Population genomic dynamics of mesopelagic lanternfishes Diaphus dumerilii, Lepidophanes guentheri, and Ceratoscopelus warmingii (Family: Myctophidae) in the Gulf of Mexico

Andrea Bernard; Kimberly A Finnegan; Tracey Sutton; Ron Eytan; Max Weber; Mahmood Shivji

doi:10.1016/j.dsr.2022.103786

Population genomic dynamics of mesopelagic lanternfishes Diaphus dumerilii, Lepidophanes guentheri, and Ceratoscopelus warmingii (Family: Myctophidae) in the Gulf of Mexico

Andrea Bernard, Kimberly A Finnegan, Tracey Sutton, Ron Eytan, Max Weber, Mahmood Shivji

Research output: Contribution to journal › Article › peer-review

Abstract

Assessing the impacts of the Deepwater Horizon oil spill (DWHOS) on deep-sea fish assemblages of the Gulf of Mexico (GOM) has been hindered by an absence of baseline (pre-spill) data concerning the population genetic dynamics of these fishes. The lanternfishes (Myctophidae) are a speciose, yet understudied, taxonomic group, that comprise a significant portion of the global deep-sea biomass, making them integral members of meso- and bathy-pelagic food webs. Herein, we used a genomic approach (double digest restriction site associated DNA sequencing) to investigate the temporal genetic dynamics of three species of lanternfishes within the northern GOM in the region of the oil spill: Ceratoscopelus warmingii (N = 65, SNP = 1804), Diaphus dumerilii (N = 42, SNP = 2577), and Lepidophanes guentheri (N = 44, SNP = 3462). Fishes were sampled in 2011, and then again in 2015, and 2016, and genotyped using single nucleotide polymorphisms (SNP) markers. An additional 22 C. warmingii samples collected in 2014 from the western North Atlantic were used to assess genetic connectivity between these two regions. Overall, all three species were characterized by low levels of genetic diversity and high inbreeding coefficients, and within two of the three species ( C. warmingii and L. guentheri ), little (if any) evidence of population genetic structure was found within northern GOM waters. Conversely, significant intra-GOM genetic population structure was found for D. dumerilii , highlighting the need for a more robust population genetic survey of these fishes within the GOM to understand how populations of these fishes may respond to future environmental perturbations. In addition, significant genetic population structure was also found between sub-populations of C. warmingii from the northern GOM and western North Atlantic; with evidence of a mixture of two genetic populations co-occurring within the western North Atlantic. Given the potential for future environmental perturbations caused by expanding oil and gas extraction and climate change on GOM mesopelagic communities, rigorous population genetic assessments are required to understand the population dynamics of fishes and to safeguard the genetic diversity and resilience of this functionally important group of deep-sea fishes.

Original language	American English
Article number	103786
Journal	Deep Sea Research Part I: Oceanographic Research Papers
Volume	185
DOIs	https://doi.org/10.1016/j.dsr.2022.103786
State	Published - Apr 22 2022

Funding

This research was made possible in part by a grant from the National Oceanic and Atmospheric Administration's RESTORE Science Program under award NA19NOS4510193 to Nova Southeastern University, in part by The Gulf of Mexico Research Initiative (SA 15?21), and accessory financial support from the Save Our Seas Foundation Program Grant 157 and Guy Harvey Ocean Foundation. Data are publicly available through the Gulf of Mexico Research Initiative Information & Data Cooperative (GRIIDC) at https://data.gulfresearchinitiative.org [https://doi.org/10.7266/n7-67wg-mz19]. We thank Laura Timm for her technical advice when designing our SNP protocol, Jon Moore for his collection and taxonomic efforts, and April Cook, Nina Pruzinsky and Natalie Slayden for their invaluable help curating tissues samples and associated data. We would also like to thank the NOAA/NMFS Northeast Fisheries Science Center and the officers, crew, and science team on the NOAA ship Pisces for the collection of the Bear Seamount samples during their Deepwater Systematics Survey. Portions of this research were conducted with the advanced computing resources provided by the Texas A&M High Performance Research Computing Cluster. This research was made possible in part by a grant from the National Oceanic and Atmospheric Administration's RESTORE Science Program under award NA19NOS4510193 to Nova Southeastern University , in part by The Gulf of Mexico Research Initiative ( SA 15–21 ), and accessory financial support from the Save Our Seas Foundation Program Grant 157 and Guy Harvey Ocean Foundation . Data are publicly available through the Gulf of Mexico Research Initiative Information & Data Cooperative (GRIIDC) at https://data.gulfresearchinitiative.org [ https://doi.org/10.7266/n7-67wg-mz19] . We thank Laura Timm for her technical advice when designing our SNP protocol, Jon Moore for his collection and taxonomic efforts, and April Cook, Nina Pruzinsky and Natalie Slayden for their invaluable help curating tissues samples and associated data. We would also like to thank the NOAA/NMFS Northeast Fisheries Science Center and the officers, crew, and science team on the NOAA ship Pisces for the collection of the Bear Seamount samples during their Deepwater Systematics Survey. Portions of this research were conducted with the advanced computing resources provided by the Texas A&M High Performance Research Computing Cluster.

