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At least 1,189 records · Page 66Linked to original sources

USGS2020

Daily nest predation rates decrease with body size in passerine birds

Body size evolution is generally framed by the benefits of being large, while costs are largely overlooked. An important putative cost of being large is the need to extend development periods, which should increase exposure to predation and potentially select against larger size. In birds, this selection pressure can be important because predation is the main source of offspring mortality and predators should more readily detect the larger nests associated with larger body sizes. Here, we show for diverse passerine birds across the world that counter to expectations, larger species suffer lower daily nest predation rates than smaller species. This pattern is consistent despite latitudinal variation in predation and does not seem to reflect a tendency of larger species to use more protected nests or less exposed nest locations. Evidence instead suggests that larger species attack a wider array of predator sizes, which could reduce predation rates in nests of large-bodied species. Regardless of the mechanism, the lower daily nest predation rates of larger species yield slightly lower predation rates over the entire development period compared with smaller species. These results highlight the importance of behavior as a mechanism to alter selection pressures and have implications for body size evolution.

The American Naturalist↗

USGS2015

Female sea lamprey shift orientation toward a conspecific chemical cue to escape a sensory trap

The sensory trap model of signal evolution hypothesizes that signalers adapt to exploit a cue used by the receiver in another context. Although exploitation of receiver biases can result in conflict between the sexes, deceptive signaling systems that are mutually beneficial drive the evolution of stable communication systems. However, female responses in the nonsexual and sexual contexts may become uncoupled if costs are associated with exhibiting a similar response to a trait in both contexts. Male sea lamprey ( Petromyzon marinus ) signal with a mating pheromone, 3-keto petromyzonol sulfate (3kPZS), which may be a match to a juvenile cue used by females during migration. Upstream movement of migratory lampreys is partially guided by 3kPZS, but females only move toward 3kPZS with proximal accuracy during spawning. Here, we use in-stream behavioral assays paired with gonad histology to document the transition of female preference for juvenile- and male-released 3kPZS that coincides with the functional shift of 3kPZS as a migratory cue to a mating pheromone. Females became increasingly biased toward the source of synthesized 3kPZS as their maturation progressed into the reproductive phase, at which point, a preference for juvenile odor (also containing 3kPZS naturally) ceased to exist. Uncoupling of female responses during migration and spawning makes the 3kPZS communication system a reliable means of synchronizing mate search. The present study offers a rare example of a transition in female responses to a chemical cue between nonsexual and sexual contexts, provides insights into the origins of stable communication signaling systems.

Behavioral Ecology↗

USGS2023

Evolutionary fire ecology: An historical account and future directions

The idea that fire acts as an evolutionary force contributing to shaping species traits started a century ago, but had not been widely recognized until very recently. Among the first to realize this force were E dward B . Poulton, R. D ale Guthrie, and E dwin V . Komarek in animals and W illis L . Jepson, W alter W . Hough, T om M . Harris, P hilip V . Wells, and R obert W . Mutch in plants. They were all ahead of their time in their evolutionary thinking. Since then, evolutionary fire ecology has percolated very slowly into the mainstream ecology and evolutionary biology; in fact, this topic is still seldom mentioned in textbooks of ecology or evolution. Currently, there is plenty of evidence suggesting that we cannot understand the biodiversity of our planet without considering the key evolutionary role of fire. But there is still research to be done in order to fully understand fire's contribution to species evolution and to predicting species responses to rapid global changes.

BioScience↗

USGS2023

A reference genome assembly for the continentally distributed ring-necked snake, Diadophis punctatus

Snakes in the family Colubridae include more than 2,000 currently recognized species, and comprise roughly 75% of the global snake species diversity on Earth. For such a spectacular radiation, colubrid snakes remain poorly understood ecologically and genetically. Two subfamilies, Colubrinae (788 species) and Dipsadinae (833 species), comprise the bulk of colubrid species richness. Dipsadines are a speciose and diverse group of snakes that largely inhabit Central and South America, with a handful of small-body-size genera that have invaded North America. Among them, the ring-necked snake, Diadophis punctatus , has an incredibly broad distribution with 14 subspecies. Given its continental distribution and high degree of variation in coloration, diet, feeding ecology, and behavior, the ring-necked snake is an excellent species for the study of genetic diversity and trait evolution. Within California, six subspecies form a continuously distributed “ring species” around the Central Valley, while a seventh, the regal ring-necked snake, Diadophis punctatus regalis is a disjunct outlier and Species of Special Concern in the state. Here, we report a new reference genome assembly for the San Diego ring-necked snake, D. p. similis , as part of the California Conservation Genomics Project. This assembly comprises a total of 444 scaffolds spanning 1,783 Mb and has a contig N50 of 8.0 Mb, scaffold N50 of 83 Mb, and BUSCO completeness score of 94.5%. This reference genome will be a valuable resource for studies of the taxonomy, conservation, and evolution of the ring-necked snake across its broad, continental distribution.

