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Results for “Molecular Ecology”

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At least 181 records · Page 10Linked to original sources
USGS2006

Arsenic and selenium in microbial metabolism

Arsenic and selenium are readily metabolized by prokaryotes, participating in a full range of metabolic functions including assimilation, methylation, detoxification, and anaerobic respiration. Arsenic speciation and mobility is affected by microbes through oxidation/reduction reactions as part of resistance and respiratory processes. A robust arsenic cycle has been demonstrated in diverse environments. Respiratory arsenate reductases, arsenic methyltransferases, and new components in arsenic resistance have been recently described. The requirement for selenium stems primarily from its incorporation into selenocysteine and its function in selenoenzymes. Selenium oxyanions can serve as an electron acceptor in anaerobic respiration, forming distinct nanoparticles of elemental selenium that may be enriched in (76)Se. The biogenesis of selenoproteins has been elucidated, and selenium methyltransferases and a respiratory selenate reductase have also been described. This review highlights recent advances in ecology, biochemistry, and molecular biology and provides a prelude to the impact of genomics studies.

Annual Review of Microbiology↗
USGS1995

What is Falco Altaicus Menzbier?

The systematics of the Altay falcon (Falco altaicus/lorenzi) remains enigmatic. First reported in 1811, it has been treated as a gyrfalcon (F. rusticolus), a saker (F. cherrug), and two separate species (F. lorenzi and F. altaicus). Of 53 'altaicus' specimens examined, at least two are misidentified gyrfalcons, many are typical sakers, but 34 (the core group) are considered to be the true Altay falcon type. Adults have red, brown, and gray color morphs. The red (backed) morph closely resembles some eastern sakers; the chocolate and gray morphs resemble respective gyrfalcon morphs. While the true affinities of the Altay falcon will be resolved by molecular genetics, the ecological, geographical, and morphological information suggest that the core group represents a gyrfalcon-saker cross that is being swamped through back crosses with the saker. The breeding range of the core group (i.e., the Altay and Sayan Mountains) is much smaller than previously reported.

Journal of Raptor Research↗
USGS2011

Molecular insights into the biology of Greater Sage-Grouse

Recent research on Greater Sage-Grouse ( Centrocercus urophasianus ) genetics has revealed some important findings. First, multiple paternity in broods is more prevalent than previously thought, and leks do not comprise kin groups. Second, the Greater Sage-Grouse is genetically distinct from the congeneric Gunnison sage-grouse ( C. minimus ). Third, the Lyon-Mono population in the Mono Basin, spanning the border between Nevada and California, has unique genetic characteristics. Fourth, the previous delineation of western ( C. u. phaios ) and eastern Greater Sage-Grouse ( C. u. urophasianus ) is not supported genetically. Fifth, two isolated populations in Washington show indications that genetic diversity has been lost due to population declines and isolation. This chapter examines the use of molecular genetics to understand the biology of Greater Sage-Grouse for the conservation and management of this species and put it into the context of avian ecology based on selected molecular studies.

Book chapter↗
USGS2017

Characterization of microsatellite loci for the Gulf Coast waterdog (Necturus beyeri) using paired-end Illumina shotgun sequencing and cross-amplification in other Necturus

