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169 records · Page 10Linked to original sources
USGS2010

Occam's shadow: levels of analysis in evolutionary ecology - where to next?

Evolutionary ecology is the study of evolutionary processes, and the ecological conditions that influence them. A fundamental paradigm underlying the study of evolution is natural selection. Although there are a variety of operational definitions for natural selection in the literature, perhaps the most general one is that which characterizes selection as the process whereby heritable variation in fitness associated with variation in one or more phenotypic traits leads to intergenerational change in the frequency distribution of those traits. The past 20 years have witnessed a marked increase in the precision and reliability of our ability to estimate one or more components of fitness and characterize natural selection in wild populations, owing particularly to significant advances in methods for analysis of data from marked individuals. In this paper, we focus on several issues that we believe are important considerations for the application and development of these methods in the context of addressing questions in evolutionary ecology. First, our traditional approach to estimation often rests upon analysis of aggregates of individuals, which in the wild may reflect increasingly non-random (selected) samples with respect to the trait(s) of interest. In some cases, analysis at the aggregate level, rather than the individual level, may obscure important patterns. While there are a growing number of analytical tools available to estimate parameters at the individual level, and which can cope (to varying degrees) with progressive selection of the sample, the advent of new methods does not reduce the need to consider carefully the appropriate level of analysis in the first place. Estimation should be motivated a priori by strong theoretical analysis. Doing so provides clear guidance, in terms of both (i) assisting in the identification of realistic and meaningful models to include in the candidate model set, and (ii) providing the appropriate context under which the results are interpreted. Second, while it is true that selection (as defined) operates at the level of the individual, the selection gradient is often (if not generally) conditional on the abundance of the population. As such, it may be important to consider estimating transition rates conditional on both the parameter values of the other individuals in the population (or at least their distribution), and population abundance. This will undoubtedly pose a considerable challenge, for both single- and multi-strata applications. It will also require renewed consideration of the estimation of abundance, especially for open populations. Thirdly, selection typically operates on dynamic, individually varying traits. Such estimation may require characterizing fitness in terms of individual plasticity in one or more state variables, constituting analysis of the norms of reaction of individuals to variable environments. This can be quite complex, especially for traits that are under facultative control. Recent work has indicated that the pattern of selection on such traits is conditional on the relative rates of movement among and frequency of spatially heterogeneous habitats, suggesting analyses of evolution of life histories in open populations can be misleading in some cases.

Journal of Applied Statistics↗
USGS1999

Geochemistry of Florida Bay sediments: Nutrient history at five sites in eastern and central Florida Bay

Recent seagrass dieoff and massive microalgal blooms have focused attention on the health of the Florida Bay ecosystem. Changes in nutrient input and the nutrient dynamics of Florida Bay are hypothesized to be linked to these problems, but crucial baseline information is still lacking. Efforts to restore Florida Bay to its natural condition will require information on the nutrient history of the bay. The purpose of this study was to examine distributions of organic C, total N, and total P in carbonate sediments from sites of continuous and known sedimentation rate (210Pb and 137Cs dated), in eastern and central Florida Bay. These sediments provide a record of historical changes in the C, N, and P load to the eastern and central bay. Analyses were conducted on sediments from cores collected at five sites, and on buried seagrass fragments at two sites. At three of the sites, sediments from seagrass-covered and adjacent barren areas were examined to determine differences in sedimentary geochemistry. Stable isotope analyses (??13C and ??15N) of sedimentary organic C and total N and of buried seagrass fragments were also carried out at two sites to examine possible changes in nutrient sources to the estuary. Results were consistent with recent increases in N and P in eastern Florida Bay, beginning in the early to mid 1980's. The timing of the increase in nutrient load observed in the sediment data directly preceded the first observations of massive microalgal blooms and seagrass dieoff in Florida Bay in 1987. The observed nutrification was greater for P than N, and was most pronounced at the most northeasterly site sampled (Pass Key). Isotope data (??15N) suggested that an increase in algal production accompanied the increase in N load at the Pass Key site. Along record of organic C, total N, and total P distributions from Whipray Basin in central Florida Bay showed historical peaks (mid 1700's and late 1800's) in organic C and total N, but not total P; these enrichments were nearly equivalent to recent inputs to the estuary. Barren areas were observed to have generally lower concentrations of organic C, total N, and total P in near surface sediments compared to seagrass-covered areas, but had generally similar concentrations in deeper sediments. This suggested that barren areas adjacent to seagrass-covered sites were places where relict sediment was physically transported and covered seagrass beds. This dataset provides an historical view of changes in nutrient inputs to Florida Bay, and baseline information needed for nutrient modeling of the bay.

