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At least 1,549 records · Page 86Linked to original sources

USGS2014

Development of ten microsatellite loci in the invasive giant African land snail, Achatina (=Lissachatina) fulica Bowdich, 1822

A suite of tetra-nucleotide microsatellite loci were developed for the invasive giant African land snail, Achatina (=Lissachatina) fulica Bowdich, 1822, from Ion Torrent next-generation sequencing data. Ten of the 96 primer sets tested amplified consistently in 30 snails from Miami, Florida, plus 12 individuals representative of their native East Africa, Indian and Pacific Ocean regions. The loci displayed moderate levels of allelic diversity (average 5.6 alleles/locus) and heterozygosity (average 42 %). Levels of genetic diversity were sufficient to produce unique multi-locus genotypes and detect phylogeographic structuring among regional samples. The invasive A. fulica can cause extensive damage to important food crops and natural resources, including native flora and fauna. The loci characterized here will be useful for determining the origins and tracking the spread of invasions, detecting fine-scale spatial structuring and estimating demographic parameters.

Conservation Genetics Resources↗

USGS2015

Rapid isolation of microsatellite DNAs and identification of polymorphic mitochondrial DNA regions in the fish rotan (Perccottus glenii) invading European Russia

Human-mediated translocations and subsequent large-scale colonization by the invasive fish rotan (Perccottus glenii Dybowski, 1877; Perciformes, Odontobutidae), also known as Amur or Chinese sleeper, has resulted in dramatic transformations of small lentic ecosystems. However, no detailed genetic information exists on population structure, levels of effective movement, or relatedness among geographic populations of P. glenii within the European part of the range. We used massively parallel genomic DNA shotgun sequencing on the semiconductor-based Ion Torrent Personal Genome Machine (PGM) sequencing platform to identify nuclear microsatellite and mitochondrial DNA sequences in P. glenii from European Russia. Here we describe the characterization of nine nuclear microsatellite loci, ascertain levels of allelic diversity, heterozygosity, and demographic status of P. glenii collected from Ilev, Russia, one of several initial introduction points in European Russia. In addition, we mapped sequence reads to the complete P. glenii mitochondrial DNA sequence to identify polymorphic regions. Nuclear microsatellite markers developed for P. glenii yielded sufficient genetic diversity to: (1) produce unique multilocus genotypes; (2) elucidate structure among geographic populations; and (3) provide unique perspectives for analysis of population sizes and historical demographics. Among 4.9 million filtered P. glenii Ion Torrent PGM sequence reads, 11,304 mapped to the mitochondrial genome (NC_020350). This resulted in 100 % coverage of this genome to a mean coverage depth of 102X. A total of 130 variable sites were observed between the publicly available genome from China and the studied composite mitochondrial genome. Among these, 82 were diagnostic and monomorphic between the mitochondrial genomes and distributed among 15 genome regions. The polymorphic sites (N = 48) were distributed among 11 mitochondrial genome regions. Our results also indicate that sequence reads generated from two three-hour runs on the Ion Torrent PGM can generate a sufficient number of nuclear and mitochondrial markers to improve understanding of the evolutionary and ecological dynamics of non-model and in particular, invasive species.

European Russia↗

USGS2015

Development of twelve microsatellite loci in the red tree corals Primnoa resedaeformis and Primnoa pacifica

A suite of tetra-, penta-, and hexa-nucleotide microsatellite loci were developed from Roche 454 pyrosequencing data for the cold-water octocorals Primnoa resedaeformis and P . pacifica . Twelve of 98 primer sets tested consistently amplified in 30 P . resedaeformis samples from Baltimore Canyon (western North Atlantic Ocean) and in 24 P . pacifica samples (Shutter Ridge, eastern Gulf of Alaska). The loci displayed moderate levels of allelic diversity (average 7.5 alleles/locus) and heterozygosity (average 47 %). Levels of genetic diversity were sufficient to produce unique multi-locus genotypes and to distinguish species. These common species are long-lived (hundreds of years) and provide essential fish habitat ( P . pacifica ), yet populations are provided little protection from human activities. These loci will be used to determine regional patterns of population connectivity to inform effective marine spatial planning and ecosystem-based fisheries management.