Funders	Funder number
Gulf of Mexico Research Initiative Information & Data Cooperative
NMFS Northeast Fisheries Science Center
Save Our Seas Foundation Program	157
National Oceanic and Atmospheric Administration	NA19NOS4510193
Gulf of Mexico Research Initiative	SA 15–21
Nova Southeastern University
Guy Harvey Ocean Foundation

ASJC Scopus Subject Areas

Aquatic Science
Oceanography

Keywords

Gulf of Mexico
Single nucleotide polymorphism
Genetic Connectivity
Genetic diversity
Myctophid
Genetic connectivity

Disciplines

Genetics and Genomics
Marine Biology
Oceanography and Atmospheric Sciences and Meteorology

Access to Document

10.1016/j.dsr.2022.103786

https://nsuworks.nova.edu/cgi/viewcontent.cgi?article=2261&context=occ_facarticlesLicense: CC BY

Cite this

Bernard, A., Finnegan, K. A., Sutton, T., Eytan, R., Weber, M., & Shivji, M. (2022). Population genomic dynamics of mesopelagic lanternfishes Diaphus dumerilii, Lepidophanes guentheri, and Ceratoscopelus warmingii (Family: Myctophidae) in the Gulf of Mexico. Deep Sea Research Part I: Oceanographic Research Papers, 185, Article 103786. https://doi.org/10.1016/j.dsr.2022.103786

Population genomic dynamics of mesopelagic lanternfishes Diaphus dumerilii, Lepidophanes guentheri, and Ceratoscopelus warmingii (Family: Myctophidae) in the Gulf of Mexico. / Bernard, Andrea; Finnegan, Kimberly A; Sutton, Tracey et al.
In: Deep Sea Research Part I: Oceanographic Research Papers, Vol. 185, 103786, 22.04.2022.

Research output: Contribution to journal › Article › peer-review

@article{1301fe488a484cb691498811bf83448b,

title = "Population genomic dynamics of mesopelagic lanternfishes Diaphus dumerilii, Lepidophanes guentheri, and Ceratoscopelus warmingii (Family: Myctophidae) in the Gulf of Mexico",

abstract = " Assessing the impacts of the Deepwater Horizon oil spill (DWHOS) on deep-sea fish assemblages of the Gulf of Mexico (GOM) has been hindered by an absence of baseline (pre-spill) data concerning the population genetic dynamics of these fishes. The lanternfishes (Myctophidae) are a speciose, yet understudied, taxonomic group, that comprise a significant portion of the global deep-sea biomass, making them integral members of meso- and bathy-pelagic food webs. Herein, we used a genomic approach (double digest restriction site associated DNA sequencing) to investigate the temporal genetic dynamics of three species of lanternfishes within the northern GOM in the region of the oil spill: Ceratoscopelus warmingii (N = 65, SNP = 1804), Diaphus dumerilii (N = 42, SNP = 2577), and Lepidophanes guentheri (N = 44, SNP = 3462). Fishes were sampled in 2011, and then again in 2015, and 2016, and genotyped using single nucleotide polymorphisms (SNP) markers. An additional 22 C. warmingii samples collected in 2014 from the western North Atlantic were used to assess genetic connectivity between these two regions. Overall, all three species were characterized by low levels of genetic diversity and high inbreeding coefficients, and within two of the three species ( C. warmingii and L. guentheri ), little (if any) evidence of population genetic structure was found within northern GOM waters. Conversely, significant intra-GOM genetic population structure was found for D. dumerilii , highlighting the need for a more robust population genetic survey of these fishes within the GOM to understand how populations of these fishes may respond to future environmental perturbations. In addition, significant genetic population structure was also found between sub-populations of C. warmingii from the northern GOM and western North Atlantic; with evidence of a mixture of two genetic populations co-occurring within the western North Atlantic. Given the potential for future environmental perturbations caused by expanding oil and gas extraction and climate change on GOM mesopelagic communities, rigorous population genetic assessments are required to understand the population dynamics of fishes and to safeguard the genetic diversity and resilience of this functionally important group of deep-sea fishes.",

keywords = "Gulf of Mexico, Single nucleotide polymorphism, Genetic Connectivity, Genetic diversity, Myctophid, Genetic connectivity",

author = "Andrea Bernard and Finnegan, {Kimberly A} and Tracey Sutton and Ron Eytan and Max Weber and Mahmood Shivji",

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doi = "10.1016/j.dsr.2022.103786",

language = "American English",

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T1 - Population genomic dynamics of mesopelagic lanternfishes Diaphus dumerilii, Lepidophanes guentheri, and Ceratoscopelus warmingii (Family: Myctophidae) in the Gulf of Mexico

