Geology topics

Darren Johnson

Publications and source records attributed to Darren Johnson.

28 records · Page 2Linked to original sources

USGS2020

The incubation environment of nests deposited by a genetically distinct group of loggerhead sea turtles in Northwest Florida

The warming climate presents a challenge to conservation of all threatened and endangered species but particularly to those that exhibit temperature-dependent sex determination such as sea turtles. Changes in temperature may result in changes in the sex ratio of the population which can directly affect reproductive rate, abundance and population dynamics. The NW Atlantic loggerhead turtle population is listed as threatened under the U.S. Endangered Species Act, and one of the smallest subpopulations in this assemblage nests in the northern Gulf of Mexico. Here, we describe the incubation environment of northern Gulf of Mexico loggerheads nesting at several different beaches in Northwest Florida. Temperature dataloggers were placed inside and adjacent to nests on different nesting beaches across Northwest Florida. In addition, incubation durations were recorded from nests deposited on those same beaches. Internal nest temperatures were higher than those in the sand, however sand temperatures were correlated with incubation durations. Sand temperatures differed along the vertical beach profile and according to depth. Temperatures also differed along a geographic gradient across Northwest Florida and in relation to distance from the Apalachicola River. Incubation durations followed a similar pattern. Mean monthly temperatures at all sites were at or lower than 29 °C (range 23.1 °C–29.6 °C at the dunes; 23.8 °C–29.4 °C at mid-beach) which suggests nests in Northwest Florida may be producing a significant number of males, in contrast to the large number of females being produced on Florida's Atlantic coast. The temperatures and incubation durations on these nesting beaches may be regulated by differing sources of sand and beach orientations across Northwest Florida.

Northwest Florida↗

USGS2020

Growth rates for immature Kemp’s ridley sea turtles from a foraging area in the northern Gulf of Mexico

Examining vital rates helps clarify how environmental characteristics, biological resources and human activities affect population growth. Carapace lengths were gathered for 241 Kemp’s ridley Lepidochelys kempii sea turtles that were marked and recaptured (n = 23) between 2011 and 2019 at a foraging location in northwest Florida, USA. There was a strong correlation between length, width and weight of captured turtles. Mean ± SD size of all captured turtles was 36.6 ± 7.6 cm. Mean recapture interval was 499 ± 475.4 d. Straight-line carapace lengths at initial capture ranged from 20.6 to 53.3 cm. Growth rates from 0.21 to 12.44 cm yr -1 (mean 3.15 ± 2.64 cm) were documented and were greatest for turtles in the 20.0-29.9 cm size class. Growth rates from northwest Florida were slower than those reported from other sites in the Gulf of Mexico. These results indicate that Kemp’s ridleys recruit from oceanic habitat into coastal bays in northwest Florida, where they remain until they reach adulthood. However, some adult-sized turtles may continue to use the nearshore habitat. A gradient in growth rates in the Gulf of Mexico may occur from faster growth in the south to slower growth in the north. Fine-scale variations in resources and environmental conditions may drive regional differences in growth rates, and research on what drives these differences is needed.

Marine Ecology Progress Series↗

USGS2019

Morphology and genetics of Lythrum salicaria from latitudinal gradients of the Northern Hemisphere grown in cold and hot common gardens

