Genetics, Environmental DNA (eDNA), Python/Biopython scripting, Molecular ecology, Bioinformatics
Professional Experience
2021 - Present Research Geneticist, USGS, Alaska Science Center, Anchorage, Alaska
2015 - 2021 Geneticist, USGS, Alaska Science Center, Anchorage, Alaska
Education and Certifications
Ph.D. 2014 University of South Florida, Tampa FL Cell and Molecular Biology
B.S. 2006 Texas A&M University at Galveston, Galveston TX Marine Biology
Science and Products
Detection of Multiple Fish Species Using Environmental DNA (eDNA), Alaska 2018
This release provides results of an environmental DNA (eDNA) study of fish identified in seven Alaskan lakes, three streams, and a positive control. Samples included replicates for multiple sampling dates and locations. The reference list and conserved primer sets to identify species present were developed using publicly available data (https://www.ncbi.nlm.nih.gov/genbank/). Highly conserved prim
Detection of Seagrass Pathogens using Environmental DNA (eDNA), North Pacific, 2016-Present
This data set is comprised of one table with sampling information and NCBI BioProject accession numbers for sequence information of this amplicon-based study targeting Labyrinthula, Phytophthora, and Halophytophthora of known pathogenic and non-pathogenic [to eelgrass (Zostera marina)] strains from eDNA samples. eDNA samples included water, sediment, and eelgrass from Notsuke Wan (Cove) Japan, Saf
Shrew (Sorex sp.) Gut Contents Identified by DNA Metabarcoding, North America, 1968-2016
This data package contains four tables related to helminths and bacteria identified in the guts of North American shrews (Genus: Sorex). Tables include: two tables of specimen information about each shrew, such as species, museum collection identification, and NCBI accession IDs; one table of NBCI GenBank accession numbers of previously identified DNA sequences used in this study to design the hel
Genetic Data from Arctic, Polar, and Saffron Cod and Walleye Pollock, Alaska and Canada, 2011-2017
Fragment data from 11 nuclear microsatellite loci and sequence data from the mitochondrial cytochrome b gene were gathered from Arctic cod (Boreogadus saida) in the Beaufort and Chukchi seas. Mitogenomic analyses of Arctic cod and three other co-distributed gadoids (Polar cod [Arctogadus glacialis], Saffron cod [Eleginus gracilis], Walleye Pollock [Gadus chalcogrammus]) were also completed. Transc
Using next generation sequencing of alpine plants to improve fecal metabarcoding diet analysis for Dall’s sheep
ObjectivesDall’s sheep (Ovis dalli dalli) are important herbivores in the mountainous ecosystems of northwestern North America, and recent declines in some populations have sparked concern. Our aim was to improve capabilities for fecal metabarcoding diet analysis of Dall’s sheep and other herbivores by contributing new sequence data for arctic and alpine plants. This expanded reference library wil
Abundance of a recently discovered Alaskan rhodolith bed in a shallow, seagrass-dominated lagoon
Rhodoliths are important foundation species of the benthic photic zone but are poorly known and rarely studied in Alaska. A bed of Lithothamnion soriferum rhodoliths was discovered in 2008 in Kinzarof Lagoon, Alaska, a shallow-water embayment dominated by eelgrass (Zostera marina). Rhodolith presence and biomass were estimated to assess trends and environmental factors that may influence rhodoli
Metabarcoding of environmental samples suggest wide distribution of eelgrass (Zostera marina) pathogens in the north Pacific
Seagrass meadows provide important ecological services to the marine environment but are declining worldwide. Although eelgrass meadows in the north Pacific are thought to be relatively healthy, few studies have assessed the presence of known disease pathogens in these meadows. In a pilot study to test the efficacy of the methods and to provide foundational disease biodiversity data in the north P
Microbiomes from biorepositories? 16S rRNA bacterial amplicon sequencing of archived and contemporary intestinal samples of wild mammals (Eulipotyphla: Soricidae)
Interest in gut microbial community composition has exploded recently as a result of the increasing ability to characterize these organisms and a growing understanding of their role in host fitness. New technologies, such as next generation amplicon (16S rRNA) sequencing, have enabled identification of bacterial communities from samples of diverse origin (e.g., fecal, skin, genital, environmental,
Environmental DNA: An emerging tool for understanding aquatic biodiversity
Field surveys for aquatic organisms provide critical information that is important for robust resource management. However, such surveys are expensive and labor intensive, particularly in large, remote landscapes like those that characterize much of Alaska. Traditionally, characterizing aquatic biodiversity necessitated the physical capture and identification of individual organisms, which require
Are migratory waterfowl vectors of seagrass pathogens?