Journal of Coastal Research↗
USGS2016

Feline immunodeficiency virus cross-species transmission: Implications for emergence of new lentiviral infections

Owing to a complex history of host-parasite coevolution, lentiviruses exhibit a high degree of species specificity. Given the well-documented viral archeology of HIV emergence following human exposures to SIV, understanding processes that promote successful cross-species lentiviral transmissions is highly relevant. We have previously reported natural cross-species transmission of a subtype of feline immunodeficiency virus, puma lentivirus A (PLVA), between bobcats ( Lynx rufus ) and mountain lions ( Puma concolor ) in a small number of animals in California and Florida. In this study we investigate host-specific selection pressures, within-host viral fitness, and inter- vs. intra-species transmission patterns among a larger collection of PLV isolates from free-ranging bobcats and mountain lions. Analysis of proviral and viral RNA levels demonstrates that PLVA fitness is severely restricted in mountain lions compared to bobcats. We document evidence of diversifying selection in three of six PLVA genomes from mountain lions, but did not detect selection among twenty PLVA isolates from bobcats. These findings support that PLVA is a bobcat-adapted virus, which is less fit in mountain lions and under intense selection pressure in the novel host. Ancestral reconstruction of transmission events reveals intraspecific PLVA transmission has occurred among panthers ( Puma concolor coryi ) in Florida following initial cross-species infection from bobcats. In contrast, interspecific transmission from bobcats to mountain lions predominates in California. These findings document outcomes of cross-species lentiviral transmission events among felids that compare to emergence of HIV from nonhuman primates. IMPORTANCE Cross-species transmission episodes can be singular, dead-end events or can result in viral replication and spread in the new species. The factors that determine which outcome will occur are complex, and the risk of new virus emergence is therefore difficult to predict. Here we use molecular techniques to evaluate transmission, fitness, and adaptation of puma lentivirus A (PLVA) between bobcats and mountain lions in two geographic regions. Our findings illustrate that mountain lion exposure to PLVA is relatively common, but does not routinely result in infections communicable in the new host. This is attributed to efficient species barriers that largely prevent lentiviral adaptation. However, the evolutionary capacity for lentiviruses to adapt to novel environments may ultimately overcome host restriction mechanisms over time and under certain ecological circumstances. This phenomenon provides a unique opportunity to examine cross-species transmission events leading to new lentiviral emergence.

California, Florida↗
USGS2017

Developing an effective Agassiz's Desert Tortoise monitoring program: Final report to the Coachella Valley Conservation Commission

Agassiz’s desert tortoise (Gopherus agassizii) is a conservation-reliant species with populations north and west of the Colorado River protected as threatened under the Endangered Species Act (Averill-Murray et al. 2012). Since it was listed under this category in 1990, a great deal has been learned about the natural history of the species, and it is now one of the best-studied turtles in the United States (Lovich and Ennen 2013). However, the accumulated body of scientific data available for the species has not yet been translated into recovery or delisting of the species. Successful conservation of any species requires knowledge of their natural history and how vital rates affect their ability to maintain stable populations in the face of natural and anthropogenic stresses. Agassiz’s desert tortoises occur from southwestern Utah to near the Mexican border in California – a distance of over 450 km – but population densities vary greatly across this immense landscape (U.S. Fish and Wildlife Service 2015). Tortoises occur in the Sonoran Desert of California, including the eastern and western ends of the Coachella Valley, where it is one of 27 species covered under the Coachella Valley Multiple Species Habitat Conservation Plan and Natural Community Conservation Plan (CVMSHCP/NCCP). The southern portion of Joshua Tree National Park (JTNP) lies within this 1.1 million acre planning area, and was predicted to be an area of low-density tortoise populations using habitat suitability modeling (Barrows 2011). JTNP is near the southern distributional limit of G. agassizii, yet very little has been published regarding the ecology of tortoises in the Sonoran Desert of California. Reproductive output is an important gross measure of the ability of a population to persist. When integrated with data on fertility and survivorship, this information forms a foundation for assessing population status and formulating effective management strategies (e.g., Congdon et al. 1993, 1994), especially for imperiled species. One aspect of the biology of G. agassizii that has been particularly well-studied is reproductive output. However, most of what we know about this topic comes from research in the Mojave Desert portion of the species’ range (Ernst and Lovich 2009). Comparatively little has been published on the reproductive ecology of populations living in the Sonoran Desert ecosystem of California. Publications by Lovich et al. (1999, 2011, 2012, 2014, 2015) constitute the main body of literature on desert tortoise reproductive ecology in the Sonoran Desert of California, with one study population located at the western end of the CVMSHCP/NCCP area. Collecting data on Agassiz’s desert tortoise ecology in the Sonoran Desert ecosystem is important due to significant differences between the two adjacent desert ecosystems, especially the timing and amounts of annual precipitation, and their potential effects on reproductive output (e.g., Lovich et al. 5 2015). There are also differences in the vulnerability of tortoises to the effects of a warming, drying climate between the two deserts (Barrows 2011; Zylstra et al. 2012). The overall goal of this study was to collect data on demography, reproductive output, and genetic affinities at a study site in the Sonoran Desert portion of JTNP in the eastern end of the CVMSHCP/NCCP area. Specific objectives included: 1) Collect data to establish baselines on tortoise populations and/or their habitat suitability in core habitat within the CVNCCP area, including biotic and abiotic variables affecting persistence of tortoise populations; 2) Compare and contrast with data collected on desert tortoises at USGS/BLM study site near Palm Springs over 16 years; 3) Support long-term modeling efforts needed to determine tortoise population viability; 4) Refine modeled relationships with identified threats such as fire, invasive species and climate change; and 5) Prioritize adaptive management needs for the desert tortoise in and beyond the CVNCCP area. The data from this study will aid in determining baseline estimates of the desert tortoise population size within the planning area as well as establish a marked population of Agassiz’s desert tortoises for future monitoring. Data will be integrated with habitat modeling in order to refine model output. Genetic data will be collected on both the north and south sides of Interstate 10 to determine the potential effects of habitat fragmentation and genetic mixing. Analyses are ongoing and results beyond those presented in this report will be published in peer-reviewed scientific journals following inclusion of additional data collected on the south side of Shavers Valley in 2017-2018.