Journal of Heredity↗

USGS2013

The population history of endogenous retroviruses in mule deer (Odocoileus heminous)

Mobile elements are powerful agents of genomic evolution and can be exceptionally informative markers for investigating species and population-level evolutionary history. While several studies have utilized retrotransposon-based insertional polymorphisms to resolve phylogenies, few population studies exist outside of humans. Endogenous retroviruses are LTR-retrotransposons derived from retroviruses that have become stably integrated in the host genome during past infections and transmitted vertically to subsequent generations. They offer valuable insight into host-virus co-evolution and a unique perspective on host evolutionary history because they integrate into the genome at a discrete point in time. We examined the evolutionary history of a cervid endogenous gammaretrovirus (CrERVγ) in mule deer ( Odocoileus hemionus ). We sequenced 14 CrERV proviruses (CrERV-in1 to -in14), and examined the prevalence and distribution of 13 proviruses in 262 deer among 15 populations from Montana, Wyoming, and Utah. CrERV absence in white-tailed deer ( O. virginianus ), identical 5′ and 3′ long terminal repeat (LTR) sequences, insertional polymorphism, and CrERV divergence time estimates indicated that most endogenization events occurred within the last 200000 years. Population structure inferred from CrERVs (F ST = 0.008) and microsatellites (θ = 0.01) was low, but significant, with Utah, northwestern Montana, and a Helena herd being particularly differentiated. Clustering analyses indicated regional structuring, and non-contiguous clustering could often be explained by known translocations. Cluster ensemble results indicated spatial localization of viruses, specifically in deer from northeastern and western Montana. This study demonstrates the utility of endogenous retroviruses to elucidate and provide novel insight into both ERV evolutionary history and the history of contemporary host populations.

Montana;Utah;Wyoming↗

USGS2019

Replicated landscape genomics identifies evidence of local adaptation to urbanization in wood frogs

Native species that persist in urban environments may benefit from local adaptation to novel selection factors. We used double-digest restriction-side associated DNA (RAD) sequencing to evaluate shifts in genome-wide genetic diversity and investigate the presence of parallel evolution associated with urban-specific selection factors in wood frogs ( Lithobates sylvaticus ). Our replicated paired study design involved 12 individuals from each of 4 rural and urban populations to improve our confidence that detected signals of selection are indeed associated with urbanization. Genetic diversity measures were less for urban populations; however, the effect size was small, suggesting little biological consequence. Using an F ST outlier approach, we identified 37 of 8344 genotyped single nucleotide polymorphisms with consistent evidence of directional selection across replicates. A genome-wide association study analysis detected modest support for an association between environment type and 12 of the 37 F ST outlier loci. Discriminant analysis of principal components using the 37 F ST outlier loci produced correct reassignment for 87.5% of rural samples and 93.8% of urban samples. Eighteen of the 37 F ST outlier loci mapped to the American bullfrog ( Rana [Lithobates] catesbeiana ) genome, although none were in coding regions. This evidence of parallel evolution to urban environments provides a powerful example of the ability of urban landscapes to direct evolutionary processes.