The aim of this project was to compare the phenotypic responses of global populations of Lythrum salicaria in cold/dry and hot/humid environments to determine if phenotypic plasticity varied between the native and invasive ranges, and secondarily if this variation was linked to genetic diversity. Common garden studies were conducted in Třeboň, Czech Republic, and Lafayette, Louisiana, USA (cold/dry vs. hot/humid garden, respectively), using populations from latitudinal gradients in Eurasia and North America. Lythrum salicaria seeds collected from the same maternal plants across these latitudinal gradients were germinated and grown in Třeboň and Lafayette. Tissue masses (above-, below-ground, inflorescence and total) of these individuals were assessed at the end of each growing season (2006–2008). Worldwide field measurements of L . salicaria height were made by volunteers from 2004–2016. Biomass and height data were analyzed using the General Linear Model framework and multivariate techniques. Molecular markers (amplified fragment length polymorphisms) of individuals used in the common garden study were analyzed using traditional genetic diversity metrics and Bayesian clustering algorithms in STRUCTURE. Reaction norms were developed from differences in maternal plant responses in Třeboň versus Lafayette. In the common garden studies, stem/leaf, root and total biomass generally were highest for individuals grown from seeds collected in the southern part of the range in the cold garden, particularly by the third year of the study. In contrast, inflorescence biomass in the cold garden was higher by the third year in individuals from mid-latitude populations. As measured by volunteers, plants were taller in Eurasia than in North America moving from north to south with the pattern switching southward of 40°N latitude. Genetic diversity was similar between native and non-native invasive populations regardless of geographical origin of the seed and was not significantly different in the GLM Select model (p > 0.05). Reaction norm slopes showed that Eurasia had larger values than North America for reaction norms for above-ground and total biomass. Plants from the seeds of mother plants from Turkey had wide variation in total biomass when grown in Třeboň versus Lafayette; this variation in response within certain populations may have contributed to the lack of population-level differences in plasticity. These results indicate no loss of genetic diversity for L . salicaria during its North American invasion, nor reduction in plastic tissue allocation responses to a varying environment, which may help explain some of its invasive qualities and which could be of adaptive value under changing future environments.

PLoS ONE↗

USGS2019

Defensible standardized ploidy assessments for Grass Carp (Ctenopharyngodon idella, Cyprinidae) intercepted from the commercial supply chain

Although methods are in place through the U.S. Fish and Wildlife (USFWS) program for ploidy testing of feral caught Grass Carp ( Ctenopharyngodon idella ) and black carp ( Mylopharyngodon piceus ), no guidelines exist for carp hauled across state lines. Using 1200 Grass Carp purchased by undercover Ohio law enforcement during 2015–2016, we developed a standardized protocol for discriminating ploidy by using two parameters, nuclear size and DNA content. Bead standards at 2 μm or 4 μm were used to establish nuclear size from Nile Tilapia ( Oreochromis niloticus ), known diploid ( n = 20) and triploid (n = 20) Grass Carp blood, and cells derived from eyeballs of purchased field carp. The control for establishing DNA content was cryopreserved or fresh tilapia blood (2.40 pg). Time postmortem indicated nuclear size was similar over 4 days, but DNA quality from triploids was best at 24 h. Occasionally, only size or DNA content was measurable. Tilapia mean nuclear size ( n = 501 samples) was 4.61 μm (SE 0.05) (R 2 = 0.94). Known diploid and triploid blood nuclear sizes, compared with tilapia size, were 3.62 μm (SE 0.13) (R 2 = 0.96) and 7.58 μm (SE 0.27) (R 2 = 0.96), respectively. Mean field carp eye nuclear size was 5.83 μm (SE 0.13). Mean DNA content of cells from field carp eyes ( n = 698 fish) was 3.51 pg (SE 0.06). No diploid Grass Carp were detected in the USFWS certified triploid Grass Carp transports. This standard protocol reliably discriminates ploidy and can be used for enforcement of regulations that differ among state jurisdictions.

Journal of Great Lakes Research↗

USGS2019

The potential resiliency of a created tidal marsh to sea-level rise

The purpose of this study was to determine the elevation dynamics of a created tidal marsh on the North Carolina coast. Deep rod surface elevation tables (RSET) and feldspar marker horizons (MH) were installed in plots to measure net surface elevation changes and to quantify contributing processes. Twelve total plots were placed on four elevation gradient transects (three transects within the created marsh and one within a reference marsh) with three plots along each transect. Elevation gradient transects included a low marsh plot dominated by Spartina alterniflora, a middle marsh plot dominated by Juncus roemerianus, and a high marsh plot dominated by Spartina patens. RSET and MH measurements were taken in December 2012, January 2014, April 2017, and March 2018. Elevation change ranged from 0.7 to 4.0 mm yr -1 within the created marsh and -0.6 to 2.1 mm yr -1 within the reference marsh. When compared to the long-term linear trend in local relative sea level rise (RSLR) of 3.10 +/- 0.35 mm yr -1 , the middle marsh plots within the created marsh trended toward survival with an observed elevation increase of 3.1 +/- 0.2 mm yr -1 . Alternatively, the low and high marsh plots within the created marsh trended towards submergence with observed elevation increases of 2.1+/- 0.2 and 1.3 +/- 0.2 mm yr -1 , respectively. These results indicate that a created marsh can display elevation dynamics similar to natural marshes. Surface elevation changes were observed over a short time period and in a relatively young marsh, so it is uncertain if these trends will continue or how the longer-term relationship with RSLR will develop. While this study provided the initial data on the ability of created tidal marshes to respond to observed sea-level rise, long-term observations will be continued to evaluate long-term elevation dynamics.