Report↗
USGS2017

Life history and status of Shortnose Sturgeon (Acipenser brevirostrum LeSueur, 1818)

Shortnose Sturgeon = SNS (Acipenser brevirostrum) is a small diadromous species with most populations living in large Atlantic coast rivers and estuaries of North America from New Brunswick, Canada, to GA, USA. There are no naturally landlocked populations, so all populations require access to fresh water and salt water to complete a natural life cycle. The species is amphidromous with use of fresh water and salt water (the estuary) varied across the species range, a pattern that may reflect whether freshwater or saltwater habitats provide optimal foraging and growth conditions. Migration is a dominant behavior during life history, beginning when fish are hatchling free embryos (southern SNS) or larvae (northeastern and far northern SNS). Migration continues by juveniles and nonspawning adult life stages on an individual time schedule with fish moving between natal river and estuary to forage or seek refuge, and by spawning adults migrating to and from riverine spawning grounds. Coastal movements by adults throughout the range (but particularly in the Gulf of Maine = GOM and among southern rivers) suggest widespread foraging, refuge use, and widespread colonization of new rivers. Colonization may also be occurring in the Potomac River, MD–VA–DC (midAtlantic region). Genetic studies (mtDNA and nDNA) identified distinct individual river populations of SNS, and recent rangewide nDNA studies identified five distinct evolutionary lineages of SNS in the USA: a northern metapopulation in GOM rivers; the Connecticut River; the Hudson River; a Delaware River–Chesapeake Bay metapopulation; and a large southern metapopulation (SC rivers to Altamaha River, GA). The Saint John River, NB, Canada, in the Bay of Fundy (north of the GOM), is the sixth distinct genetic lineage within SNS. Life history information from telemetry tracking supports the genetic information documenting extensive movement of adults among rivers within the three metapopulations. However, individual river populations with spawning adults are still the best basal unit for management and recovery planning. The focus on individual river populations should be complemented with attention to migratory processes and corridors that foster metapopulation level risks and benefits. The species may be extirpated at the center of the range, i.e., the midAtlantic region (Chesapeake Bay, MD–VA, and probably, NC), but large rivers in VA, including the James and Potomac rivers, need study. The largest SNS populations in GOM and northeastern rivers, like the Kennebec, Hudson, and Delaware rivers, typically have tens of thousands of adults. This contrasts with southern rivers, where rivers typically have much fewer (<2500) adults, except for the Altamaha River (>6000 adults). River damming in the 19th and 20th Centuries extirpated some populations, and also, created two dysfunctional segmented populations: the Connecticut River SNS in CT–MA and the SanteeCooper rivers–Lake Marion SNS in SC. The major anthropogenic impact on SNS in marine waters is fisheries bycatch. The major impacts that determine annual recruitment success occur in freshwater firstly, where adult spawning migrations and spawning are blocked or spawning success is affected by river regulation and secondly, where poor survival of early life stages is caused by river dredging, pollution, and unregulated impingement/entrainment in water withdrawal facilities. Climate warming has the potential to reduce abundance or eliminate SNS in many rivers, particularly in the South. In 1998, the National Marine Fisheries Service (NMFS) recommended management of 19 rivers as distinct population segments (DPSs) based on strong fidelity to natal rivers. A Biological Assessment completed in 2010 reaffirmed this approach. NMFS has not formally listed DPSs under the ESA and the species remains listed as endangered rangewide in the USA.

