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Nathan A Johnson, Ph.D.

Nathan Johnson is a Research Biologist at the USGS Wetland and Aquatic Research Center. 

EDUCATION

Ph.D., Fisheries and Aquatic Sciences, University of Florida

M.S., Fisheries and Wildlife Sciences, Virginia Tech University

B.S., Fisheries Science, Virginia Tech University

RESEARCH

Nathan Johnson's research focuses on investigating species boundaries, distributions, and conservation priorities of freshwater mussels in the Southeast.  Raised in eastern Virginia, Nate received both his bachelor’s and master’s degrees from the Fisheries and Wildlife Department at Virginia Tech and earned his Ph.D. at the University of Florida.  His undergraduate research focused on conservation genetics and propagation of endangered freshwater mussels and fishes.  For his master’s, Nate looked at the genetics of disease resistance in rainbow trout at the USDA-National Center for Cool and Coldwater Aquaculture in Leetown, WV. By developing new molecular markers to trace pedigrees and populations structure, he identified associations between major histocompatibility genes and disease resistance. His dissertation research resolved long-standing uncertainties about the systematics of freshwater mussels that will aid in the development of more effective conservation management strategies.  This includes documenting mussel diversity in rivers of the North American Coastal Plain using DNA barcoding and evaluating the processes responsible for their current geographic distribution (phylogeography).  He is active in a variety of professional societies including the American Fisheries Society and the Freshwater Mollusk Conservation Society and currently partnered with the Florida Museum, the Smithsonian Institute, Florida Fish and Wildlife Conservation Commission, and the US Fish and Wildlife Service. Outside of professional interests, he enjoys traveling, mountain biking, fishing, and surfing.

Science and Products

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Inflated Heelsplitter (Potamilus inflatus)

Development and Implementation of Environmental DNA (eDNA) Tools to Aid Listing and Recovery Efforts for Imperiled and Common Freshwater Mussels

Researchers will develop and optimize an eDNA assay to delineate the current distribution of P. inflatus. The assay will then be used to provide up-to-date distributional information and detection rates for P. inflatus in the Pearl River basin.
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Species Management Research Program, Wetland and Aquatic Research Center
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Development and Implementation of Environmental DNA (eDNA) Tools to Aid Listing and Recovery Efforts for Imperiled and Common Freshwater Mussels

Researchers will develop and optimize an eDNA assay to delineate the current distribution of P. inflatus. The assay will then be used to provide up-to-date distributional information and detection rates for P. inflatus in the Pearl River basin.
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Figure 2. Photo illustrating difficulties distinguishing between federally endangered and common freshwater mussel species

Using Molecular Tools to Recalibrate Freshwater Mussel Taxonomy with a Focus on Imperiled Species

Freshwater mussels of the family Unionidae, also known as naiads, pearly mussels, freshwater clams, or unionids, are a diverse group of bivalve mollusks that are distributed on every continent except Antarctica. Approximately 300 species are known from the United States, with most of this diversity residing in rivers of the Southeast where many endemic taxa have evolved.
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Ecosystems Mission Area, Species Management Research Program, Wetland and Aquatic Research Center
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Using Molecular Tools to Recalibrate Freshwater Mussel Taxonomy with a Focus on Imperiled Species

Freshwater mussels of the family Unionidae, also known as naiads, pearly mussels, freshwater clams, or unionids, are a diverse group of bivalve mollusks that are distributed on every continent except Antarctica. Approximately 300 species are known from the United States, with most of this diversity residing in rivers of the Southeast where many endemic taxa have evolved.
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Map of habitat for Imperiled Freshwater Mussel Species in the S

Life History Characterization and Host Fish Identification for Federally Listed and Imperiled Freshwater Mussel Species in the Suwannee River Basin in Georgia and Florida