Maine↗

USGS1995

The generation of oceanic rhyolites by crystal fractionation: the basalt-rhyolite association at Volcán Alcedo, Galápagos archipelago

Alcedo volcano is one of six shield volcanoes on Isabela Island in the western Galápagos Islands. Although Alcedo is dominantiy basaltic, it is unusual in that it also has erupted ∼1 km 3 of rhyolite. The rhyolitic phase marked a 10-fold decrease in the mass-eruption rate of the volcano, and the volcano has returned to erupting basalt. The basalts are tholeiitic and range from strongly to sparsely porphyritic. Olivine and plagiodase are the liquidus phases in the most primitive basalts. The MgO and Ni concentrations in the most primitive basalts indicate that they have undergone substantial differentiation since extraction from the mantle. The rhyolites contain the assemblage oligoclase-augite-titanomagnetite-fayalite-apatite and sparse xenoliths of quenched basalt and cumulate gabbros. Intermediate rocks are very rare, but some are apparently basaltrhyolite hybrids, and others resulted from differentiation of tholeiitic magma. Several modeling approaches and Sr-, Nd-, and O-isotopic data indicate that the rhyolites resulted from ∼ 90% fractionation (by weight) of plagiodase, augite, titanomagnetite, olivine, and apatite from the most primitive olivine tholeiite. The data are inconsistent with the rhyolites originating by crustal anatexis. The extreme Daly gap may be caused by the large increase in viscosity as the basaltic magma differentiates to intermediate and siliceous compositions; highly evolved magmas are eruptible only after they become saturated with volatiles by second boiling. The close association of the hybrid intermediate magmas and magmatic inclusions with the climactic plinian eruption indicates mixing between mafic and silicic magmas immediately before eruption. Rhyolite production was favored by the decrease in supply of basaltic magma as Alcedo was carried away from the focus of the Galápagos hotspot. A three-stage model for the magmatic evolution of a Galápagos volcano is proposed. In the first stage, the supply of basaltic magma is large. Basaltic magma continually intrudes the subcaldera magma chamber, buffering the magmas' compositional and thermal evolution. As the volcano is carried away from the basaltic source, the magma chamber is allowed to cool and differentiate, as exemplified by Alcedo's rhyolitic phase. Finally, the volcano receives even smaller influx of basalt, so a large magma chamber cannot be sustained, and the volcano shifts to isolated basaltic eruptions.

Galapagos Islands↗

USGS2002

The Fish Canyon magma body, San Juan volcanic field, Colorado: Rejuvenation and eruption of an upper-crustal batholith

More than 5000 km 3 of nearly compositionally homogeneous crystal-rich dacite (∼68 wt % SiO 2 : ∼45% Pl + Kfs + Qtz + Hbl + Bt + Spn + Mag + Ilm + Ap + Zrn + Po) erupted from the Fish Canyon magma body during three phases: (1) the pre-caldera Pagosa Peak Dacite (an unusual poorly fragmented pyroclastic deposit, ∼200 km 3 ); (2) the syn-collapse Fish Canyon Tuff (one of the largest known ignimbrites, ∼5000 km 3 ); (3) the post-collapse Nutras Creek Dacite (a volumetrically minor lava). The late evolution of the Fish Canyon magma is characterized by rejuvenation of a near-solidus upper-crustal intrusive body (mainly crystal mush) of batholithic dimensions. The necessary thermal input was supplied by a shallow intrusion of more mafic magma represented at the surface by sparse andesitic enclaves in late-erupted Fish Canyon Tuff and by the post-caldera Huerto Andesite. The solidified margins of this intrusion are represented by holocrystalline xenoliths with Fish Canyon mineralogy and mineral chemistry and widely dispersed partially remelted polymineralic aggregates, but dehydration melting was not an important mechanism in the rejuvenation of the Fish Canyon magma. Underlying mafic magma may have evolved H 2 O–F–S–Cl-rich fluids that fluxed melting in the overlying crystal mush. Manifestations of the late up-temperature magma evolution are: (1) resorbed quartz, as well as feldspars displaying a wide spectrum of textures indicative of both resorption and growth, including Rapakivi textures and reverse growth zoning (An 27–28 to An 32–33 ) at the margins of many plagioclase phenocrysts; (2) high Sr, Ba, and Eu contents in the high-SiO 2 rhyolite matrix glass, which are inconsistent with extreme fractional crystallization of feldspar; (3) oscillatory and reverse growth zoning toward the margins of many euhedral hornblende phenocrysts (rimward increases from ∼5·5–6 to 7·7–8·5 wt % Al 2 O 3 ). Homogeneity in magma composition at the chamber-wide scale, contrasting with extreme textural and chemical complexities at the centimeter–millimeter scale, is consistent with a dynamic environment, wherein crystals with a variety of growth and resorption histories were juxtaposed shortly before eruption by convective currents.