Conservation Genetics Resources↗

USGS2017

Novel RAD sequence data reveal a lack of genomic divergence between dietary ecotypes in a landlocked salmonid population

Preservation of heritable ecological diversity within species and populations is a key challenge for managing natural resources and wild populations. Salmonid fish are iconic and socio-economically important species for commercial, aquaculture, and recreational fisheries across the globe. Many salmonids are known to exhibit ecological divergence within species, including distinct feeding ecotypes within the same lakes. Here we used 5559 SNPs, derived from RAD sequencing, to perform population genetic comparisons between two dietary ecotypes of sockeye salmon ( Oncorhynchus nerka ) in Jo-Jo Lake, Alaska (USA). We tested the standing hypothesis that these two ecotypes are currently diverging as a result of adaptation to distinct dietary niches; results support earlier conclusions of a single panmictic population. The RAD sequence data revealed 40 new SNPs not previously detected in the species, and our sequence data can be used in future studies of ecotypic diversity in salmonid species.

Alaska↗

USGS2012

Local and landscape associations between wintering dabbling ducks and wetland complexes in Mississippi

Landscape features influence distribution of waterbirds throughout their annual cycle. A conceptual model, the wetland habitat complex, may be useful in conservation of wetland habitats for dabbling ducks (Anatini). The foundation of this conceptual model is that ducks seek complexes of wetlands containing diverse resources to meet dynamic physiological needs. We included flooded croplands, wetlands and ponds, public-land waterfowl sanctuary, and diversity of habitats as key components of wetland habitat complexes and compared their relative influence at two spatial scales (i.e., local, 0.25-km radius; landscape, 4-km) on dabbling ducks wintering in western Mississippi, USA during winters 2002–2004. Distribution of mallard ( Anas platyrhynchos ) groups was positively associated with flooded cropland at local and landscape scales. Models representing flooded croplands at the landscape scale best explained occurrence of other dabbling ducks. Habitat complexity measured at both scales best explained group size of other dabbling ducks. Flooded croplands likely provided food that had decreased in availability due to conversion of wetlands to agriculture. Wetland complexes at landscape scales were more attractive to wintering ducks than single or structurally simple wetlands. Conservation of wetland complexes at large spatial scales (≥5,000 ha) on public and private lands will require coordination among multiple stakeholders.

Mississippi↗

USGS2013

Phragmites australis expansion in a restored brackish marsh: documentation at different time scales

Invasive plants in restored habitats can alter the system such that restoration goals are not met. Non-native lineages of Phragmites australis (hereafter Phragmites) are invasive in North American wetlands, and their presence can be problematic because of decreased species diversity and altered physicochemical processes. Phragmites is a challenging species for restoration because both native and non-native lineages can co-occur. We documented Phragmites expansion in a brackish marsh in Louisiana, USA that was restored with dredged sediments. Invasive Phragmites clones were inadvertently planted at the site. Phragmites expansion was documented through field measurements and aerial imagery. No growth differences were apparent between lineages during the first growing season. Horizontal expansion of 2.27 ± 0.15 m (mean ± 1SE) 5 months after planting occurred through rhizome growth. Seven years after planting, three patches with a combined aerial cover of about 0.7 ha were delineated. The study verified that Phragmites can grow relatively rapidly and persist on dredged sediments. Long-term rapid growth of invasive Phragmites may be a positive attribute in areas subject to high erosion and subsidence rates, despite reductions in species diversity. Acceptability of the presence of invasive Phragmites will depend on restoration goals.

