Jonathan Whitney
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View article: Metabarcoding Primers for Indo‐Pacific Fishes
Metabarcoding Primers for Indo‐Pacific Fishes Open
Environmental DNA (eDNA) metabarcoding offers an effective solution to determine fish species compositions in communities across diverse environments. However, it is not clear how different metabarcoding primers perform in terms of recover…
View article: The Role of Wind on the Simulated Dispersal and Recruitment of a Commercially Important Hawaiʻi Bottomfish
The Role of Wind on the Simulated Dispersal and Recruitment of a Commercially Important Hawaiʻi Bottomfish Open
Variability in larval transport has long been hypothesized to drive recruitment fluctuations in fishes, yet evidence for these hypotheses is often lacking. Further, the origins of many of these hypotheses come from temperate to subpolar re…
View article: assessPool: a flexible pipeline for population genomic analyses of pooled sequencing data
assessPool: a flexible pipeline for population genomic analyses of pooled sequencing data Open
Despite the dramatic decrease in high-throughput sequencing costs over time, sequencing the ideal number of individuals for population genetic inference remains prohibitively expensive. When research questions require only population-level…
View article: Skimming the skaters: genome skimming improves phylogenetic resolution of Halobatinae (Hemiptera: Gerridae)
Skimming the skaters: genome skimming improves phylogenetic resolution of Halobatinae (Hemiptera: Gerridae) Open
Gerromorpha Popov, 1971 is a fascinating and diverse insect lineage that evolved about 200 Mya to spend their entire life cycle on the air–water interface and have since colonized all types of aquatic habitats. The subfamily Halobatinae Bi…
View article: Microplastics absent from reef fish in the Marshall Islands: Multistage screening methods reduced false positives
Microplastics absent from reef fish in the Marshall Islands: Multistage screening methods reduced false positives Open
Island communities, like the Republic of the Marshall Islands (RMI), depend on marine resources for food and economics, so plastic ingestion by those resources is a concern. The gastrointestinal tracts of nine species of reef fish across f…
View article: Near-island enhancement in mesopelagic micronekton assemblages off Hawaiʻi
Near-island enhancement in mesopelagic micronekton assemblages off Hawaiʻi Open
The west coast of Hawaiʻi Island hosts elevated primary production compared to offshore waters and an abundance of large pelagic animals for reasons that are not entirely understood. Here we show that the nearshore environment off the west…
View article: Genomic evidence indicates small island-resident populations and sex-biased behaviors of Hawaiian reef Manta Rays
Genomic evidence indicates small island-resident populations and sex-biased behaviors of Hawaiian reef Manta Rays Open
Background Reef manta rays ( Mobula alfredi ) are globally distributed in tropical and subtropical seas. Their life history traits (slow growth, late maturity, low reproductive output) make them vulnerable to perturbations and therefore re…
View article: The complete mitochondrial genome of the Reef Manta Ray, <i>Mobula alfredi</i>, from Hawaii
The complete mitochondrial genome of the Reef Manta Ray, <i>Mobula alfredi</i>, from Hawaii Open
We provide the complete mitochondrial genome of the reef manta ray, Mobula alfredi, using an ezRAD approach. The total length of the mitogenome was 18,166 bp and contained 13 protein-coding genes, 22 transfer RNAs genes, two ribosomal RNA …
View article: Data to support Whitney JL, Coleman RR, Deakos MH "Genomic evidence indicates small island-resident populations and sex-biased behaviors of Hawaiian Reef Manta Rays"
Data to support Whitney JL, Coleman RR, Deakos MH "Genomic evidence indicates small island-resident populations and sex-biased behaviors of Hawaiian Reef Manta Rays" Open
Datasets supporting the manuscript: Whitney JL, Coleman RR, Deakos MH "Genomic evidence indicates small island-resident populations and sex-biased behaviors of Hawaiian Reef Manta Rays". BMC Ecology and Evolution 23, 31 (2023). https://doi…
View article: Data to support Whitney JL, Coleman RR, Deakos MH "Genomic evidence indicates small island-resident populations and sex-biased behaviors of Hawaiian Reef Manta Rays"
Data to support Whitney JL, Coleman RR, Deakos MH "Genomic evidence indicates small island-resident populations and sex-biased behaviors of Hawaiian Reef Manta Rays" Open
Datasets supporting the manuscript: Whitney JL, Coleman RR, Deakos MH "Genomic evidence indicates small island-resident populations and sex-biased behaviors of Hawaiian Reef Manta Rays". BMC Ecology and Evolution 23, 31 (2023). https://doi…
View article: Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing
Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing Open
DNA barcoding is critical to conservation and biodiversity research, yet public reference databases are incomplete. Existing barcode databases are biased toward cytochrome oxidase subunit I (COI) and frequently lack associated voucher spec…
View article: Peer Review #1 of "Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing (v0.1)"
Peer Review #1 of "Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing (v0.1)" Open
skimming is an efficient and (at scale) cost-effective method to generate all mitochondrial and common nuclear DNA barcoding loci for multiple species simultaneously, which has great potential to scale for future projects and facilitate co…
View article: Peer Review #1 of "Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing (v0.2)"
Peer Review #1 of "Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing (v0.2)" Open
skimming is an efficient and (at scale) cost-effective method to generate all mitochondrial and common nuclear DNA barcoding loci for multiple species simultaneously, which has great potential to scale for future projects and facilitate co…
View article: Physical mechanisms driving biological accumulation in surface lines on coastal Hawaiian waters
Physical mechanisms driving biological accumulation in surface lines on coastal Hawaiian waters Open
Lines of smooth ocean surface water known as "slicks" appear in coastal waters worldwide and can be caused by a number of natural mechanisms. Off the western coast of the island of Hawai'i, USA, internal waves, submarine groundwater discha…
View article: Preassembly of Tylosurus crocodilus (USNM 442362)
Preassembly of Tylosurus crocodilus (USNM 442362) Open
Preassembly of Tylosurus crocodilus (USNM 442362) based on SRA data (SRR14433895), derived using SPAdes 3.15.2. All contigs less than 200 bp removed.