Migratory waterfowl vector plant seeds and other tissues, but little attention has focused on the potential of avian vectoring of plant pathogens. Extensive meadows of eelgrass (Zostera marina) in southwest Alaska support hundreds of thousands of waterfowl during fall migration and may be susceptible to plant pathogens. We recovered DNA of organisms pathogenic to eelgrass from environmental samp
Micro-geographic population genetic structure within Arctic cod (Boreogadus saida) in Beaufort Sea of Alaska
Many marine organisms show significant levels of genetic heterogeneity on local spatial scales despite exhibiting limited genetic structure at large geographic scales which can be produced through a variety of mechanisms. The Arctic cod (Boreogadus saida) is a circumpolar species and is a vital species in Arctic food webs. To examine population genetic structure of Arctic cod at macro- and micro-g
Using redundant primer sets to detect multiple native Alaskan fish species from environmental DNA
Accurate and timely data regarding freshwater fish communities is important for informed decision-making by local, state, tribal, and federal land and resource managers; however, conducting traditional gear-based fish surveys can be an expensive and time-consuming process, particularly in remote areas, like those that characterize much of Alaska. To help address this challenge, we developed and te
Museum metabarcoding: a novel method revealing gut helminth communities of small mammals across space and time
Natural history collections spanning multiple decades provide fundamental historical baselines to measure and understand changing biodiversity. New technologies such as next generation DNA sequencing (NGS) have considerably increased the potential of museum specimens to address significant questions regarding the impact of environmental changes on host and parasite/pathogen dynamics. We developed
A transcriptome resource for the Arctic Cod (Boreogadus saida)
Arctic Cod (Boreogadus saida) serve as an important link in Arctic food webs and are thus considered an important species for environmental monitoring. RNA-Seq was conducted on samples from wild-collected individuals representing various age classes and tissue types to obtain as complete a transcriptome as possible on an Illumina MiSeq, which resulted in a total of 64,457 transcripts with an avera
Genomics of Arctic cod
The Arctic cod (Boreogadus saida) is an abundant marine fish that plays a vital role in the marine food web. To better understand the population genetic structure and the role of natural selection acting on the maternally-inherited mitochondrial genome (mitogenome), a molecule often associated with adaptations to temperature, we analyzed genetic data collected from 11 biparentally-inherited nuclea
Non-USGS Publications**
Quasem, I., A. N. Achille, B. A. Caddick, T. A. Carter, C. Daniels, J. A. Delaney, V. Delic, K. A. Denton, M. C. Duran, M. K. Fatica, C. M. Ference, J. P. Galkiewicz, A. M. Garcia, J. D. Hendrick, S. A. Horton, M. S. Kun, P. W. Koch, T. M. Lee, C. R. McCabe, S. McHale, L. D. McDaniel, D. M. Menning, K. J. Menning, H. Mirzaei-Souderjani, S. Mostajabian, D. A. Nicholson, C. K. Nugent, N. P. Osman, D. I. Pappas, A. M. Rocha, K. Rosario, H. Rubelmann, J. A. Schwartz, K. W. Seeley, C. M. Staley, E. M. Wallace, T. M. Wong, B. L. Zielinski, T. E. Hanson, and K. M. Scott. 2017. Peculiar citric acid cycle of hydrothermal vent chemolithoautotroph Hydrogenovibrio crunogenus, and insights into carbon metabolism by obligate autotrophs. FEMS Microbiology Letters 364(14):fnx148. doi:10.1093/femsle/fnx148
Menning, D. M., W. A. Carraher-Stross, E. D. Graham, D. N. Thomas, A. R. Phillips, R. J. Scharping, and J. R. Garey. 2017. Aquifer Discharge Drives Microbial Community Change in Karst Estuaries. Estuaries and Coasts 41(2):430-443. doi:10.1007/s12237-017-0281-7
Menning, D. M., J. G. Wynn, and J. R. Garey. 2015. Karst estuaries are governed by interactions between inland hydrological conditions and sea level. Journal of Hydrology 527:718-733. doi:10.1016/j.jhydrol.2015.05.021
Menning, D. M., L. M. Boop, E. D. Graham, and J. R. Garey. 2014. Molecular analyses of microbial abundance and diversity in the water column of anchialine caves in Mallorca, Spain. International Journal of Speleology 43:217-226. doi:10.5038/1827-806X.43.2.9
Garey, J. R. and D. M. Menning. 2012. The dynamics of community structure within a submarine coastal spring with an anchialine source. Natura Croatica 21(1):43-46.