Louisiana↗

USGS2013

Genetic structuring of northern myotis (Myotis septentrionalis) at multiple spatial scales

Although groups of bats may be genetically distinguishable at large spatial scales, the effects of forest disturbances, particularly permanent land use conversions on fine-scale population structure and gene flow of summer aggregations of philopatric bat species are less clear. We genotyped and analyzed variation at 10 nuclear DNA microsatellite markers in 182 individuals of the forest-dwelling northern myotis ( Myotis septentrionalis ) at multiple spatial scales, from within first-order watersheds scaling up to larger regional areas in West Virginia and New York. Our results indicate that groups of northern myotis were genetically indistinguishable at any spatial scale we considered, and the collective population maintained high genetic diversity. It is likely that the ability to migrate, exploit small forest patches, and use networks of mating sites located throughout the Appalachian Mountains, Interior Highlands, and elsewhere in the hibernation range have allowed northern myotis to maintain high genetic diversity and gene flow regardless of forest disturbances at local and regional spatial scales. A consequence of maintaining high gene flow might be the potential to minimize genetic founder effects following population declines caused currently by the enzootic White-nose Syndrome.

Acta Theriologica↗

USGS2012

Ecology and evolution of pine life histories

Introduction - Pinus is a diverse genus of trees widely distributed throughout the Northern Hemisphere. Understanding pine life history is critical to both conservation and fire management. Objectives - Here I lay out the different pathways of pine life history adaptation and a brief overview of pine evolution and the very significant role that fire has played. Results - Pinus originated ~150 Ma in the mid-Mesozoic Era and radiated across the northern continent of Laurasia during the Cretaceous Period. Pines have followed two evolutionary strategies interpreted as responses to competition by the newly emerging angiosperms. The Strobus lineage mostly has radiated into stressful sites of low nutrient soils and extremes in cold or heat. The Pinus (subgenus) lineage has radiated into fire-prone landscapes with diverse fire regimes. Examination of life history traits illustrates syndromes associated with fire-avoider, fire-tolerater, fire-embracer, and fire-refuge strategies. Conclusion - Understanding the current pattern of pine distribution requires interpreting their evolution in terms of climate, geology, and fire. All three of these factors have played a role since the Mesozoic origin of the genus. All are important to the appropriate management of these resources.

Annals of Forest Science↗

USGS1991

Gaylussite formation at Mono Lake, California

The salinity of Mono Lake has steadily increased since 1941 from 50%. to about 90%. due to diversion of tributary streams. This increase has resulted in the newly discovered precipitation of gaylussite (Na 2 Ca(CO 3 ) 2 · 5H 2 O). Chemical modeling of the lake water using Pitzer equations suggests that gaylussite has been forming year round since about 1970 when the salinity first exceeded 80%., and that it was earlier forming intermittently at lower salinities in the winter shortly after diversion began, breaking down incongruently to aragonite during summers. Lake water appears to remain at a constant 9-fold supersaturation with aragonite at all salinities, perhaps buffered by monohydrocalcite which appears to be just at saturation for all salinities. Other saline lakes also appear to be buffered by monohydrocalcite.

California↗

USGS1970

Latitudinal gradients in tertiary molluscan faunas of the Pacific coast

Tertiary molluscan faunas of the middle latitudes of the marginal eastern North Pacific are characterized by warm-water taxa whose descendants now live in more southerly latitudes. A series of profiles in which cumulative percentages of warm-water faunal elements are plotted against latitude show progressive northward decreases in the percentage of these elements in the faunas of Pacific coast Tertiary stages. Systematic changes in the relative position of these latitudinal gradients during the Middle and Late Tertiary are related to climatic change in the Pacific Basin. Widespread tropical marine climate in the middle latitudes of the eastern North Pacific during the Eocene is indicated by widespread faunal units characterized by high levels of taxonomic diversity. Succeeding Early Oligocene faunas are less diverse, suggesting cooler climatic conditions. Unusually low representations of warm-water genera characterize the molluscan faunas of the Acila shumardi Zone in central California (latitude 34°–37°N). The anomalously cool-water aspect of these faunas may record the occurrence of upwelling along a bold linear segment of the Pacific coast. During the Late Oligocene or the Early Miocene, they are replaced by faunas of unusually warm-water aspect resulting in positive anomalies in Miocene latitudinal faunal gradients in central California. The Miocene anomalies seem to result from the development of an irregular Neogene coastline with extensive, newly established shallow-water embayments.