Journal of Applied Ichthyology↗
USGS2001

Mars Global Surveyor Thermal Emission Spectrometer experiment: Investigation description and surface science results

The Thermal Emission Spectrometer (TES) investigation on Mars Global Surveyor (MGS) is aimed at determining (1) the composition of surface minerals, rocks, and ices; (2) the temperature and dynamics of the atmosphere; (3) the properties of the atmospheric aerosols and clouds; (4) the nature of the polar regions; and (5) the thermophysical properties of the surface materials. These objectives are met using an infrared (5.8- to 50-μm) interferometric spectrometer, along with broadband thermal (5.1- to 150-μm) and visible/near-IR (0.3- to 2.9-μm) radiometers. The MGS TES instrument weighs 14.47 kg, consumes 10.6 W when operating, and is 23.6×35.5×40.0 cm in size. The TES data are calibrated to a 1-σ precision of 2.5 −6 ×10 −8 W cm −2 sr −1 /cm −1 , 1.6×10 −6 W cm −2 sr −1 , and ∼0.5 K in the spectrometer, visible/near-IR bolometer, and IR bolometer, respectively. These instrument subsections are calibrated to an absolute accuracy of ∼4×10 −8 W cm −2 sr −1 /cm −1 (0.5 K at 280 K), 1–2%, and ∼1–2 K, respectively. Global mapping of surface mineralogy at a spatial resolution of 3 km has shown the following: (1) The mineralogic composition of dark regions varies from basaltic, primarily plagioclase feldspar and clinopyroxene, in the ancient, southern highlands to andesitic, dominated by plagioclase feldspar and volcanic glass, in the younger northern plains. (2) Aqueous mineralization has produced gray, crystalline hematite in limited regions under ambient or hydrothermal conditions; these deposits are interpreted to be in-place sedimentary rock formations and indicate that liquid water was stable near the surface for a long period of time. (3) There is no evidence for large-scale (tens of kilometers) occurrences of moderate-grained (>50-μm) carbonates exposed at the surface at a detection limit of ∼10%. (4) Unweathered volcanic minerals dominate the spectral properties of dark regions, and weathering products, such as clays, have not been observed anywhere above a detection limit of ∼10%; this lack of evidence for chemical weathering indicates a geologic history dominated by a cold, dry climate in which mechanical, rather than chemical, weathering was the significant form of erosion and sediment production. (5) There is no conclusive evidence for sulfate minerals at a detection limit of ∼15%. The polar region has been studied with the following major conclusions: (1) Condensed CO 2 has three distinct end-members, from fine-grained crystals to slab ice. (2) The growth and retreat of the polar caps observed by MGS is virtually the same as observed by Viking 12 Martian years ago. (3) Unique regions have been identified that appear to differ primarily in the grain size of CO 2 ; one south polar region appears to remain as black slab CO 2 ice throughout its sublimation. (4) Regional atmospheric dust is common in localized and regional dust storms around the margin and interior of the southern cap. Analysis of the thermophysical properties of the surface shows that (1) the spatial pattern of albedo has changed since Viking observations, (2) a unique cluster of surface materials with intermediate inertia and albedo occurs that is distinct from the previously identified low-inertia/bright and high-inertia/dark surfaces, and (3) localized patches of high-inertia material have been found in topographic lows and may have been formed by a unique set of aeolian, fluvial, or erosional processes or may be exposed bedrock.

Journal of Geophysical Research E: Planets↗
USGS2001

The geology of a part of Acadia and the nature of the Acadian orogeny across Central and Eastern Maine