Amphibians are one of the most threatened groups of vertebrates (Stuart et al. 2004; Wake and Vredenburg 2008), and the application of molecular techniques to amphibian ecology and genetics has dramatically improved our ability to conserve species and populations (see Shaffer et al. [2015] for review). Microsatellites, tandem repeats of two to six nucleotides in the nuclear genome, are highly variable molecular markers that can be used to describe gene flow and genetic diversity, each of which is positively correlated with population persistence (Allendorf and Luikart 2007; Allentoft and O’Brien 2010; Avise 2004; Selkoe and Toonen 2006). Microsatellite loci have frequently been applied to studies involving terrestrial and pond breeding amphibians (Emel and Storfer 2012), but fewer studies have focused on taxa inhabiting lotic systems (Emel and Storfer 2012). For example, studies characterizing microsatellite loci are completely lacking for a group of permanently aquatic salamanders, the waterdogs and mudpuppies (Family Proteidae, Genus Necturus ) (Rafinesque 1819). The genus Necturus consists of several species of perennibranch salamanders that can be found throughout many freshwater streams, rivers, and lakes in North America (Petranka 1998). Some authorities recognize five species (Crother 2012; Petranka 1998), including the Mudpuppy ( Necturus maculosus ) (Rafinesque 1819), Gulf Coast Waterdog ( N. beyeri ) (Viosca 1937), Black Warrior Waterdog ( N. alabamensis ) (Viosca 1937), Neuse River Waterdog ( N. lewisi ) (Brimley 1924), and Dwarf Waterdog ( N. punctatus ) (Gibbes 1850). This taxonomy also recognizes two subspecies within N. maculosus , including the Common Mudpuppy ( N. m. maculosus ) and the Red River Waterdog ( N. m. louisianensis ) (Crother 2012; Petranka 1998; Schmidt 1953). Other authorities suggest that there are six or seven species within Necturus (Collins 1990; Frost 2016; Powell et al. 2016). These more diverse schemes recognize each of the aforementioned five species while also elevating the Red River Waterdog ( N. louisianensis ) (Collins 1990; Frost 2016; Powell et al. 2016; Viosca 1938) and Löding’s Waterdog ( N. lödingi or N. cf. beyeri ) (Bart et al. 1997; Guyer 2005a; Viosca 1938). Allozyme work by Guttman et al. (1990) suggests that there is at least one cryptic species of Necturus in drainages east of the Mobile Basin and south of the Alabama River, and both Bart et al. (1997) and Guyer (2005a) advise that these populations should be referred to as N. cf. beyeri . However, until range wide studies incorporating genetic and other data are published, we will follow the five species taxonomy outlined by Crother (2012) while acknowledging that certain taxa, such as N. maculosus and N. beyeri , may require systematic revision.

Herpetological Review↗
USGS2010

Linking microbial and ecosystem ecology using ecological stoichiometry: a synthesis of conceptual and empirical approaches

Currently, one of the biggest challenges in microbial and ecosystem ecology is to develop conceptual models that organize the growing body of information on environmental microbiology into a clear mechanistic framework with a direct link to ecosystem processes. Doing so will enable development of testable hypotheses to better direct future research and increase understanding of key constraints on biogeochemical networks. Although the understanding of phenotypic and genotypic diversity of microorganisms in the environment is rapidly accumulating, how controls on microbial physiology ultimately affect biogeochemical fluxes remains poorly understood. We propose that insight into constraints on biogeochemical cycles can be achieved by a more rigorous evaluation of microbial community biomass composition within the context of ecological stoichiometry. Multiple recent studies have pointed to microbial biomass stoichiometry as an important determinant of when microorganisms retain or recycle mineral nutrients. We identify the relevant cellular components that most likely drive changes in microbial biomass stoichiometry by defining a conceptual model rooted in ecological stoichiometry. More importantly, we show how X-ray microanalysis (XRMA), nanoscale secondary ion mass spectroscopy (NanoSIMS), Raman microspectroscopy, and in situ hybridization techniques (for example, FISH) can be applied in concert to allow for direct empirical evaluation of the proposed conceptual framework. This approach links an important piece of the ecological literature, ecological stoichiometry, with the molecular front of the microbial revolution, in an attempt to provide new insight into how microbial physiology could constrain ecosystem processes.

Ecosystems↗
USGS1999

Tadpoles: the Biology of Anuran Larvae

The recent alarming declines in amphibian populations worldwide and the suitability of amphibians for use in answering research questions in disciplines as diverse as molecular systematics, animal behavior, ecology, and evolutionary biology have focused enormous attention on tadpoles. Yet despite this growing interest, relatively little is known about these fascinating creatures. n this invaluable reference, leading experts on tadpole biology relate what we currently know about tadpoles and what we might learn from them in the future. Tadpoles provides detailed summaries of tadpole morphology, development, behavior, ecology, and environmental physiology; explores the evolutionary consequences of the tadpole stage; synthesizes available information on their biodiversity, and presents a standardized terminology and an exhaustive literature review of tadpole biology.