**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
Python Scripts for Bioinformatics, 2017
Bioinformatics software repository containing python scripts intended for search and download of genetic information obtained from GenBank NCBI genetics data resources in support of developing PCR primers, targeted genetic databases, genetic analyses, and data interpretation. Includes multiple functions to streamline this process.
This repository represents an effort to strengthen the software c
Science and Products
- Science
- Data
Detection of Multiple Fish Species Using Environmental DNA (eDNA), Alaska 2018
This release provides results of an environmental DNA (eDNA) study of fish identified in seven Alaskan lakes, three streams, and a positive control. Samples included replicates for multiple sampling dates and locations. The reference list and conserved primer sets to identify species present were developed using publicly available data (https://www.ncbi.nlm.nih.gov/genbank/). Highly conserved primDetection of Seagrass Pathogens using Environmental DNA (eDNA), North Pacific, 2016-Present
This data set is comprised of one table with sampling information and NCBI BioProject accession numbers for sequence information of this amplicon-based study targeting Labyrinthula, Phytophthora, and Halophytophthora of known pathogenic and non-pathogenic [to eelgrass (Zostera marina)] strains from eDNA samples. eDNA samples included water, sediment, and eelgrass from Notsuke Wan (Cove) Japan, SafShrew (Sorex sp.) Gut Contents Identified by DNA Metabarcoding, North America, 1968-2016
This data package contains four tables related to helminths and bacteria identified in the guts of North American shrews (Genus: Sorex). Tables include: two tables of specimen information about each shrew, such as species, museum collection identification, and NCBI accession IDs; one table of NBCI GenBank accession numbers of previously identified DNA sequences used in this study to design the helGenetic Data from Arctic, Polar, and Saffron Cod and Walleye Pollock, Alaska and Canada, 2011-2017
Fragment data from 11 nuclear microsatellite loci and sequence data from the mitochondrial cytochrome b gene were gathered from Arctic cod (Boreogadus saida) in the Beaufort and Chukchi seas. Mitogenomic analyses of Arctic cod and three other co-distributed gadoids (Polar cod [Arctogadus glacialis], Saffron cod [Eleginus gracilis], Walleye Pollock [Gadus chalcogrammus]) were also completed. Transc - Multimedia
- Publications
Using next generation sequencing of alpine plants to improve fecal metabarcoding diet analysis for Dall’s sheep
ObjectivesDall’s sheep (Ovis dalli dalli) are important herbivores in the mountainous ecosystems of northwestern North America, and recent declines in some populations have sparked concern. Our aim was to improve capabilities for fecal metabarcoding diet analysis of Dall’s sheep and other herbivores by contributing new sequence data for arctic and alpine plants. This expanded reference library wilAbundance of a recently discovered Alaskan rhodolith bed in a shallow, seagrass-dominated lagoon
Rhodoliths are important foundation species of the benthic photic zone but are poorly known and rarely studied in Alaska. A bed of Lithothamnion soriferum rhodoliths was discovered in 2008 in Kinzarof Lagoon, Alaska, a shallow-water embayment dominated by eelgrass (Zostera marina). Rhodolith presence and biomass were estimated to assess trends and environmental factors that may influence rhodoliMetabarcoding of environmental samples suggest wide distribution of eelgrass (Zostera marina) pathogens in the north Pacific
Seagrass meadows provide important ecological services to the marine environment but are declining worldwide. Although eelgrass meadows in the north Pacific are thought to be relatively healthy, few studies have assessed the presence of known disease pathogens in these meadows. In a pilot study to test the efficacy of the methods and to provide foundational disease biodiversity data in the north PMicrobiomes from biorepositories? 16S rRNA bacterial amplicon sequencing of archived and contemporary intestinal samples of wild mammals (Eulipotyphla: Soricidae)
Interest in gut microbial community composition has exploded recently as a result of the increasing ability to characterize these organisms and a growing understanding of their role in host fitness. New technologies, such as next generation amplicon (16S rRNA) sequencing, have enabled identification of bacterial communities from samples of diverse origin (e.g., fecal, skin, genital, environmental,Environmental DNA: An emerging tool for understanding aquatic biodiversity
Field surveys for aquatic organisms provide critical information that is important for robust resource management. However, such surveys are expensive and labor intensive, particularly in large, remote landscapes like those that characterize much of Alaska. Traditionally, characterizing aquatic biodiversity necessitated the physical capture and identification of individual organisms, which requireAre migratory waterfowl vectors of seagrass pathogens?