Colorado↗

USGS2016

Probing the volcanic-plutonic connection and the genesis of crystal-rich rhyolite in a deeply dissected supervolcano in the Nevada Great Basin: Source of the late Eocene Caetano Tuff

Late Cenozoic faulting and large-magnitude extension in the Great Basin of the western USA has created locally deep windows into the upper crust, permitting direct study of volcanic and plutonic rocks within individual calderas. The Caetano caldera in north–central Nevada, formed during the mid-Tertiary ignimbrite flare-up, offers one of the best exposed and most complete records of caldera magmatism. Integrating whole-rock geochemistry, mineral chemistry, isotope geochemistry and geochronology with field studies and geologic mapping, we define the petrologic evolution of the magmatic system that sourced the >1100 km 3 Caetano Tuff. The intra-caldera Caetano Tuff is up to ∼5 km thick, composed of crystal-rich (30–45 vol. %), high-silica rhyolite, overlain by a smaller volume of comparably crystal-rich, low-silica rhyolite. It defies classification as either a monotonous intermediate or crystal-poor zoned rhyolite, as commonly ascribed to ignimbrite eruptions. Crystallization modeling based on the observed mineralogy and major and trace element geochemistry demonstrates that the compositional zonation can be explained by liquid–cumulate evolution in the Caetano Tuff magma chamber, with the more evolved lower Caetano Tuff consisting of extracted liquids that continued to crystallize and mix in the upper part of the chamber following segregation from a cumulate-rich, and more heterogeneous, source mush. The latter is represented in the caldera stratigraphy by the less evolved upper Caetano Tuff. Whole-rock major, trace and rare earth element geochemistry, modal mineralogy and mineral chemistry, O, Sr, Nd and Pb isotope geochemistry, sanidine Ar–Ar geochronology, and zircon U–Pb geochronology and trace element geochemistry provide robust evidence that the voluminous caldera intrusions (Carico Lake pluton and Redrock Canyon porphyry) are genetically equivalent to the least evolved Caetano Tuff and formed from magma that remained in the lower chamber after ignimbrite eruption and caldera collapse. Thus, the Caetano Tuff contradicts models for the mutually exclusive origins of voluminous volcanic and plutonic magmas in the upper crust. Crystal-scale O isotope data indicate that the Caetano Tuff is one of the most 18 O-enriched rhyolites in the Great Basin (δ 18 O magma = 10·2 ± 0·2‰), supporting anatexis of local metasedimentary basement crust. Metapelite xenoliths in the Carico Lake pluton and ubiquitous xenocrystic zircons in the Caetano Tuff provide constraints for the anatexis process; these data point to shallow (<15 km) dehydration melting of a protolith similar to the Proterozoic McCoy Creek Group siliciclastic sediments in eastern Nevada, projected beneath Caetano in fault-stacked shelf sediments that were thickened during Mesozoic crustal shortening. Mean zircon U–Pb ages for different stratigraphic levels of the intra-caldera Caetano Tuff are 34·2–34·5 Ma, 0·2–0·5 Myr older than the caldera sanidine 40 Ar/ 39 Ar age of 34·00 ± 0·03 Ma, documenting protracted duration of assembly and homogenization of isotopically diverse upper crustal melts, followed by crystallization and zonation to generate the Caetano Tuff magma chamber. Sanidine rims in the least evolved Caetano Tuff and in the Carico Lake pluton and Redrock Canyon porphyry have sharply zoned Ba domains that point to crystal growth during magmatic recharge events. The recharge magma is inferred to have been compositionally similar to the Caetano Tuff magma, with increased Ba resulting from remelting of Ba-rich sanidine cumulates. Mush reactivation to generate the Caetano Tuff eruption was sufficiently rapid to preserve compositional gradients in the intracaldera ignimbrite, calling into question models that predict homogeneity as a prerequisite for remobilizing crystal-rich ignimbrite magmas.