Book↗
USGS2019

Successful molecular detection studies require clear communication among diverse research partners

Molecular detection techniques are powerful tools used in ecological applications ranging from diet analyses to pathogen surveillance. Research partnerships that use these tools often involve collaboration among professionals with expertise in field biology, laboratory techniques, quantitative modeling, wildlife disease, and natural resource management. However, in many cases, each of these collaborators lacks specific knowledge about the approaches, decisions, methods, and terminology used by their research partners, which can impede effective communication and act as a barrier to the efficient use of molecular data for ecological inferences and subsequent conservation decision making. We outline a collaborative framework to assist colleagues with diverse types of expertise to effectively translate their scientific and management needs to research partners from other specialties. The molecular techniques used to detect organisms will continue to advance both in sophistication and in the breadth of ecological applications. Our objective is to enable ecologists to harness the full utility of these methods by developing effective collaborative partnerships.

Frontiers in Ecology and the Environment↗
USGS1998

Molecular contributions to conservation

Recent advances in molecular technology have opened a new chapter in species conservation efforts, as well as population biology. DNA sequencing, MHC (major histocompatibility complex), minisatellite, microsatellite, and RAPD (random amplified polymorphic DNA) procedures allow for identification of parentage, more distant relatives, founders to new populations, unidentified individuals, population structure, effective population size, population-specific markers, etc. PCR (polymerase chain reaction) amplification of mitochondrial DNA, nuclear DNA, ribosomal DNA, chloroplast DNA, and other systems provide for more sophisticated analyses of metapopulation structure, hybridization events, and delineation of species, subspecies, and races, all of which aid in setting species recovery priorities. Each technique can be powerful in its own right but is most credible when used in conjunction with other molecular techniques and, most importantly, with ecological and demographic data collected from the field. Surprisingly few taxa of concern have been assayed with any molecular technique. Thus, rather than showcasing exhaustive details from a few well-known examples, this paper attempts to present a broad range of cases in which molecular techniques have been used to provide insight into conservation efforts.

Ecology↗
USGS2006

Taxonomic and geographic variation in oviposition by tailed frogs ( Ascaphus spp )

Tailed frogs ( Ascaphus spp.) oviposit in cryptic locations in streams of the Pacific Northwest and Rocky Mountains. This aspect of their life history has restricted our understanding of their reproductive ecology. The recent split of A. montanus in the Rocky Mountains from A. truei was based on molecular differentiation, and comparisons of their ecology are limited. Our objectives were to provide a range-wide summary of information on Ascaphus oviposition, compare some aspects of the reproductive ecology of the 2 species, and examine geographic variation in their reproductive traits. Reproductive ecology of the 2 species differed. Ascaphus truei had smaller clutches, oviposited later in the summer, and had a longer duration of oviposition than A. montanus . A greater number of communal oviposition sites were attributed to A. montanus . These ecological differences support the recent taxonomic revision of Ascaphus and suggest that different management strategies may be necessary for each species where conservation is a priority.

Northwestern Naturalist↗
USGS2012

Molecular detection of hematozoa infections in tundra swans relative to migration patterns and ecological conditions at breeding grounds