Palaeogeography, Palaeoclimatology, Palaeoecology↗

USGS1996

Shallow marine event sedimentation in a volcanic arc-related setting: The Ordovician Suri Formation, Famatina Range, northwest Argentina

The Loma del Kilómetro Member of the Lower Ordovician Suri Formation records arc-related shelf sedimentation in the Famatina Basin of northwest Argentina. Nine facies, grouped into three facies assemblages, are recognized. Facies assemblage 1 [massive and parallel-laminated mudstones (facies A) locally punctuated by normally graded or parallel-laminated silty sandstones (facies B] records deposition from suspension fall-out and episodic storm-induced turbidity currents in an outer shelf setting. Facies assemblage 2 [massive and parallel-laminated mudstones (facies A) interbedded with rippled-top very fine-grained sandstones (facies D)] is interpreted as the product of background sedimentation alternating with distal storm events in a middle shelf environment. Facies assemblage 3 [normally graded coarse to fine-grained sandstones (facies C); parallel-laminated to low angle cross-stratified sandstones (facies E); hummocky cross-stratified sandstones and siltstones (facies F); interstratified fine-grained sandstones and mudstones (facies G); massive muddy siltstones and sandstones (facies H); tuffaceous sandstones (facies 1); and interbedded thin units of massive and parallel-laminated mudstones (facies A)] is thought to represent volcaniclastic mass flow and storm deposition coupled with subordinated suspension fall-out in an inner-shelf to lower-shoreface setting. The Loma del Kilómetro Member records regress ive-transgressive sedimentation in a storm- and mass flow-dominated high-gradient shelf. Volcano-tectonic activity was the important control on shelf morphology, while relative sea-level change influenced sedimentation. The lower part of the succession is attributed to mud blanketing during high stand and volcanic quiescence. Progradation of the inner shelf to lower shoreface facies assemblage in the middle part represents an abrupt basinward shoreline migration. An erosive-based, non-volcaniclastic, turbidite unit at the base of this package suggests a sea level fall. Pyroclastic detritus, andesites, and a non-volcanic terrain were eroded and their detritus was transported basinward and redeposited by sediment gravity flows during the low stand. The local coexistence of juvenile pyroclastic detritus and fossils suggests reworking of rare ash-falls. The upper part of the Loma del Kilómetro Member records a transgression with no evidence of contemporaneous volcanism. Biostratinomic, paleoecologic, and ichnologic analyses support this paleoenvironmental interpretations and provide independent evidence for the dominance of episodic sedimentation in an arc-related shallow marine setting. Fossil concentrations were mainly formed by event processes, such as storms and volcaniclastic mass flows. High depositional rates inhibited formation of sediment-starved biogenic concentrations. Collectively, trace fossils belong to the Cruziana ichnofacies. Low diversity, scarcity, and presence of relatively simple forms indicate benthic activity under stressful conditions, most probably linked to high sedimentation rates. Contrasting sedimentary dynamics between ‘normal shelves’ and their volcaniclastic counterparts produce distinct and particular signatures in the stratigraphic record. Arc-related shelves are typified by event deposition with significant participation of sediment gravity flows, relatively high sedimentation rates, textural and mineralogical immaturity of sediments, scarcity and low diversity of trace fossils, and dominance of transported and reworked faunal assemblages genetically related to episodic processes.