Journal of Petrology↗

USGS2014

A depth-averaged debris-flow model that includes the effects of evolving dilatancy. I. Physical basis

To simulate debris-flow behaviour from initiation to deposition, we derive a depth-averaged, two-phase model that combines concepts of critical-state soil mechanics, grain-flow mechanics and fluid mechanics. The model's balance equations describe coupled evolution of the solid volume fraction, m , basal pore-fluid pressure, flow thickness and two components of flow velocity. Basal friction is evaluated using a generalized Coulomb rule, and fluid motion is evaluated in a frame of reference that translates with the velocity of the granular phase, v s . Source terms in each of the depth-averaged balance equations account for the influence of the granular dilation rate, defined as the depth integral of ∇⋅ v s . Calculation of the dilation rate involves the effects of an elastic compressibility and an inelastic dilatancy angle proportional to m − m eq , where m eq is the value of m in equilibrium with the ambient stress state and flow rate. Normalization of the model equations shows that predicted debris-flow behaviour depends principally on the initial value of m − m eq and on the ratio of two fundamental timescales. One of these timescales governs downslope debris-flow motion, and the other governs pore-pressure relaxation that modifies Coulomb friction and regulates evolution of m . A companion paper presents a suite of model predictions and tests.

Proceedings of the Royal Society A↗

USGS2014

A depth-averaged debris-flow model that includes the effects of evolving dilatancy: II. Numerical predictions and experimental tests.

We evaluate a new depth-averaged mathematical model that is designed to simulate all stages of debris-flow motion, from initiation to deposition. A companion paper shows how the model’s five governing equations describe simultaneous evolution of flow thickness, solid volume fraction, basal pore-fluid pressure, and two components of flow momentum. Each equation contains a source term that represents the influence of state-dependent granular dilatancy. Here we recapitulate the equations and analyze their eigenstructure to show that they form a hyperbolic system with desirable stability properties. To solve the equations we use a shock-capturing numerical scheme with adaptive mesh refinement, implemented in an open-source software package we call D-Claw. As tests of D-Claw, we compare model output with results from two sets of large-scale debris-flow experiments. One set focuses on flow initiation from landslides triggered by rising pore-water pressures, and the other focuses on downstream flow dynamics, runout, and deposition. D-Claw performs well in predicting evolution of flow speeds, thicknesses, and basal pore-fluid pressures measured in each type of experiment. Computational results illustrate the critical role of dilatancy in linking coevolution of the solid volume fraction and pore-fluid pressure, which mediates basal Coulomb friction and thereby regulates debris-flow dynamics.

Proceedings of the Royal Society A↗

USGS2007

Chromosome painting among Proboscidea, Hyracoidea and Sirenia: Support for Paenungulata (Afrotheria, Mammalia) but not Tethytheria

Despite marked improvements in the interpretation of systematic relationships within Eutheria, particular nodes, including Paenungulata (Hyracoidea, Sirenia and Proboscidea), remain ambiguous. The combination of a rapid radiation, a deep divergence and an extensive morphological diversification has resulted in a limited phylogenetic signal confounding resolution within this clade both at the morphological and nucleotide levels. Cross-species chromosome painting was used to delineate regions of homology between Loxodonta africana (2n = 56), Procavia capensis (2n=54), Trichechus manatus latirostris (2n = 48) and an outgroup taxon, the aardvark (Orycteropus afer, 2n = 20). Changes specific to each lineage were identified and although the presence of a minimum of 11 synapomorphies confirmed the monophyly of Paenungulata, no change characterizing intrapaenungulate relationships was evident. The reconstruction of an ancestral paenungulate karyotype and the estimation of rates of chromosomal evolution indicate a reduced rate of genomic repatterning following the paenungulate radiation. In comparison to data available for other mammalian taxa, the paenungulate rate of chromosomal evolution is slow to moderate. As a consequence, the absence of a chromosomal character uniting two paenungulates (at the level of resolution characterized in this study) may be due to a reduced rate of chromosomal change relative to the length of time separating successive divergence events. ?? 2007 The Royal Society.

Proceedings of the Royal Society B: Biological Sci↗

USGS2019

Is there convergence of gut microbes in blood-feeding vertebrates?

Animal microbiomes play an important role in dietary adaptation, yet the extent to which microbiome changes exhibit parallel evolution is unclear. Of particular interest is an adaptation to extreme diets, such as blood, which poses special challenges in its content of proteins and lack of essential nutrients. In this study, we assessed taxonomic signatures (by 16S rRNA amplicon profiling) and potential functional signatures (inferred by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt)) of haematophagy in birds and bats. Our goal was to test three alternative hypotheses: no convergence of microbiomes, convergence in taxonomy and convergence in function. We find a statistically significant effect of haematophagy in terms of microbial taxonomic convergence across the blood-feeding bats and birds, although this effect is small compared to the differences found between haematophagous and non-haematophagous species within the two host clades. We also find some evidence of convergence at the predicted functional level, although it is possible that the lack of metagenomic data and the poor representation of microbial lineages adapted to haematophagy in genome databases limit the power of this approach. The results provide a paradigm for exploring convergent microbiome evolution replicated with independent contrasts in different host lineages.