Tundra swans ( Cygnus columbianus ) are broadly distributed in North America, use a wide variety of habitats, and exhibit diverse migration strategies. We investigated patterns of hematozoa infection in three populations of tundra swans that breed in Alaska using satellite tracking to infer host movement and molecular techniques to assess the prevalence and genetic diversity of parasites. We evaluated whether migratory patterns and environmental conditions at breeding areas explain the prevalence of blood parasites in migratory birds by contrasting the fit of competing models formulated in an occupancy modeling framework and calculating the detection probability of the top model using Akaike Information Criterion (AIC). We described genetic diversity of blood parasites in each population of swans by calculating the number of unique parasite haplotypes observed. Blood parasite infection was significantly different between populations of Alaska tundra swans, with the highest estimated prevalence occurring among birds occupying breeding areas with lower mean daily wind speeds and higher daily summer temperatures. Models including covariates of wind speed and temperature during summer months at breeding grounds better predicted hematozoa prevalence than those that included annual migration distance or duration. Genetic diversity of blood parasites in populations of tundra swans appeared to be relative to hematozoa prevalence. Our results suggest ecological conditions at breeding grounds may explain differences of hematozoa infection among populations of tundra swans that breed in Alaska.

Alaska↗
USGS2024

Molecular sexing of birds using quantitative PCR (qPCR) of sex-linked genes and logistic regression models

The ability to sex individuals is an important component of many behavioural and ecological investigations and provides information for demographic models used in conservation and species management. However, many birds are difficult to sex using morphological characters or traditional molecular sexing methods. In this study, we developed probabilistic models for sexing birds using quantitative PCR (qPCR) data. First, we quantified distributions of gene copy numbers at a set of six sex-linked genes, including the sex-determining gene DMRT1 , for individuals across 17 species and seven orders of birds ( n = 150). Using these data, we built predictive logistic models for sex identification and tested their performance with independent samples from 51 species and 13 orders ( n = 209). Models using the two loci most highly correlated with sex had greater accuracy than models using the full set of sex-linked loci, across all taxonomic levels of analysis. Sex identification was highly accurate when individuals to be assigned were of species used in model building. Our analytical approach was widely applicable across diverse neognath bird lineages spanning millions of years of evolutionary divergence. Unlike previous methods, our probabilistic framework incorporates uncertainty around qPCR measurements as well as biological variation within species into decision-making rules. We anticipate that this method will be useful for sexing birds, including those of high conservation concern and/or subsistence value, that have proven difficult to sex using traditional approaches. Additionally, the general analytical framework presented in this paper may also be applicable to other organisms with sex chromosomes.

Molecular Ecology Resources↗
USGS2000

Microsatellites: Evolutionary and methodological background and empirical applications at individual, population, and phylogenetic levels

The recent proliferation and greater accessibility of molecular genetic markers has led to a growing appreciation of the ecological and evolutionary inferences that can be drawn from molecular characterizations of individuals and populations (Burke et al. 1992, Avise 1994). Different techniques have the ability to target DNA sequences which have different patterns of inheritance, different modes and rates of evolution and, concomitantly, different levels of variation. In the quest for 'the right marker for the right job', microsatellites have been widely embraced as the marker of choice for many empirical genetic studies. The proliferation of microsatellite loci for various species and the voluminous literature compiled in very few years associated with their evolution and use in various research applications, exemplifies their growing importance as a research tool in the biological sciences. The ability to define allelic states based on variation at the nucleotide level has afforded unparalleled opportunities to document the actual mutational process and rates of evolution at individual microsatellite loci. The scrutiny to which these loci have been subjected has resulted in data that raise issues pertaining to assumptions formerly stated, but largely untestable for other marker classes. Indeed this is an active arena for theoretical and empirical work. Given the extensive and ever-increasing literature on various statistical methodologies and cautionary notes regarding the uses of microsatellites, some consideration should be given to the unique characteristics of these loci when determining how and under what conditions they can be employed.