Famatina Range, northwest Argentina↗

USGS1995

The role of palynology in paleoecological analyses of Tertiary coals

Pollen, spores, and other plant microfossils are important constituents of Tertiary coals, both as petrographic components (the maceral sporinite) and as distinctive indicators of the nature of the depositional environment in which the coal-forming peat accumulated. Palynological analyses, which have been conducted on Tertiary coals since the 1930's, play an increasingly important role in modern paleoecological analyses of coals. Among the most important factors controlling the petrographic composition and facies characteristics of coal deposits are the types and relative abundances of plants that composed the peat. At present, wetland environments in which peat accumulates (mires) range from marshes and bogs to forested swamps; each is inhabited by distinctive plant communities. These plant communities are associated with varied conditions of climate, water depth, chemistry, and nutrient supply, and the floras can be indicative of these conditions. In the Tertiary Period, plant communities of mires were also highly diverse and specialized (especially as compared with those of the Carboniferous). The dominant species in some Paleocene mire floras were gymnosperms, but continuing a trend begun in Late Cretaceous time, angiosperms became increasingly prominent through the Tertiary. The diverse: angiosperm-dominated mire floras produced coals that vary significantly in facies and hence in quality. Such contrasts are evident in contemporaneous coals from different paleolatitudes, as well as among, coals of different ages within the Tertiary, as exemplified by selected deposits in the western United. States. The palynofloras of these coals reflect the floristic composition of the plant communities of the ancient mires.

International Journal of Coal Geology↗

USGS1995

Latest Quaternary foraminifers and sediment transport in Pervenets Canyon, Bering Sea

A combination of microfossil and sediment analysis has been used in an attempt to understand oceanographic processes and the late Quaternary history of the Pervenets Canyon region. The primary sedimentation process in Pervenets Canyon is downslope transport. Near the shelfbreak, there is evidence of turbidite and debris-flow activity, but at the distal end of the upper canyon and on the continental slope there is no macroscopic evidence for these processes. Analysis of the foraminiferal assemblages shows that the fauna is 97.6% from the Suborder Rotaliina and about 2.0% from the Suborder Textulariina. The Suborder Miliolina accounts for approximately 0.4% of the fauna. The Pervenets Canyon fauna is most similar to other faunas from the Bering Sea, indicating a North Pacific Ocean influence on the fauna. Foraminiferal abundance and species diversity vary widely in the samples studied. The major factors controlling these values are downslope transport of sediment, disintegration of arenaceous taxa, dissolution of calcareous taxa, and diversity limited by low-oxygen bottom waters. Downslope transport of shelf species is indicated by the presence of Elphidium clavatum and E. excavatum . Shallow-shelf and low-oxygen foraminiferal faunas are often intermixed in the samples. The distribution of these low-oxygen faunas in Core 81-65 suggests that the oxygen-minimum zone fluctuated with sea level.

Marine Micropaleontology↗

USGS2013

Hormonal control of euryhalinity

Hormones play a critical role in maintaining body fluid balance in euryhaline fishes during changes in environmental salinity. The neuroendocrine axis senses osmotic and ionic changes, then signals and coordinates tissue-specific responses to regulate water and ion fluxes. Rapid-acting hormones, e.g. angiotensins, cope with immediate challenges by controlling drinking rate and the activity of ion transporters in the gill, gut, and kidney. Slow-acting hormones, e.g. prolactin and growth hormone/insulin-like growth factor-1, reorganize the body for long-term acclimation by altering the abundance of ion transporters and through cell proliferation and differentiation of ionocytes and other osmoregulatory cells. Euryhaline species exist in all groups of fish, including cyclostomes, and cartilaginous and teleost fishes. The diverse strategies for responding to changes in salinity have led to differential regulation and tissue-specific effects of hormones. Combining traditional physiological approaches with genomic, transcriptomic, and proteomic analyses will elucidate the patterns and diversity of the endocrine control of euryhalinity.

