jan Šumpich ◽  
Peter Huemer ◽  
Oleksiy Bidzilya
Keyword(s):  
New Species ◽  
Molecular Data ◽  
Dna Barcodes ◽  
Altai Mountains ◽  
Cytochrome C Oxidase I ◽  
Altai Republic ◽  
Two New Species ◽  
A New Species ◽  
I Gene ◽  
Russian Altai

In total, thirteen species of the genus Caryocolum Gregor & Povolný, 1954 (Lepidoptera: Gelechiidae) have been recorded from the Altai mountains in Russia so far. All available faunistic data are summarized and presented in detail. DNA barcodes of the mtCOI (cytochrome c oxidase I) gene of the majority of recorded species were studied. Molecular data and morphology support the following two species, which are described here as new to science: Caryocolum procurvella sp. nov. and C. atrum sp. nov. Caryocolum tetrameris (Meyrick, 1926) is recorded as a new species for Russia. Caryocolum blandella (Douglas, 1852) and C. viscariella (Stainton, 1855) are removed from the fauna of the Altai Republic due to misidentifications.

A new species of lambdarina (rhynchonellida, brachiopoda) from the viséan of central sudetes (Poland) and its phylogenetic position

2014 ◽  
Vol 64 (1) ◽  
pp. 1-12 ◽  
Author(s):  
Jolanta Muszer
Keyword(s):  
New Species ◽  
Full Range ◽  
Morphological Features ◽  
Phylogenetic Position ◽  
Growth Stages ◽  
Tropical Waters ◽  
Marginal Seas ◽  
Sw Poland ◽  
A New Species

Abstract A new species of micromorphic articulate brachiopod (Rhynchonellida) Lambdarina jugowiensis sp. nov., from the upper Visean (Sokolec Beds) of central Sudetes, SW Poland, is described. The studied specimens are calcified, what makes them unique in respect of their state of preservation. The material is represented by a full range of growth stages; from brephic to gerontic. Based on its morphological features and the palaeogeographical distribution of all its known species, two main evolutionary lines are proposed for the genus; the Australian and the European ones. Lambdarina was widely distributed in the equatorial-tropical waters of marginal seas of the Palaeotethys Ocean, mostly during Mississippian time.

scholarly journals Helarchaeota and co-occurring sulfate-reducing bacteria in subseafloor sediments from the Costa Rica Margin

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Rui Zhao ◽  
Jennifer F. Biddle
Keyword(s):  
Costa Rica ◽  
Metabolic Pathways ◽  
Phylogenetic Analyses ◽  
Sulfate Reducing Bacteria ◽  
Sulfate Reducing ◽  
Hydrocarbon Emission ◽  
Costa Rica Margin ◽  
Reducing Bacteria ◽  
Electron Transfers ◽  
Deep Sediments

AbstractDeep sediments host many archaeal lineages, including the Asgard superphylum which contains lineages predicted to require syntrophic partnerships. Our knowledge about sedimentary archaeal diversity and their metabolic pathways and syntrophic partners is still very limited. We present here new genomes of Helarchaeota and the co-occurring sulfate-reducing bacteria (SRB) recovered from organic-rich sediments off Costa Rica Margin. Phylogenetic analyses revealed three new metagenome-assembled genomes (MAGs) affiliating with Helarchaeota, each of which has three variants of the methyl-CoM reductase-like (MCR-like) complex that may enable them to oxidize short-chain alkanes anaerobically. These Helarchaeota have no multi-heme cytochromes but have Group 3b and Group 3c [NiFe] hydrogenases, and formate dehydrogenase, and therefore have the capacity to transfer the reducing equivalents (in the forms of hydrogen and formate) generated from alkane oxidation to external partners. We also recovered five MAGs of SRB affiliated with the class of Desulfobacteria, two of which showed relative abundances (represented by genome coverages) positively correlated with those of the three Helarchaeota. Genome analysis suggested that these SRB bacteria have the capacity of H2 and formate utilization and could facilitate electron transfers from other organisms by means of these reduced substances. Their co-occurrence and metabolic features suggest that Helarchaeota may metabolize synergistically with some SRB, and together exert an important influence on the carbon cycle by mitigating the hydrocarbon emission from sediments to the overlying ocean.

scholarly journals De Novo Genome Assembly of Limpet Bathyacmaea lactea (Gastropoda: Pectinodontidae): The First Reference Genome of a Deep-Sea Gastropod Endemic to Cold Seeps

2020 ◽  
Vol 12 (6) ◽  
pp. 905-910 ◽  
Author(s):  
Ruoyu Liu ◽  
Kun Wang ◽  
Jun Liu ◽  
Wenjie Xu ◽  
Yang Zhou ◽  
...  
Keyword(s):  
Deep Sea ◽  
Metal Ion ◽  
De Novo ◽  
Demographic History ◽  
Gene Families ◽  
Phylogenetic Position ◽  
Cold Seeps ◽  
Nitrogen And Phosphorus ◽  
De Novo Genome Assembly ◽  
A Genome

Abstract Cold seeps, characterized by the methane, hydrogen sulfide, and other hydrocarbon chemicals, foster one of the most widespread chemosynthetic ecosystems in deep sea that are densely populated by specialized benthos. However, scarce genomic resources severely limit our knowledge about the origin and adaptation of life in this unique ecosystem. Here, we present a genome of a deep-sea limpet Bathyacmaea lactea, a common species associated with the dominant mussel beds in cold seeps. We yielded 54.6 gigabases (Gb) of Nanopore reads and 77.9-Gb BGI-seq raw reads, respectively. Assembly harvested a 754.3-Mb genome for B. lactea, with 3,720 contigs and a contig N50 of 1.57 Mb, covering 94.3% of metazoan Benchmarking Universal Single-Copy Orthologs. In total, 23,574 protein-coding genes and 463.4 Mb of repetitive elements were identified. We analyzed the phylogenetic position, substitution rate, demographic history, and TE activity of B. lactea. We also identified 80 expanded gene families and 87 rapidly evolving Gene Ontology categories in the B. lactea genome. Many of these genes were associated with heterocyclic compound metabolism, membrane-bounded organelle, metal ion binding, and nitrogen and phosphorus metabolism. The high-quality assembly and in-depth characterization suggest the B. lactea genome will serve as an essential resource for understanding the origin and adaptation of life in the cold seeps.

scholarly journals A New Species of Galipea (Rutaceae-Cuspariinae) from Costa Rica and Nicaragua

1994 ◽  
Vol 4 (4) ◽  
pp. 347
Author(s):  
Jorge Gómez-Laurito ◽  
Quírico Jiménez Madrigal ◽  
Jorge Gomez-Laurito ◽  
Quirico Jimenez Madrigal
Keyword(s):  
New Species ◽  
Costa Rica ◽  
A New Species
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