Freshwater mussels are considered the most imperiled group of animals in the United States. These animals provide valuable ecological services by filtering water, sequestering nutrients, and providing forage for migratory birds, small mammals, and turtles. They also have a unique and complex life cycle that makes them especially vulnerable to human disturbances. It includes a parasitic larval...
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Ecosystems Mission Area, Species Management Research Program, Wetland and Aquatic Research Center
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Life History Characterization and Host Fish Identification for Federally Listed and Imperiled Freshwater Mussel Species in the Suwannee River Basin in Georgia and Florida

Freshwater mussels are considered the most imperiled group of animals in the United States. These animals provide valuable ecological services by filtering water, sequestering nutrients, and providing forage for migratory birds, small mammals, and turtles. They also have a unique and complex life cycle that makes them especially vulnerable to human disturbances. It includes a parasitic larval...
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Evaluation of Stream Reaches for Mussel Reintroduction in the Upper Coosa Watershed, NW Georgia

Evaluation of Stream Reaches for Mussel Reintroduction in the Upper Coosa Watershed, NW Georgia

The Conasauga River in northwest Georgia and southeast Tennessee harbors the majority of mussel diversity still found in the Georgia portion of the Upper Coosa Basin. While the Conasauga historically supported at least 44 mussel species, only about 20 species remain.
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Ecosystems Mission Area, Species Management Research Program, Wetland and Aquatic Research Center
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Evaluation of Stream Reaches for Mussel Reintroduction in the Upper Coosa Watershed, NW Georgia

The Conasauga River in northwest Georgia and southeast Tennessee harbors the majority of mussel diversity still found in the Georgia portion of the Upper Coosa Basin. While the Conasauga historically supported at least 44 mussel species, only about 20 species remain.
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Molecular and distributional data used to investigate misidentifications, population genetic diversity, and spatiotemporal trends in distribution for Pleurobema riddellii to help guide ESA listing decisions

We provide genetic and distribution data for the Louisiana Pigtoe, Pleorubema riddellii, to guide decisions related to federal protection for the species under the U.S. Endangered Species Act. Our final dataset includes 125 COI sequences generated as part of our study representing P. riddellii from eight North American river basins. This includes the COI sequence we generated from a museum specime
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Wetland and Aquatic Research Center

Molecular data and results needed to better understand codiversification of freshwater mussels (Unionidae: Quadrulini) and their parasitic larval hosts

The North American freshwater mussel tribe Quadrulini has a suite of life history adaptations, however, the evolution of life histories in this group has yet to be explored using comparative phylogenetic methods. Here we provide the AHE DNA sequence alignment representing 27 species from the subfamily Ambleminae that was used to estimate a phylogenomic reconstruction of Quadrulini. Additionally, w
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Wetland and Aquatic Research Center

Molecular, morphological, and distributional data supporting the recognition of an undescribed freshwater mussel endemic to the Edwards Plateau in the Colorado River basin

The widespread distribution of Strophitus undulatus, as well as high intraspecific morphological variation, has led previous authors to doubt the taxon is representative of a single species. Here we provide detailed information for all the freshwater mussels and associated DNA sequence data utilized to test species boundaries in S. undulatus. These molecular data, in combination with morphological
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Wetland and Aquatic Research Center

Molecular resources for investigating relationships among freshwater mussels (Bivalvia: Unionoida) with a focus on the genus Alasmidonta

Longstanding taxonomic uncertainties have limited conservation efforts for species currently assigned to the freshwater mussel genus Alasmidonta. Here, we present mitochondrial and nuclear DNA sequence data needed to assess the genus- and species-level taxonomy of Alasmidonta. These molecular data allowed us to test whether cryptic diversity exists within Alasmidonta and whether A. triangulata and
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Wetland and Aquatic Research Center

Red Lionfish DNA data collected from Florida, USA and around the invasive distribution from 2007 to 2016

Red lionfish (Pterois volitans) have become a successful invasive predator across the Northwestern Atlantic, Caribbean, and Gulf of Mexico (GoM). Previous investigations have identified the southeast coast of Florida as the original site of introduction, but no region-wide genetic study has directly addressed the question of introduction location(s). This dataset includes previously unpublished re
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Wetland and Aquatic Research Center

