Geology topics

John M. Pfeiffer

Publications and source records attributed to John M. Pfeiffer.

11 recordsLinked to original sources

USGS2026

Body size, dispersal potential, range size and habitat fragmentation are linked to extinction risk of freshwater mussels

Aim: Trait-based approaches are increasingly recognized as a tool for understanding species’ vulnerabilities to intensifying global change. For species with complex life histories that involve a parasitic life stage, a combination of traits associated with either the host or parasite could influence extinction risk. Location: United States of America Taxon: Freshwater mussels are a highly threatened assemblage of bivalves with an obligate ectoparasitic larval stage requiring a host fish. Adult mussels are sedentary, with long-distance dispersal dictated by the dispersal ability of the host fish during the parasitic larval life phase. Methods: We integrate several open-source spatial and trait datasets for freshwater mussels and host fishes to test hypotheses about the relationship between species-level traits such as body size, area of occupancy (AOO), host fish dispersal, habitat fragmentation, and mussel extinction risk. Results: Imperiled mussels were smaller, had smaller areas of occupancy, used small-bodied, dispersal-limited host fishes, and had higher densities of large dams in their AOO compared to non-imperiled mussels. Conclusions: Body size, along with AOO and dispersal potential, appear to have cascading effects on imperilment where decreases in these traits potentiate population fragmentation via large dams. Thus, in contrast to many other groups, freshwater mussel body size is inversely related to extinction risk and small-bodied mussels should be closely monitored to prevent future extinctions.

Journal of Biogeography↗

USGS2024

Integrative phylogenetic, phylogeographic and morphological characterisation of the Unio crassus species complex reveals cryptic diversity with important conservation implications

The global decline of freshwater mussels and their crucial ecological services highlight the need to understand their phylogeny, phylogeography and patterns of genetic diversity to guide conservation efforts. Such knowledge is urgently needed for Unio crassus , a highly imperilled species originally widespread throughout Europe and southwest Asia. Recent studies have resurrected several species from synonymy based on mitochondrial data, revealing U. crassus to be a complex of cryptic species. To address long-standing taxonomic uncertainties hindering effective conservation, we integrate morphometric, phylogenetic, and phylogeographic analyses to examine species diversity within the U. crassus complex across its entire range. Phylogenetic analyses were performed using cytochrome c oxidase subunit I (815 specimens from 182 populations) and, for selected specimens, whole mitogenome sequences and Anchored Hybrid Enrichment (AHE) data on ∼600 nuclear loci. Mito-nuclear discordance was detected, consistent with mitochondrial DNA gene flow between some species during the Pliocene and Pleistocene. Fossil-calibrated phylogenies based on AHE data support a Mediterranean origin for the U. crassus complex in the Early Miocene. The results of our integrative approach support 12 species in the group: the previously recognised Unio bruguierianus , Unio carneus, Unio crassus , Unio damascensis , Unio ionicus , Unio sesirmensis , and Unio tumidiformis , and the reinstatement of five nominal taxa: Unio desectus stat. rev. , Unio gontierii stat. rev. , Unio mardinensis stat. rev. , Unio nanus stat. rev. , and Unio vicarius stat. rev. Morphometric analyses of shell contours reveal important morphospace overlaps among these species, highlighting cryptic, but geographically structured, diversity. The distribution, taxonomy, phylogeography, and conservation of each species are succinctly described.

Molecular Phylogenetics and Evolution↗

USGS2023

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 life history adaptations including highly specialized patterns of host use, infection strategies, and variable larval morphologies. However, the evolution of life histories has yet to be explored using phylogenetic comparative methods. In this study, we use a holistic approach incorporating biogeographical, ecological, molecular, and morphological datasets to reconstruct the evolution of Quadrulini. Comparative phylogenetic analyses suggested the diversification of Quadrulini has been driven, at least in part, by codiversification with their primary host fishes in Ictaluridae. Major diversification events in both ictalurids and quadrulines were estimated to have occurred in the Mississippi River basin throughout the Miocene. Life history characteristics associated with parasitism were supported to have coevolved with host repertories, supporting the hypothesis that ecological interactions with host fishes have shaped the evolution of highly specialized traits in this group. Our findings demonstrate the importance of ecological interactions with host resources in shaping the evolutionary history of freshwater mussels.