Migratory waterfowl vector plant seeds and other tissues, but little attention has focused on the potential of avian vectoring of plant pathogens. Extensive meadows of eelgrass (Zostera marina) in southwest Alaska support hundreds of thousands of waterfowl during fall migration and may be susceptible to plant pathogens. We recovered DNA of organisms pathogenic to eelgrass from environmental sampMicro-geographic population genetic structure within Arctic cod (Boreogadus saida) in Beaufort Sea of Alaska
Many marine organisms show significant levels of genetic heterogeneity on local spatial scales despite exhibiting limited genetic structure at large geographic scales which can be produced through a variety of mechanisms. The Arctic cod (Boreogadus saida) is a circumpolar species and is a vital species in Arctic food webs. To examine population genetic structure of Arctic cod at macro- and micro-gUsing redundant primer sets to detect multiple native Alaskan fish species from environmental DNA
Accurate and timely data regarding freshwater fish communities is important for informed decision-making by local, state, tribal, and federal land and resource managers; however, conducting traditional gear-based fish surveys can be an expensive and time-consuming process, particularly in remote areas, like those that characterize much of Alaska. To help address this challenge, we developed and teMuseum metabarcoding: a novel method revealing gut helminth communities of small mammals across space and time
Natural history collections spanning multiple decades provide fundamental historical baselines to measure and understand changing biodiversity. New technologies such as next generation DNA sequencing (NGS) have considerably increased the potential of museum specimens to address significant questions regarding the impact of environmental changes on host and parasite/pathogen dynamics. We developedA transcriptome resource for the Arctic Cod (Boreogadus saida)
Arctic Cod (Boreogadus saida) serve as an important link in Arctic food webs and are thus considered an important species for environmental monitoring. RNA-Seq was conducted on samples from wild-collected individuals representing various age classes and tissue types to obtain as complete a transcriptome as possible on an Illumina MiSeq, which resulted in a total of 64,457 transcripts with an averaGenomics of Arctic cod
The Arctic cod (Boreogadus saida) is an abundant marine fish that plays a vital role in the marine food web. To better understand the population genetic structure and the role of natural selection acting on the maternally-inherited mitochondrial genome (mitogenome), a molecule often associated with adaptations to temperature, we analyzed genetic data collected from 11 biparentally-inherited nucleaNon-USGS Publications**
Quasem, I., A. N. Achille, B. A. Caddick, T. A. Carter, C. Daniels, J. A. Delaney, V. Delic, K. A. Denton, M. C. Duran, M. K. Fatica, C. M. Ference, J. P. Galkiewicz, A. M. Garcia, J. D. Hendrick, S. A. Horton, M. S. Kun, P. W. Koch, T. M. Lee, C. R. McCabe, S. McHale, L. D. McDaniel, D. M. Menning, K. J. Menning, H. Mirzaei-Souderjani, S. Mostajabian, D. A. Nicholson, C. K. Nugent, N. P. Osman, D. I. Pappas, A. M. Rocha, K. Rosario, H. Rubelmann, J. A. Schwartz, K. W. Seeley, C. M. Staley, E. M. Wallace, T. M. Wong, B. L. Zielinski, T. E. Hanson, and K. M. Scott. 2017. Peculiar citric acid cycle of hydrothermal vent chemolithoautotroph Hydrogenovibrio crunogenus, and insights into carbon metabolism by obligate autotrophs. FEMS Microbiology Letters 364(14):fnx148. doi:10.1093/femsle/fnx148Menning, D. M., W. A. Carraher-Stross, E. D. Graham, D. N. Thomas, A. R. Phillips, R. J. Scharping, and J. R. Garey. 2017. Aquifer Discharge Drives Microbial Community Change in Karst Estuaries. Estuaries and Coasts 41(2):430-443. doi:10.1007/s12237-017-0281-7Menning, D. M., J. G. Wynn, and J. R. Garey. 2015. Karst estuaries are governed by interactions between inland hydrological conditions and sea level. Journal of Hydrology 527:718-733. doi:10.1016/j.jhydrol.2015.05.021Menning, D. M., L. M. Boop, E. D. Graham, and J. R. Garey. 2014. Molecular analyses of microbial abundance and diversity in the water column of anchialine caves in Mallorca, Spain. International Journal of Speleology 43:217-226. doi:10.5038/1827-806X.43.2.9Garey, J. R. and D. M. Menning. 2012. The dynamics of community structure within a submarine coastal spring with an anchialine source. Natura Croatica 21(1):43-46.**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
- Software
Python Scripts for Bioinformatics, 2017
Bioinformatics software repository containing python scripts intended for search and download of genetic information obtained from GenBank NCBI genetics data resources in support of developing PCR primers, targeted genetic databases, genetic analyses, and data interpretation. Includes multiple functions to streamline this process. This repository represents an effort to strengthen the software c