Novel genetic resources for Clubshell freshwater mussels (Pleurobema clava, P. oviforme) for enhanced conservation

Here we provide public access to two mitochondrial DNA sequence alignments, multi-locus microsatellite DNA genotypes, morphometric measurements and details on all specimens utilized in Morrison et al., 2021 (In press).
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Eastern Ecological Science Center

Molecular data to investigate phylogeographic patterns, species boundaries, and demographic history of a North American freshwater mussel species complex (Bivalvia: Unionidae)

Here we provide public access to three DNA sequence alignments (COI, ND1, ITS1) and details on all specimens utilized in Keogh et al. (in review).
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Wetland and Aquatic Research Center

Novel genetic resources to facilitate future molecular studies in freshwater mussels (Bivalvia: Unionidae)

Here we provide public access to six DNA sequence alignments and details on all specimens utilized in Smith and Johnson (2020).
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Wetland and Aquatic Research Center

Molecular and morphological data to resolve species boundaries in the critically imperiled freshwater mussel species, Fusconaia mitchelli

We generated multilocus DNA sequence data and traditional morphometric measurements to evaluate species boundaries in Fusconaia mitchelli. We sequenced three loci: the protein-coding mitochondrial DNA genes cytochrome oxidase subunit 1 and NADH dehydrogenase 1, and the nuclear ribosomal internal transcribed spacer 1. We also took three measurements, maximum length, maximum width, and maximum heigh
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Wetland and Aquatic Research Center

Anchored hybrid enrichment in Potamilus mussels

Freshwater mussels are a species-rich group with biodiversity patterns shaped by life history strategies that include an obligate parasitic larval stage. Anchored hybrid enrichment (AHE) and ancestral character reconstruction (ACR) revealed convergence of life history strategies involving larval morphologies that reduce size to increase fecundity and require growth during encapsulation to increase
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Wetland and Aquatic Research Center

Molecular, morphometric, and distribution information for the freshwater mussel genus Potamilus and newly described species, Potamilus streckersoni sp. nov.

Inaccurate systematics confound our ability to determine evolutionary processes that have led to the diversification of many taxa. The North American freshwater mussel tribe Lampsilini, Ihering, 1901, is one of the more well-studied groups in Unionidae; however, many supraspecific relationships between lampsiline genera remain unresolved. Two genera that have been largely overlooked are Leptodea a
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Wetland and Aquatic Research Center

Cytonuclear discordance in the Florida Everglades invasive Burmese python (Python bivitatus) population indicates possible hybridization with the Indian python (Python molurus)

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Wetland and Aquatic Research Center
Man and child in camouflage smiling for camera with hunted deer in foreground
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Filter Total Items: 46

Molecular data validate historical and contemporary distributions of Pleurobema riddellii (Bivalvia: Unionidae) and help guide conservation and recovery efforts

Accurate taxonomic and distributional information are arguably the most critical components of conservation status assessments but can be greatly affected by misidentifications. The Louisiana pigtoe Pleurobema riddellii is a freshwater mussel proposed as threatened under the US Endangered Species Act. The species belongs to the tribe Pleurobemini, which includes multiple taxa that are inherently c
Authors
Nathan Johnson, Caitlin Beaver, Alexander H. Kiser, Matthew A. Duplessis, Matthew D. Wagner, Robert J. Ellwanger, Clinton R. Robertson, Sean D. Kinney, Beau B. Gregory, Steve Wolverton, Charles R. Randklev, Paul D. Hartfield, James D. Williams, Chase H. Smith
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Ecosystems Mission Area, Wetland and Aquatic Research Center

U.S. Geological Survey science vision for native freshwater mussel research in the United States