North Carolina↗

USGS2018

Exotic invasive Pomacea maculata (Giant Apple Snail) will depredate eggs of frog and toad species of the Southeastern US

Pomacea maculata (Perry) (Giant Apple Snail) is a freshwater snail native to South America ( Hayes et al. 2015 ) that is an invasive species in the freshwater wetlands and waterways of the northern Gulf of Mexico, peninsular Florida ( Benson 2017 , Burks 2017 ) and globally ( Hayes et al. 2015 ). Karraker and Dudgeon ( 2014 ) found that Pomacea canaliculata (Lamarck) (Channeled Apple Snail) opportunistically ate frog eggs. The Giant Apple Snail is a sister species to the Channeled Apple Snail and shares similar life-history attributes ( Hayes et al. 2015 ). However, the literature indicates that Giant Apple Snail is presumed to be an herbivore (e.g., Burke et al. 2017 , Burlakova et al. 2009 ). Will Giant Apple Snail eat amphibian eggs? If they do, they could have a negative impact on anuran populations throughout their introduced range. In this study, we presented Giant Apple Snails with frog and toad eggs to determine if they would eat them.

Southeastern Naturalist↗

USGS2018

Quantifying relative importance: Computing standardized effects in models with binary outcomes

Scientists commonly ask questions about the relative importances of processes, and then turn to statistical models for answers. Standardized coefficients are typically used in such situations, with the goal being to compare effects on a common scale. Traditional approaches to obtaining standardized coefficients were developed with idealized Gaussian variables in mind. When responses are binary, complications arise that impact standardization methods. In this paper, we review, evaluate, and propose new methods for standardizing coefficients from models that contain binary outcomes. We first consider the interpretability of unstandardized coefficients and then examine two main approaches to standardization. One approach, which we refer to as the Latent-Theoretical or LT method, assumes that underlying binary observations there exists a latent, continuous propensity linearly related to the coefficients. A second approach, which we refer to as the Observed-Empirical or OE method, assumes responses are purely discrete and estimates error variance empirically via reference to a classical R2 estimator. We also evaluate the standard formula for calculating standardized coefficients based on standard deviations. Criticisms of this practice have been persistent, leading us to propose an alternative formula that is based on user-defined “relevant ranges”. Finally, we implement all of the above in an open-source package for the statistical software R. Results from simulation studies show that both the LT and OE methods of standardization support a similarly-broad range of coefficient comparisons. The LT method estimates effects that reflect underlying latent-linear propensities, while the OE method computes a linear approximation for the effects of predictors on binary responses. The contrast between assumptions for the two methods is reflected in persistently weaker standardized effects associated with OE standardization. Reliance on standard deviations for standardization (the traditional approach) is critically examined and shown to introduce substantial biases when predictors are non-Gaussian. The use of relevant ranges in place of standard deviations has the capacity to place LT and OE standardized coefficients on a more comparable scale. As ecologists address increasingly complex hypotheses, especially those that involve comparing the influences of different controlling factors (e.g., top-down versus bottom-up or biotic versus abiotic controls), comparable coefficients become a necessary component for evaluations.