View article: Preassembly of Canthigaster amboinensis (USNM 442417)
Preassembly of Canthigaster amboinensis (USNM 442417) Open
Preassembly of Canthigaster amboinensis (USNM 442417) based on SRA data (SRR14163830, SRR14432035), derived using SPAdes 3.15.2. All contigs less than 200 bp removed.
View article: Preassembly of Saurida nebulosa (USNM 442473)
Preassembly of Saurida nebulosa (USNM 442473) Open
Preassembly of Saurida nebulosa (USNM 442473) based on SRA data (SRR14433894), derived using SPAdes 3.15.2. All contigs less than 200 bp removed.
View article: Preassembly of Neoniphon sammara (USNM 442483)
Preassembly of Neoniphon sammara (USNM 442483) Open
Preassembly of Neoniphon sammara (USNM 442483) based on SRA data (SRR14433902), derived using SPAdes 3.15.2. All contigs less than 200 bp removed.
View article: Preassembly of Brosme brosme (USNM 433199)
Preassembly of Brosme brosme (USNM 433199) Open
Preassembly of Brosme brosme (USNM 433199) based on SRA data (SRR14433899), derived using SPAdes 3.15.2. All contigs less than 200 bp removed.
View article: Preassembly of Scomberoides lysan (USNM 442297)
Preassembly of Scomberoides lysan (USNM 442297) Open
Preassembly of Scomberoides lysan (USNM 442297) based on SRA data (SRR14433897), derived using SPAdes 3.15.2. All contigs less than 200 bp removed.
View article: Preassembly of Forcipiger flavissimus (USNM 411089)
Preassembly of Forcipiger flavissimus (USNM 411089) Open
Preassembly of Forcipiger flavissimus (USNM 411089) based on SRA data (SRR14433901), derived using SPAdes 3.15.2. All contigs less than 200 bp removed.
View article: Preassembly of Saurida nebulosa (USNM 442473)
Preassembly of Saurida nebulosa (USNM 442473) Open
Preassembly of Saurida nebulosa (USNM 442473) based on SRA data (SRR14433894), derived using SPAdes 3.15.2. All contigs less than 200 bp removed.
View article: Preassembly of Gymnothorax fimbriatus (UNSM 395396)
Preassembly of Gymnothorax fimbriatus (UNSM 395396) Open
Preassembly of Gymnothorax fimbriatus (UNSM 395396) based on SRA data (SRR14433904), derived using SPAdes 3.15.2. All contigs less than 200 bp removed.
View article: Preassembly of Neoniphon sammara (USNM 442483)
Preassembly of Neoniphon sammara (USNM 442483) Open
Preassembly of Neoniphon sammara (USNM 442483) based on SRA data (SRR14433902), derived using SPAdes 3.15.2. All contigs less than 200 bp removed.
View article: Preassembly of Canthigaster amboinensis (USNM 442417)
Preassembly of Canthigaster amboinensis (USNM 442417) Open
Preassembly of Canthigaster amboinensis (USNM 442417) based on SRA data (SRR14163830, SRR14432035), derived using SPAdes 3.15.2. All contigs less than 200 bp removed.
View article: Preassembly of Brosme brosme (USNM 433199)
Preassembly of Brosme brosme (USNM 433199) Open
Preassembly of Brosme brosme (USNM 433199) based on SRA data (SRR14433899), derived using SPAdes 3.15.2. All contigs less than 200 bp removed.
View article: Preassembly of Gymnothorax undulatus (USNM 442319)
Preassembly of Gymnothorax undulatus (USNM 442319) Open
Preassembly of Gymnothorax undulatus (USNM 442319) based on SRA data (SRR14433896), derived using SPAdes 3.15.2. All contigs less than 200 bp removed.
View article: Preassembly of Gymnura altavela (USNM 433343)
Preassembly of Gymnura altavela (USNM 433343) Open
Preassembly of Gymnura altavela (USNM 433343) based on SRA data (SRR14433898), derived using SPAdes 3.15.2. All contigs less than 200 bp removed.