Bulletin of the Society of Systematic Biologists↗

USGS2023

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 for capture and de novo assembly of the targeted regions using whole genome re-sequencing reads. This new pipeline captured targeted loci accurately, and given its unbiased nature, can be used with any target capture probe set. Moreover, due to its low computational demand, this new pipeline may be ideal for users with limited resources and when high-coverage sequencing outputs are required. We demonstrate the utility of our approach by incorporating WGS data into the first comprehensive phylogenomic reconstruction of the freshwater mussel family Margaritiferidae. We also provide a catalogue of well-curated functional annotations of these previously uncharacterized freshwater mussel-specific target regions, representing a complementary tool for scrutinizing phylogenetic inferences while expanding future applications of the probe set.

Molecular Ecology Resources↗

USGS2022

Occurrence of a reproducing wild population of Channa aurolineata (Pisces: Channidae) in the Manatee River drainage, Florida

We report on the discovery of a wild, reproducing population of Channa aurolineata (Pisces: Channidae) in west-central Florida (USA), and first documented occurrence of snakeheads in the Gulf Coast region. Channa aurolineata is a large, predatory fish of the bullseye snakehead “Marulius group” species complex from Asia. Adult and juvenile specimens were captured in June 2020 in a 1.8-hectare pond that connects during high water to a small stream within the Manatee River-Tampa Bay Basin. The pond site is 250-km from the only other wild C. aurolineata population in the USA (present in southeast Florida since ca. 2000) and is considered a separate introduction and not the result of natural dispersal. Morphological and molecular comparisons revealed high overlap between the two Florida populations, evidence humans may have transported fish between sites. To verify identification, we compared Florida samples to C. aurolineata from Thailand and found mtDNA-COI barcode sequences to be identical or to differ by only a single base pair. Life body coloration of Florida samples matched their Asian counterparts, but Florida specimens averaged fewer dorsal fin rays (53.6 vs. 56.0), anal fin rays (34.2 vs 36.1), lateral line scales (65.3 vs. 67.4), and vertebrae (62.1 vs. 64.3), differences implying possible founder effect or sampling bias. Existence of this invasive predator is a concern because of the risk of spread and negative ecological effects, including an observation of terrestrial hunting behavior. In 2020–2021, several hundred C. aurolineata were removed from the pond by nets and electrofishing, and surveys suggested the population had not spread to nearby waters. In May 2021 the pond was treated with rotenone and 48 more specimens were recovered. No additional snakeheads have been sighted since the piscicide operation, although verification of eradication will require monitoring of the watershed.

Florida↗

USGS2020

Comparative phylogenomics reveal complex evolution of life history strategies in a clade of bivalves with parasitic larvae (Bivalvia: Unionoida: Ambleminae)

Freshwater mussels are a species‐rich group with biodiversity patterns strongly shaped by a life history strategy that includes an obligate parasitic larval stage. In this study, we set out to reconstruct the life history evolution and systematics in a clade of freshwater mussels adapted to parasitizing a molluscivorous host fish. Anchored hybrid enrichment and ancestral character reconstruction revealed a complex pattern of life history evolution with host switching and multiple instances of convergence, including reduction in size of larvae, increased fecundity, and growth during encapsulation. Our phylogenomic analyses also recovered non‐monophyly of taxa exhibiting multiple traits used as the basis for previous taxonomic hypotheses. Taxa with axe‐head shaped glochidia were resolved as paraphyletic, but our results strongly suggest the complex morphology is an adaptation to reduce larval size, with reduction in size further accentuated in taxa previously assigned to Leptodea . To more accurately reflect the evolutionary history of this group, we make multiple systematic changes, including the description of a new genus, Atlanticoncha gen. nov. , and the synonymy of the genus Leptodea under Potamilus . Our findings contribute to the growing body of literature showing that cladistic hypotheses based solely on morphological characters, including larval morphology, can be flawed in freshwater mussels.