Book chapter↗
USGS2014

Tick control: Trapping, bio-control, host management and other alternative strategies

Biology of Ticks is the most comprehensive work on tick biology and tick-borne diseases. This second edition is a multi-authored work, featuring the research and analyses of renowned experts across the globe. Spanning two volumes, the book examines the systematics, biology, structure, ecological adaptations, evolution, genomics and the molecular processes that underpin the growth, development and survival of these important disease-transmitting parasites. Also discussed is the remarkable array of diseases transmitted (or caused) by ticks, as well as modern methods for their control. This book should serve as a modern reference for students, scientists, physicians, veterinarians and other specialists. Volume II includes chapters on the ecology of non-nidicolous and nidicolous ticks, genetics and genomics (including the genome of the Lyme disease vector Ixodes scapularis) and immunity, including host immune responses to tick feeding and tick-host interactions, as well as the tick's innate immune system that prevents and/or controls microbial infections. Six chapters cover in depth the many diseases caused by the major tick-borne pathogens, including tick-borne protozoa, viruses, rickettsiae of all types, other types of bacteria (e.g., the Lyme disease agent) and diseases related to tick paralytic agents and toxins. The remaining chapters are devoted to tick control using vaccines, acaricides, repellents, biocontrol, and, finally, techniques for breeding ticks in order to develop tick colonies for scientific study.

Book chapter↗
USGS2024

A guide to environmental DNA extractions for non-molecular trained biologists, ecologists, and conservation scientists

Ecologists, biologists, and conservation scientists are increasingly interested in the use of environmental DNA (eDNA) data for research and potentially decision-making. While commercial DNA extraction kits are typically user-friendly and accessible, they may fail to deliver the desired results with inherently complex eDNA samples, necessitating protocol optimization or educated selection of alternative approaches. To this end, knowledge of the basic steps and principles of DNA extractions is essential, but traditional education tracks in ecology, conservation, and environmental management typically do not include in-depth training in molecular methods. The primary objective of this paper is to enable scientists with an ecological background and limited molecular training to understand the four key steps of eDNA isolations, and to use this expertise to their advantage. We describe the purpose of commonly used reagents and chemicals, point out alternatives for each key step, explain the impact of certain choices regarding isolation approaches on DNA integrity and purity, and highlight the possibility of a tailor-made “mix and match” approach. We anticipate that this paper will enable field ecologists to develop a deeper understanding of the mechanisms and chemistry underlying eDNA extractions, thus allowing them to make informed decisions regarding the best eDNA extraction method for their research goals. Our intention is not to provide comprehensive, step-by-step protocols, but to offer guiding principles while highlighting alternative solutions. Finally, we hope that this paper will act as a useful resource to support knowledge transfer and teaching.

Environmental DNA↗
USGS2023

Toward absolute abundance for conservation applications: Estimating the number of contributors via microhaplotype genotyping of mixed-DNA sample

Molecular methods including metabarcoding and quantitative polymerase chain reaction have shown promise for estimating species abundance by quantifying the concentration of genetic material in field samples. However, the relationship between specimen abundance and detectable concentrations of genetic material is often variable in practice. DNA mixture analysis represents an alternative approach to quantify specimen abundance based on the presence of unique alleles in a sample. The DNA mixture approach provides novel opportunities to inform ecology and conservation by estimating the absolute abundance of target taxa through molecular methods; yet, the challenges associated with genotyping many highly variable markers in mixed-DNA samples have prevented its widespread use. To advance molecular approaches for abundance estimation, we explored the utility of microhaplotypes for DNA mixture analysis by applying a 125-marker panel to 1179 Chinook salmon ( Oncorhynchus tshawytscha ) smolts from the Sacramento-San Joaquin Delta, California, USA. We assessed the accuracy of DNA mixture analysis through a combination of mock mixtures containing DNA from up to 20 smolts and a trophic ecological application enumerating smolts in predator diets. Mock DNA mixtures of up to 10 smolts could reliably be resolved using microhaplotypes, and increasing the panel size would likely facilitate the identification of more individuals. However, while analysis of predator gastrointestinal tract contents indicated DNA mixture analysis could discern the presence of multiple prey items, poor and variable DNA quality prevented accurate genotyping and abundance estimation. Our results indicate that DNA mixture analysis can perform well with high-quality DNA, but methodological improvements in genotyping degraded DNA are necessary before this approach can be used on marginal-quality samples.