Book chapter↗

USGS2013

Smolt physiology and endocrinology

Book chapter↗

USGS2016

Hydrologic exchange flows and their ecological consequences in river corridors

The actively flowing waters of streams and rivers remain in close contact with surrounding off-channel and subsurface environments. These hydrologic linkages between relatively fast flowing channel waters, with more slowly flowing waters off-channel and in the subsurface, are collectively referred to as hydrologic exchange flows (HEFs). HEFs include surface exchange with a channel’s marginal areas and subsurface flow through the streambed (hyporheic flow), as well as storm-driven bank storage and overbank flows onto floodplains. HEFs are important, not only for storing water and attenuating flood peaks, but also for their role in influencing water conservation, water quality improvement, and related outcomes for ecological values and services of aquatic ecosystems. Biogeochemical opportunities for chemical transformations are increased by HEFs as a result of the prolonged contact between flowing waters and geochemically and microbially active surfaces of sediments and vegetation. Chemical processing is intensified and water quality is often improved by removal of excess nutrients, metals, and organic contaminants from flowing waters. HEFs also are important regulators of organic matter decomposition, nutrient recycling, and stream metabolism that helps establish a balanced and resilient aquatic food web. The shallow and protected storage zones associated with HEFs support nursery and feeding areas for aquatic organisms that sustain aquatic biological diversity. Understanding of these varied roles for HEFs has been driven by the related disciplines of stream ecology, fluvial geomorphology, surface-water hydraulics, and groundwater hydrology. A current research emphasis is on the role that HEFs play in altered flow regimes, including restoration to achieve diverse goals, such as expanding aquatic habitats and managing dissolved and suspended river loads to reduce over-fertilization of coastal waters and offset wetland loss. New integrative concepts and models are emerging (eg, hydrologic connectivity) that emphasize HEF functions in river corridors over a wide range of spatial and temporal scales.

Book chapter↗

USGS2017

Geomorphology and sediment regimes of intermittent rivers and ephemeral streams

The geomorphology and sediment regimes of intermittent rivers and ephemeral streams (IRES) are extremely diverse, owing in large part to the substantial spatiotemporal variability of the associated hydrological regimes. We describe the geomorphological character and sediment transport processes along IRES within the context of four geomorphological zones—upland, piedmont, lowland, and floodout—to illustrate the underpinning longitudinal trends of sediment production, transfer, and deposition that exist at the landscape scale. Many geomorphological features of IRES tend to be spatially discontinuous as a result of extended no or low-flow conditions that are punctuated by high-magnitude flood events. Diversity of geomorphology and sediment regimes both within and between the four geomorphological zones therefore promotes ecological processes and patterns in IRES that can be very distinct from perennial river systems.

Book chapter↗

USGS2019

Soil warming effects on tropical forests with highly weathered soils

The tropics are a region encircling the equator, delineated to the north by the Tropic of Cancer (23°26′14.0″N) and to the south by the Tropic of Capricorn (23°26′14.0″S). While we often think of the tropics as consistently warm and wet throughout the year, in reality, the tropics maintain a myriad of climates. Of the 116 Holdridge life zones (a global bioclimatic classification scheme), the tropics contain more life zones than the sum of all the planet's other geographic regions combined ( Holdridge, 1967 ). In addition to high climatic diversity, the tropics support a wide range of parent materials, landforms, geomorphic characteristics, and soil ages, and maintain all 12 soil types of the USDA soil taxonomy system ( Palm et al., 2007 ; Porder et al., 2007 ; Quesada et al., 2010 ; Richter and Babbar, 1991 ; Sanchez, 1977 ; Soil Survey Staff, 2006 ; Townsend et al., 2008 ). Accordingly, there is no single representative tropical ecosystem. Given the diversity of tropical biomes, this chapter will focus specifically on tropical forested ecosystems and their responses to warming because of their global importance, potential sensitivity to change, and the fact that an improved understanding of how these ecosystems may respond to warmer climate conditions is of significant importance to ecology and society. Furthermore, while generally considering all tropical forest types, emphasis in this chapter is on the humid tropics for which we have most data.

Book chapter↗