Cladistics↗

USGS2019

Noninvasive identification of cryptic herpetofauna from fecal samples: A novel approach pairing conservation dog surveys and genetic analysis

Noninvasive fecal sampling combined with genetic analysis is a powerful technique allowing the study of elusive or otherwise difficult to monitor species without the need for direct contact. While this method is widely used in birds and mammals, it has never been successfully applied on a large scale in reptiles. The blunt-nosed leopard lizard (Gambelia sila) is an endangered species endemic to the San Joaquin Desert of California. Presently, acquiring data on G. sila for research and management involves more traditional methods such as live capture to obtain tissue samples for DNA analysis, or observation via visual surveys, which are also used for regulatory monitoring in accordance with wildlife agency protocols. Here we describe an innovative approach for gathering additional information, that combines use of conservation detection dogs trained to locate G. sila scat samples with genetic analysis for identifying and distinguishing among sympatric lizard species. We developed two PCR assays that produce fluorescently labelled amplicons of species-specific fragment length for six lizard species in the study area. Using these assays we genetically identifed to species 78% (255 of 327) of samples collected by dog-handler teams across four years. The majority of the genetically identifed samples (82.4%; 210 of 255) were confirmed as originating from G. sila. Beyond the immediate application of these techniques for the study and monitoring of G. sila, our ability to recover usable DNA and to differentiate among a diverse group of lizards highlights the broad potential of our methodology for noninvasive sampling in reptiles.

California↗

USGS2018

Integrative taxonomy resolves taxonomic uncertainty for freshwater mussels being considered for protection under the U.S. Endangered Species Act

Objectively delimiting species boundaries remains an important challenge in systematics and becomes urgent when unresolved taxonomy complicates conservation and recovery efforts. We examined species boundaries in the imperiled freshwater mussel genus Cyclonaias (Bivalvia: Unionidae) using morphometrics, molecular phylogenetics, and multispecies coalescent models to help guide pending conservation assessments and legislative decisions. Congruence across multiple lines of evidence indicated that current taxonomy overestimates diversity in the C. pustulosa species complex. The only genetically and morphologically diagnosable species in the C. pustulosa species complex were C. pustulosa and C. succissa and we consider C. aurea , C. houstonensis, C. mortoni , and C. refulgens to be synonyms of C. pustulosa . In contrast, all three species in the C. nodulata complex ( C. necki , C. nodulata , and C. petrina ) were genetically, geographically, and morphologically diagnosable. Our findings have important conservation and management implications, as three nominal species ( C. aurea , C. houstonensis , and C. petrina ) are being considered for protection under the Endangered Species Act.

Scientific Reports↗

USGS2018

Molecular and morphological data reveal non-monophyly and speciation in imperiled freshwater mussels (Anodontoides and Strophitus)