AU - Bernard, Andrea

AU - Finnegan, Kimberly A

AU - Sutton, Tracey

AU - Eytan, Ron

AU - Weber, Max

AU - Shivji, Mahmood

PY - 2022/4/22

Y1 - 2022/4/22

N2 - Assessing the impacts of the Deepwater Horizon oil spill (DWHOS) on deep-sea fish assemblages of the Gulf of Mexico (GOM) has been hindered by an absence of baseline (pre-spill) data concerning the population genetic dynamics of these fishes. The lanternfishes (Myctophidae) are a speciose, yet understudied, taxonomic group, that comprise a significant portion of the global deep-sea biomass, making them integral members of meso- and bathy-pelagic food webs. Herein, we used a genomic approach (double digest restriction site associated DNA sequencing) to investigate the temporal genetic dynamics of three species of lanternfishes within the northern GOM in the region of the oil spill: Ceratoscopelus warmingii (N = 65, SNP = 1804), Diaphus dumerilii (N = 42, SNP = 2577), and Lepidophanes guentheri (N = 44, SNP = 3462). Fishes were sampled in 2011, and then again in 2015, and 2016, and genotyped using single nucleotide polymorphisms (SNP) markers. An additional 22 C. warmingii samples collected in 2014 from the western North Atlantic were used to assess genetic connectivity between these two regions. Overall, all three species were characterized by low levels of genetic diversity and high inbreeding coefficients, and within two of the three species ( C. warmingii and L. guentheri ), little (if any) evidence of population genetic structure was found within northern GOM waters. Conversely, significant intra-GOM genetic population structure was found for D. dumerilii , highlighting the need for a more robust population genetic survey of these fishes within the GOM to understand how populations of these fishes may respond to future environmental perturbations. In addition, significant genetic population structure was also found between sub-populations of C. warmingii from the northern GOM and western North Atlantic; with evidence of a mixture of two genetic populations co-occurring within the western North Atlantic. Given the potential for future environmental perturbations caused by expanding oil and gas extraction and climate change on GOM mesopelagic communities, rigorous population genetic assessments are required to understand the population dynamics of fishes and to safeguard the genetic diversity and resilience of this functionally important group of deep-sea fishes.

AB - Assessing the impacts of the Deepwater Horizon oil spill (DWHOS) on deep-sea fish assemblages of the Gulf of Mexico (GOM) has been hindered by an absence of baseline (pre-spill) data concerning the population genetic dynamics of these fishes. The lanternfishes (Myctophidae) are a speciose, yet understudied, taxonomic group, that comprise a significant portion of the global deep-sea biomass, making them integral members of meso- and bathy-pelagic food webs. Herein, we used a genomic approach (double digest restriction site associated DNA sequencing) to investigate the temporal genetic dynamics of three species of lanternfishes within the northern GOM in the region of the oil spill: Ceratoscopelus warmingii (N = 65, SNP = 1804), Diaphus dumerilii (N = 42, SNP = 2577), and Lepidophanes guentheri (N = 44, SNP = 3462). Fishes were sampled in 2011, and then again in 2015, and 2016, and genotyped using single nucleotide polymorphisms (SNP) markers. An additional 22 C. warmingii samples collected in 2014 from the western North Atlantic were used to assess genetic connectivity between these two regions. Overall, all three species were characterized by low levels of genetic diversity and high inbreeding coefficients, and within two of the three species ( C. warmingii and L. guentheri ), little (if any) evidence of population genetic structure was found within northern GOM waters. Conversely, significant intra-GOM genetic population structure was found for D. dumerilii , highlighting the need for a more robust population genetic survey of these fishes within the GOM to understand how populations of these fishes may respond to future environmental perturbations. In addition, significant genetic population structure was also found between sub-populations of C. warmingii from the northern GOM and western North Atlantic; with evidence of a mixture of two genetic populations co-occurring within the western North Atlantic. Given the potential for future environmental perturbations caused by expanding oil and gas extraction and climate change on GOM mesopelagic communities, rigorous population genetic assessments are required to understand the population dynamics of fishes and to safeguard the genetic diversity and resilience of this functionally important group of deep-sea fishes.

KW - Gulf of Mexico

KW - Single nucleotide polymorphism

KW - Genetic Connectivity

KW - Genetic diversity

KW - Myctophid

KW - Genetic connectivity

UR - https://nsuworks.nova.edu/occ_facarticles/1250

U2 - 10.1016/j.dsr.2022.103786

DO - 10.1016/j.dsr.2022.103786

M3 - Article

VL - 185

JO - Deep Sea Research Part I: Oceanographic Research Papers

JF - Deep Sea Research Part I: Oceanographic Research Papers

M1 - 103786

ER -

Population genomic dynamics of mesopelagic lanternfishes Diaphus dumerilii, Lepidophanes guentheri, and Ceratoscopelus warmingii (Family: Myctophidae) in the Gulf of Mexico

Abstract

Funding

ASJC Scopus Subject Areas

Keywords

Disciplines

Access to Document

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