Executive SummaryNorth America is a global center for native freshwater mussel (order Unionida, hereinafter “mussels”) diversity, with more than 350 species. Mussels are among the most imperiled fauna on the planet. Reasons for both local and widespread declines in mussels are mostly unknown, although the threats may include habitat loss and fragmentation, diseases, environmental contaminants, alt
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Teresa J. Newton, Nathan A. Johnson, David H. Hu
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Ecosystems Mission Area, Species Management Research Program

Coevolution with host fishes shapes parasitic life histories in a group of freshwater mussels (Unionidae: Quadrulini)

Ecological interactions among species often lead to parasitic lineages coevolving with host resources, which is often suggested as the primary driver of parasite diversification. Freshwater mussels are bivalves that possess a parasitic life cycle requiring larval encystment on freshwater vertebrates to complete metamorphosis. The North American freshwater mussel tribe Quadrulini has a suite of lif
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Sakina Neemuchwala, Nathan Johnson, John M. Pfeiffer, Manuel Lopes-Lima, Andre Gomes-dos-Santos, Elsa Froufe, David M. Hillis, Chase H. Smith
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Ecosystems Mission Area, Wetland and Aquatic Research Center

Environmental, morphological, and molecular data reveal a new species of freshwater mussel, Strophitus howellsi, endemic to the Edwards Plateau in Texas

Freshwater mussels are considered the most imperiled group of organisms in North America and systematics research has played an integral role in the development and implementation of their conservation. Despite the importance of systematics in conservation planning, the evolutionary relationships between many mussel taxa remain poorly explored, clearly illustrated by Strophitus undulatus. This spe
Authors
Chase H. Smith, Alexander H. Kiser, Nathan Johnson, Charles R. Randklev
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Ecosystems Mission Area, Wetland and Aquatic Research Center

A novel assembly pipeline and functional annotations for targeted sequencing: A case study on the globally threatened Margaritiferidae (Bivalvia: Unionida)

The proliferation of genomic sequencing approaches has significantly impacted the field of phylogenetics. Target capture approaches provide a cost-effective, fast and easily applied strategy for phylogenetic inference of non-model organisms. However, several existing target capture processing pipelines are incapable of incorporating whole genome sequencing (WGS). Here, we develop a new pipeline fo
Authors
André Gomes-dos-Santos, Elsa Froufe, John M. Pfeiffer, Nathan Johnson, Chase H. Smith, André M. Machado, L. Filipe C. Castro, Van Tu Do, Akimasa Hattori, Nicole Garrison, Nathan V. Whelan, Ivan N. Bolotov, Ilya V. Vikhrev, Alexander V. Kondakov, Mohamed Ghamizi, Vincent Prié, Arthur E. Bogan, Manuel Lopes Lima
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Ecosystems Mission Area, Wetland and Aquatic Research Center

Hidden in the hills: Phylogeny of the freshwater mussel genus Alasmidonta (Bivalvia: Unionidae) and description of a new species

Inaccurate taxonomy can lead to species in need of conservation being overlooked, which makes revisionary systematics crucially important for imperilled groups. The freshwater mussel genus Alasmidonta is one such group in need of study. Here, we take a multilocus phylogenetic approach to assess species-level taxonomy of Alasmidonta and test monophyly of this genus. Phylogenetic inference resulted
Authors
Nathan V. Whelan, Nathan Johnson, Ashantye' S. Williams, Michael A. Perkins, Caitlin E. Beaver, Jason W. Mays
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Ecosystems Mission Area, Wetland and Aquatic Research Center

Biogeography of freshwater mussels (Bivalvia: Unionida) in Texas and implications on conservation biology

AimBiogeography seeks to identify and explain the spatial distributions of species and has become an important tool used by conservationists to protect and manage aquatic organisms. Texas, located in the southwestern United States, is home to 52 species of freshwater mussels, 9 of which are endemic to Texas and 7 that are endemic to Texas and neighboring states or countries. There have been two ma
Authors
Michael de Moulpied, Chase H. Smith, Clint R. Robertson, Nathan Johnson, Roel Lopez, Charles R. Randklev
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Ecosystems Mission Area, Wetland and Aquatic Research Center