Accurate taxonomic placement is vital to conservation efforts considering many intrinsic biological characteristics of understudied species are inferred from closely related taxa. The rayed creekshell, Anodontoides radiatus (Conrad, 1834), exists in the Gulf of Mexico drainages from western Florida to Louisiana and has been petitioned for listing under the Endangered Species Act. We set out to resolve the evolutionary history of A. radiatus, primarily generic placement and species boundaries, using phylogenetic, morphometric, and geographic information. Our molecular matrix contained 3 loci: cytochrome c oxidase subunit I, NADH dehydrogenase subunit I, and the nuclear-encoded ribosomal internal transcribed spacer I. We employed maximum likelihood and Bayesian inference to estimate a phylogeny and test the monophyly of Anodontoides and Strophitus. We implemented two coalescent-based species delimitation models to test seven species models and evaluate species boundaries within A. radiatus. Concomitant to molecular data, we also employed linear morphometrics and geographic information to further evaluate species boundaries. Molecular and morphological evidence supports the inclusion of A. radiatus in the genus Strophitus, and we resurrect the binomial Strophitus radiatus to reflect their shared common ancestry. We also found strong support for polyphyly in Strophitus and advocate the resurrection of the genus Pseudodontoideus to represent ‘Strophitus’ connasaugaensis and ‘Strophitus’ subvexus. Strophitus radiatus exists in six well-supported clades that were distinguished as evolutionary independent lineages using Bayesian inference, maximum likelihood, and coalescent-based species delimitation models. Our integrative approach found evidence for as many as 4 evolutionary divergent clades within S. radiatus. Therefore, we formally describe two new species from the S. radiatus species complex (Strophitus williamsi and Strophitus pascagoulaensis) and recognize the potential for a third putative species (Strophitus sp. cf. pascagoulaensis). Our findings aid stakeholders in establishing conservation and management strategies for the members of Anodontoides, Strophitus, and Pseudodontoideus.

Alabama, Florida, Louisiana, Mississippi↗

USGS2017

Molecular phylogeny of the Nearctic and Mesoamerican freshwater mussel genus Megalonaias

Megalonaias is the most geographically widespread genus of the subfamily Ambleminae and is distributed across much of the eastern half of North America, from Minnesota to Nicaragua. Despite the large geographic distribution, the species-level diversity of Megalonaias is quite depauperate (2 spp.), suggesting the genus may not be constrained by the same physical, ecological, or physiological barriers that limit dispersal in many other amblemines. However, this hypothesis is contingent on the assumption that the current taxonomy of Megalonaias accurately reflects its evolutionary history, which remains incompletely understood due to the marginalization of Mesoamerican populations in systematic research. Using one mitochondrial (COI ) and one nuclear marker ( ITS1 ) sequenced from 41 individuals distributed across both the Nearctic and Mesoamerican ecoregions, we set out to better understand the species boundaries and genetic diversity within Megalonaias . The reconstructed molecular phylogeny and the observed genetic diversity suggests that Megalonaias is a monotypic genus and that Megalonaias nickliniana , currently considered a federally endangered species, is not a valid species. These results are discussed in the context of their systematic and conservation implications, as well as how the unusual life history strategy of Megalonaias may be influencing its molecular diversity.

Hydrobiologia↗

USGS2015

Generic reclassification and species boundaries in the rediscovered freshwater mussel ‘Quadrula’ mitchelli (Simpson in Dall, 1896)

The Central Texas endemic freshwater mussel, Quadrula mitchelli (Simpson in Dall, 1896), had been presumed extinct until relict populations were recently rediscovered. To help guide ongoing and future conservation efforts focused on Q . mitchelli we set out to resolve several uncertainties regarding its evolutionary history, specifically its unknown generic position and untested species boundaries. We designed a molecular matrix consisting of two loci ( cytochrome c oxidase subunit I and internal transcribed spacer I ) and 57 terminal taxa to test the generic position of Q . mitchelli using Bayesian inference and maximum likelihood phylogenetic reconstruction. We also employed two Bayesian species validation methods to test five a priori species models (i.e. hypotheses of species delimitation). Our study is the first to test the generic position of Q. mitchelli and we found robust support for its inclusion in the genus Fusconaia. Accordingly, we introduce the binomial, Fusconaia mitchelli comb. nov., to accurately represent the systematic position of the species. We resolved F. mitchelli individuals in two well supported and divergent clades that were generally distinguished as distinct species using Bayesian species validation methods, although alternative hypotheses of species delineation were also supported. Despite strong evidence of genetic isolation within F. mitchelli , we do not advocate for species-level status of the two clades as they are allopatrically distributed and no morphological, behavioral, or ecological characters are known to distinguish them. These results are discussed in the context of the systematics, distribution, and conservation of F. mitchelli .

Conservation Genetics↗