Dataset: Etelis genetics

Name: Genetic sequence identifiers for Etelis samples collected in the Indo-Pacific Ocean between 1997 and 2012
Published: 2022-04-21
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.873427.1

Spatial Extent: N:32 E:-120.1551564 S:-35 W:29.8892

Temporal Extent: 1997 - 2012

Project:

Origins of Hawaiian Reef Fishes (Hawaiian Fish Origins)

Program:

Indo-Pac Research Coordination Network (Indo-Pac RCN)

Principal Investigator:

Brian Bowen (University of Hawaii, UH)

Scientist:

Kimberly R. Andrews (University of Hawaii, UH)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2022-04-21

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Genetic sequence identifiers for Etelis samples collected in the Indo-Pacific Ocean between 1997 and 2012

Abstract:

Genetic sequence identifiers for Etelis samples collected in the Indo-Pacific Ocean between 1997 and 2012. These data were published in Andrews et al. (2021).

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2022-04-21	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.873427.1	2022-05-10

Methods & Sampling

The holotype was purchased at Yanbu fish market after being collected by hook and line in a nearby area and was deposited at the National Museum of Marine Biology & Aquarium (NMMB-P). Fifteen paratypes were obtained from Western Australia and deposited at the fish collection of California Academy of Sciences, San Francisco (CAS). These paratypes were part of a previous study using morphological and genetic data which revealed that two morphologically similar species were being identified as E. carbunculus, leading the authors to propose an undescribed species of Etelis (Andrews et al. 2016). That study generated DNA sequence data from cytochrome b (cytb) for the paratypes, and the sequences have been deposited in GenBank (Accession numbers MW151867- MW151881). See "Related Datasets" for links to the NCBI Popsets that contain these sequences.

[See Related Dataset "Etelis morphology" https://www.bco-dmo.org/dataset/873174 for morphological measurements, meristics for the Etelis samples. The column "Field_ID" can be used to relate the Etelis genetics and Etelis morphology datasets.]

DNA sequences from cytb and cytochrome oxidase I (COI) were obtained from the E. boweni holotype and four E. radiosus specimens from the Yanbu fish market using previously described protocols (Andrews et al. 2016). The sequences were aligned with sequences used in phylogenetic analyses in Andrews et al. 2016, including cytb and COI sequences from six E. boweni and six E. carbunculus specimens collected across the Indo-Pacific, along with sequences from all other recognized Etelis species (six E. coruscans specimens, seven E. radiosus specimens, five E. oculatus specimens), and one specimen from each of two outgroups (Pristipomoides filamentosus and Aphareus rutilans). All sequences were then trimmed to a common length for each locus, for a total of 375 bp for cytb and 599 bp for COI.

Location: Indo-Pacific

Species List:

ScientificName,AphiaID,LSID

Aphareus rutilans,218468,urn:lsid:marinespecies.org:taxname:218468

Etelis boweni,1536489,urn:lsid:marinespecies.org:taxname:1536489

Etelis carbunculus,212545,urn:lsid:marinespecies.org:taxname:212545

Etelis coruscans,212544,urn:lsid:marinespecies.org:taxname:212544

Etelis oculatus,159789,urn:lsid:marinespecies.org:taxname:159789

Etelis radiosus,276518,urn:lsid:marinespecies.org:taxname:276518

Pristipomoides filamentosus,218511,urn:lsid:marinespecies.org:taxname:218511

Data Processing Description

Maximum likelihood phylogenetic analysis was conducted with concatenated cytb and COI sequences using the GTR-GAMMA model in RAxML (Stamatakis 2014) with sequence data partitioned by locus, and parameters and rates allowed to vary between partitions. We first conducted 50 maximum likelihood searches with distinct starting trees, and then performed 1,000 bootstrap replicates on the best-scoring tree. Sequence data generated for this study were deposited in GenBank (accession numbers MW138043- MW138047, MW151862- MW151866).

BCO-DMO Data Manager Processing Notes:

* Exact locations for these samples are not available due to fish market acquisition. The region is known ("Indo-Pacific"). Bounding box coordinates were calculated in python using the multipolygon from marineregions.org ( MRID: 14289).

* A unique list of scientific names in this dataset were matched using the World Register of Marine Species taxa match tool. All names exactly matched the accepted synonym of a species name on 2022-04-22.
* location names delimited with a column in the data changed to semicolon-delimited (for csv support).

Data Files

File
etelis_genetics.csv (Comma Separated Values (.csv), 4.84 KB) MD5:b267c2924dfd4e5cd9674ee1b5e2f087 Primary data file for dataset ID 873427

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1558852

Deployments

None available yet

Instruments

None available yet

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Field_ID	Field ID: sample identifier	unitless	sample
Species	Species (Genus species)	unitless	species
Status	Status: specimen status	unitless	sample_descrip
Sample_Location	Sample location	unitless	site
cytb	cytb: NCBI GenBank accession number for cytochrome b sequence	unitless	Genbank_accession
COI	COI: NCBI GenBank accession number for cytochrome oxidase I sequence	unitless	Genbank_accession
Reference	Reference: specimen citation	unitless	reference_paper

Database

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Dataset: Etelis genetics