California↗
USGS2023

Landscape transcriptomics as a tool for addressing global change effects across diverse species

Landscape transcriptomics is an emerging field studying how genome-wide expression patterns reflect dynamic landscape-scale environmental drivers, including habitat, weather, climate, and contaminants, and the subsequent effects on organismal function. This field is benefitting from advancing and increasingly accessible molecular technologies, which in turn are allowing the necessary characterization of transcriptomes from wild individuals distributed across natural landscapes. This research is especially important given the rapid pace of anthropogenic environmental change and potential impacts that span levels of biological organization. We discuss three major themes in landscape transcriptomic research: connecting transcriptome variation across landscapes to environmental variation, generating and testing hypotheses about the mechanisms and evolution of transcriptomic responses to the environment, and applying this knowledge to species conservation and management. We discuss challenges associated with this approach and suggest potential solutions. We conclude that landscape transcriptomics has great promise for addressing fundamental questions in organismal biology, ecology, and evolution, while providing tools needed for conservation and management of species.

Molecular Ecology Resources↗
USGS2016

Genetic structure and viability selection in the golden eagle (Aquila chrysaetos), a vagile raptor with a Holarctic distribution

Molecular markers can reveal interesting aspects of organismal ecology and evolution, especially when surveyed in rare or elusive species. Herein, we provide a preliminary assessment of golden eagle ( Aquila chrysaetos ) population structure in North America using novel single nucleotide polymorphisms (SNPs). These SNPs included one molecular sexing marker, two mitochondrial markers, 85 putatively neutral markers that were derived from noncoding regions within large intergenic intervals, and 74 putatively nonneutral markers found in or very near protein-coding genes. We genotyped 523 eagle samples at these 162 SNPs and quantified genotyping error rates and variability at each marker. Our samples corresponded to 344 individual golden eagles as assessed by unique multilocus genotypes. Observed heterozygosity of known adults was significantly higher than of chicks, as was the number of heterozygous loci, indicating that mean zygosity measured across all 159 autosomal markers was an indicator of fitness as it is associated with eagle survival to adulthood. Finally, we used chick samples of known provenance to test for population differentiation across portions of North America and found pronounced structure among geographic sampling sites. These data indicate that cryptic genetic population structure is likely widespread in the golden eagle gene pool, and that extensive field sampling and genotyping will be required to more clearly delineate management units within North America and elsewhere.

Conservation Genetics↗
USGS2026

DNA retention in sea lamprey digestive tracts: Insights from controlled feeding experiments

The sea lamprey ( Petromyzon marinus ), a non-native species in the Laurentian Great Lakes, has significantly impacted native fish communities and commercial fisheries, requiring population suppression efforts. While traditional control methods such as lampricides and barriers have reduced sea lamprey population abundance, questions remain regarding sea lamprey dietary composition given the focus of current damage assessments on economically and ecologically important host species. Recent advances in molecular technology offer promising methods of sea lamprey dietary assessment. Specifically, DNA metabarcoding enables species-specific identification of taxonomically diverse prey items from gut and fecal samples, and has proven effective in many taxa, including hematophagous species such as Arctic lamprey ( Lethenteron camtschaticum ) and sea lamprey. However, studies on DNA retention within digestive tracts are limited, particularly given the potential effects of environmental and dietary factors among hematophagous species. We used controlled feeding experiments to understand the effects these factors may have on DNA retention and host detectability within sea lamprey digestive tracts. Additionally, we evaluated the utility of metabarcoding for identifying multiple host species from consecutive feedings. Results indicate that host DNA can be detected up to 30 days post-feeding, with detection probability decreasing with increasing time following feeding. Temperature effects were dependent upon fasting periods, and host-switching trials indicated multiple previous host species could be detected from a single lamprey. Findings provide valuable insights for refining dietary analysis protocols for wild-caught sea lamprey within native and introduced ranges.

Environmental DNA↗