Using a multi-model ensemble approach to determine biodiversity hotspots with limited occurrence data in understudied areas: An example using freshwater mussels in México

Species distribution models (SDMs) are an increasingly important tool for conservation particularly for difficult-to-study locations and with understudied fauna. Our aims were to (1) use SDMs and ensemble SDMs to predict the distribution of freshwater mussels in the Pánuco River Basin in Central México; (2) determine habitat factors shaping freshwater mussel occurrence; and (3) use predicted occup
Authors
Alexander H. Kiser, Kevin S. Cummings, Jeremy S. Tiemann, Chase H. Smith, Nathan A. Johnson, Roel R. Lopez, Charles R. Randklev
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Ecosystems Mission Area, Wetland and Aquatic Research Center

Genetic analysis of red lionfish Pterois volitans from Florida, USA, leads to alternative North Atlantic introduction scenarios

The red lionfish Pterois volitans is a successful invasive predator across the western North Atlantic, Caribbean, and Gulf of Mexico. The southeast coast of Florida (USA) has been identified as the original introduction location, but genetic analyses including Florida lionfish have yet to investigate introduction scenarios. Here, we assessed the potential lionfish invasion pathways using 1795 sequ
Authors
Margaret Hunter, Caitlin Beaver, Nathan A. Johnson, Eleanor K. Bors, Antonio A. Mignucci-Giannoni, Brian R. Silliman, Dayne Buddo, Linda Searle, Edgardo Díaz-Ferguson
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Ecosystems Mission Area, Wetland and Aquatic Research Center

Establishing conservation units to promote recovery of two threatened freshwater mussel species (Bivalvia: Unionida: Potamilus)

Population genomics has significantly increased our ability to make inferences about microevolutionary processes and demographic histories, which have the potential to improve protection and recovery of imperiled species. Freshwater mussels (Bivalvia: Unionida) represent one of the most imperiled groups of organisms globally. Despite systemic decline of mussel abundance and diversity, studies eval
Authors
Chase H. Smith, Nathan Johnson, Clinton R. Robertson, Robert D. Doyle, Charles R. Randklev
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Ecosystems Mission Area, Wetland and Aquatic Research Center

Rediscovery and genetic confirmation of the Threeridge Mussel, Amblema plicata (Say, 1817) (Bivalvia, Unionidae), in the Choctawhatchee River, Florida, USA

Recent freshwater mussel research has resulted in rediscovery of several species presumed extinct. We report the rediscovery of Amblema plicata (Say, 1817) in 2019 from the Choctawhatchee River, Florida, USA. Amblema plicata has not been reported in the Choctawhatchee river basin since 1958, more than 61 years ago. This species was collected during the long-term monitoring of freshwater mussels in
Authors
Lauren N. Patterson, Susan R. Geda, Nathan A. Johnson
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Ecosystems Mission Area, Wetland and Aquatic Research Center

Gulf Coast vicariance shapes phylogeographic history of a North American freshwater mussel species complex

AimFreshwater mussels share habitat and are parasites of freshwater fishes during the larval life stage. Therefore, models of fish biogeography may also explain the historical biogeography of freshwater mussels. We tested this assumption using predictions of three biogeographic models constructed for northern Gulf of Mexico drainages on a freshwater mussel species complex. Specifically, we tested
Authors
Sean M. Keogh, Nathan Johnson, James D. Williams, Charles R. Randklev, Andrew Simons
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Ecosystems Mission Area, Wetland and Aquatic Research Center

Non-USGS Publications**

Grobler, P. J., Jones, J.W., Johnson, N.A., Neves, R.J., and E.M. Hallerman. 2011. Homogeneity at Nuclear Microsatellite Loci Masks Mitochondrial Haplotype Diversity in the Endangered Fanshell Pearlymussel (Cyprogenia stegaria). Journal of Heredity 102(2): 196-206. [Link]

**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.

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