The zone of Acadian collision between the Medial New England and Composite Avalon terranes is well preserved in Maine. A transect from northwest (Rome) to southeast (Camden) crosses the eastern part of Medial New England comprising the Central Maine basin, Liberty-Orrington thrust sheet, and Fredericton trough, and the western part of Composite Avalon, including the Graham Lake, Clarry Hill, and Clam Cove thrust sheets. U-Pb geochronology of events before, during, and after the Acadian orogeny helps elucidate the nature and distribution of tectonostratigraphic belts in this zone and the timing of some Acadian events in the Northern Appalachians. The Central Maine basin consists of sedimentary and volcanic rocks of Middle Ordovician (∼470 to ∼460 Ma) age overlain with probable conformity by latest Ordovician(?) through earliest Devonian marine rift and flysch sedimentary rocks; these are intruded by weakly to undeformed plutonic rocks of Early and Middle Devonian age (∼399–378 Ma). The Fredericton trough consists of Early Silurian gray pelite and sandstone to earliest Late Silurian calcareous turbidite, deformed and variably metamorphosed prior to the emplacement of Late Silurian (∼422 Ma) and Early to Late Devonian (∼418 to ∼368 Ma) plutons. The Liberty-Orrington thrust sheet consists of Cambrian(?)-Ordovician (>∼474 to ∼469 Ma and younger) clastic sedimentary and volcanic rocks intruded by highly deformed Late Silurian (∼424 to ∼422 Ma) and Devonian (∼418 to ∼389 Ma) plutons, possibly metamorphosed in Late Silurian time (prior to ∼417 Ma), and metamorphosed to amphibolite facies in Early to Middle Devonian time (∼400 to ∼381 Ma). The Graham Lake thrust sheet contains possible Precambrian rocks, Cambrian sedimentary rocks with a volcanic unit dated at ∼503 Ma, and Ordovician rocks with possible Caradocian Old World fossils, metamorphosed and deformed in Silurian time and intruded by mildly to undeformed Late Silurian (∼421 Ma) and Late Devonian (∼371 to ∼368 Ma) plutons. The Clarry Hill thrust sheet consists of poorly studied, highly metamorphosed Cambrian (?) rocks. The Clam Cove thrust sheet contains highly deformed Precambrian limestone, shale, sandstone, and conglomerate, metamorphosed to epidote amphibolite facies and intruded by a mildly deformed pluton dated at ∼421 Ma. Metamorphism, deformation, and voluminous intrusive igneous activity of Silurian age are common to both the most southeastern parts of Medial New England and the thrust sheets of Composite Avalon. In contrast to Medial New England, the thrust sheets of Composite Avalon show only modest effects of Devonian deformation and metamorphism. Regional stratigraphic relations, paleontologic findings, and U-Pb geochronology suggest that the Graham Lake, Clarry Hill, and Clam Cove thrust sheets are far-traveled allochthons that were widely separated from Medial New England in the Silurian. One hundred nine (109) new U-Pb analyses of zircon, monazite, and sphene from 25 samples of metamorphosed, stratified, and intrusive igneous rocks are used to decipher the history of events along the transect. In our view, many of the structures within Medial New England were formed during the closing of the back-arc ocean during the waning stages of the Taconian orogeny. These features include the precursors to the upright folds found in Silurian sedimentary rocks, the west-facing Liberty-Orrington thrust sheet, and the Silurian plutons of Medial New England. Acadian tectonic features, including flysch sedimentation, igneous activity, deformation with nappe emplacement, and metamorphism record the progressive loading of Medial New England by a stack of thrust nappes emplaced in latest Silurian to Middle Devonian time. The Acadian orogeny is a prolonged event, lasting from earliest Late Silurian to the Late Devonian, whose evolution involved: (1) convergence between Medial New England and Composite Avalon along an east-dipping subduction zone from earliest Late Silurian to Early Devonian time; (2) collision and concurrent delamination of lithospheric mantle beneath Medial New England in Early Devonian time resulting in deformation, high-grade metamorphism, and intrusive igneous activity in the most eastern part of Medial New England and the western parts of Composite Avalon; (3) Early to Middle Devonian northwest-migrating penetrative deformations of the Acadian Main stage, including northwest-directed thrusting and recumbent folding followed by tightening of folds possibly produced in the waning stages of the Taconian orogeny and forming folded wave trains of isoclinal folds (∼419 to ∼404 Ma), (4) asymmetrical folds produced by east-west shortening (∼399 to ∼380 Ma); and (5) final westward emplacement of Composite Avalon thrust sheets onto Medial New England in Late Devonian time (∼380 to ∼371 Ma). The present boundary between rocks of Medial New England and Composite Avalon at the surface is the Sennebec Pond fault, a high-angle fault that cuts the Graham Lake and Clarry Hill thrusts, and is intruded by the Mt. Waldo pluton (∼371), one of several Late Devonian plutons (∼371 to ∼367 Ma) that mark the end of the Acadian orogeny in coastal Maine. The thrust sheets of Composite Avalon carried rocks of peri-Gondwanan affinity and with possible Old World fauna many kilometers to the west over Medial New England, thus potentially hiding the original suture at depth under the Gulf of Maine.

Maine↗