Ecosphere↗

USGS2016

Component greenhouse gas fluxes and radiative balance from two deltaic marshes in Louisiana: Pairing chamber techniques and eddy covariance

Coastal marshes take up atmospheric CO 2 while emitting CO 2 , CH 4 , and N 2 O. This ability to sequester carbon (C) is much greater for wetlands on a per-area basis than from most ecosystems, facilitating scientific, political, and economic interest in their value as greenhouse gas sinks. However, the greenhouse gas balance of Gulf of Mexico wetlands is particularly understudied. We describe the net ecosystem exchange (NEE c ) of CO 2 and CH 4 using eddy covariance (EC) in comparison with fluxes of CO 2 , CH 4 , and N 2 O using chambers from brackish and freshwater marshes in Louisiana, USA. From EC, we found that 182 g C m -2 y -1 was lost through NEE c from the brackish marsh. Of this, 11 g C m -2 y -1 resulted from net CH 4 emissions and the remaining 171 g C m -2 y -1 resulted from net CO 2 emissions. In contrast, -290 g C m 2 y -1 was taken up through NEE c by the freshwater marsh, with 47 g C m -2 y -1 emitted as CH 4 and -337 g C m -2 y -1 taken up as CO 2 . From chambers, we discovered that neither site had large fluxes of N 2 O. Sustained-flux greenhouse gas accounting metrics indicated that both marshes had a positive (warming) radiative balance, with the brackish marsh having a substantially greater warming effect than the freshwater marsh. That net respiratory emissions of CO 2 and CH 4 as estimated through chamber techniques were 2-4 times different from emissions estimated through EC requires additional understanding of the artifacts created by different spatial and temporal sampling footprints between techniques.

Journal of Geophysical Research: Biogeosciences↗

USGS2015

Hydrologic remediation for the Deepwater Horizon incident drove ancillary primary production increase in coastal swamps

As coastal wetlands subside worldwide, there is an urgency to understand the hydrologic drivers and dynamics of plant production and peat accretion. One incidental test of the effects of high rates of discharge on forested wetland production occurred in response to the 2010 Deepwater Horizon incident, in which all diversions in Louisiana were operated at or near their maximum discharge level for an extended period to keep offshore oil from threatened coastal wetlands. Davis Pond Diversion was operated at six times the normal discharge levels for almost 4 months, so that Taxodium distichum swamps downstream of the diversion experienced greater inundation and lower salinity. After this remediation event in 2010, above-ground litter production increased by 2.7 times of production levels in 2007–2011. Biomass of the leaf and reproductive tissues of several species increased; wood litter was minimal and did not change during this period. Root production decreased in 2010 but subsequently returned to pre-remediation values in 2011. Both litter and root production remained high in the second growing season after hydrologic remediation. Annual tree growth (circumference increment) was not significantly altered by the remediation. The potential of freshwater pulses for regulating tidal swamp production is further supported by observations of higher T. distichum growth in lower salinity and/or pulsed environments across the U.S. Gulf Coast. Usage of freshwater pulses to manage altered estuaries deserves further consideration, particularly because the timing and duration of such pulses could influence both primary production and peat accretion.

Louisiana↗

USGS2012

Structural equation modeling and the analysis of long-term monitoring data

The analysis of long-term monitoring data is increasingly important; not only for the discovery and documentation of changes in environmental systems, but also as an enterprise whose fruits validate the allocation of effort and scarce funds to monitoring. In simple terms, we may distinguish between the detection of change in some ecosystem attribute versus the investigation of causes and consequences associated with that change. The statistical framework known as structural equation modeling (SEM) can contribute to both detection of changes and the search for causes. This chapter summarizes some of the capabilities of SEM and shows a few ways it can be used to model temporal change. Because of its ability to test hypotheses about whether rates of change are zero or nonzero, it can be used for change detection with repeated-measures data. As more of the capabilities of SEM are presented, its capacity for evaluating causal networks is highlighted. Here is where its potential for making a unique contribution to the analysis of long-term monitoring data is revealed. Thus, one?s primary motivation for using SEM with monitoring data will be to investigate hypotheses about what factors may be driving change. In this chapter, it will be necessary to first introduce notation to describe the elements of structural equation models (SE models) so as to permit an unambiguous presentation of their various forms. The first part of the chapter works through the fundamental features of models of increasing complexity, while the second part of the chapter illustrates several of these possibilities using a real example.

Book chapter↗