Philosophical Transactions of the Royal Society B:↗

USGS2021

The roles of antimicrobial resistance, phage diversity, isolation source, and selection in shaping the genomic architecture of Bacillus anthracis

Bacillus anthracis, the causative agent of anthrax disease, is a worldwide threat to livestock, wildlife and public health. While analyses of genetic data from across the globe have increased our understanding of this bacterium’s population genomic structure, the influence of selective pressures on this successful pathogen is not well understood. In this study, we investigate the effects of antimicrobial resistance, phage diversity, geography and isolation source in shaping population genomic structure. We also identify a suite of candidate genes potentially under selection, driving patterns of diversity across 356 globally extant B. anthracis genomes. We report ten antimicrobial resistance genes and 11 different prophage sequences, resulting in the first large-scale documentation of these genetic anomalies for this pathogen. Results of random forest classification suggest genomic structure may be driven by a combination of antimicrobial resistance, geography and isolation source, specific to the population cluster examined. We found strong evidence that a recombination event linked to a gene involved in protein synthesis may be responsible for phenotypic differences between comparatively disparate populations. We also offer a list of genes for further examination of B. anthracis evolution, based on high-impact single nucleotide polymorphisms (SNPs) and clustered mutations. The information presented here sheds new light on the factors driving genomic structure in this notorious pathogen and may act as a road map for future studies aimed at understanding functional differences in terms of B. anthracis biogeography, virulence and evolution.

Microbial Genomics↗

USGS2025

Diversity of polyomaviruses and papillomaviruses in penguins from eastern and western Antarctica

Polyomaviruses and papillomaviruses are icosahedral viruses with small circular dsDNA genomes. Limited information on their diversity and evolution in avian hosts is available, with even less known regarding Antarctic penguins. Prior to this study, only one polyomavirus and two papillomaviruses had been identified in Adélie penguins ( Pygoscelis adeliae ). To expand our knowledge of these viruses in Antarctic penguins, we collected faecal and cloacal swab samples from 246 Adélie penguins over 3 breeding seasons (2021–2024) and 10 emperor penguins ( Aptenodytes forsteri ) during the 2023–2024 season on Ross Island (Ross Sea). Additionally, we sampled 66 Adélie, 40 chinstrap ( Pygoscelis antarcticus ) and 71 gentoo ( Pygoscelis papua ) penguins during the 2022–2023 season across various sites on the Antarctic Peninsula. All samples were screened for papillomaviruses and polyomaviruses. We identified 31 polyomaviruses in Adélie, gentoo and chinstrap penguins and 4 papillomaviruses in Adélie penguins sampled in both eastern and western Antarctica. The 31 penguin polyomaviruses belong to a single species but form four distinct variants that are host species specific with strong geographic clustering. The four papillomaviruses represent three different types, of which two are new types from Adélie penguins sampled on Yalour Island in the West Antarctic Peninsula. Co-occurrence of two polyomavirus variants was identified in two individual gentoo penguins. Both of these variants appear to be circulating in gentoo penguins at Cierva Cove, Hope Bay in Trinity Peninsula along the Antarctic Peninsula, and at Hannah Point on Livingstone Island and Stranger Point on King George Island in the South Shetland Islands. Here, we expand the known diversity, host and geographical ranges of penguin polyomaviruses and, together with a previously identified polyomavirus on Ross Island from 2012 to 2013, show that they form five distinct lineages. The four papillomaviruses identified in this study, together with two previously identified from Ross Island in 2012 and 2013 breeding seasons, show substantial diversity reflecting four papillomavirus types across three viral species and two distinct genera. Continued surveillance and viral genomic analysis across a larger geographical framework will help understand the evolution, transmission and incidence rates of these viruses.

Microbial Genomics↗

USGS2003

Phylogeography of infectious haematopoietic necrosis virus in North America

Infectious hematopoietic necrosis virus (IHNV) is a rhabdoviral pathogen that infects wild and cultured salmonid fish throughout the Pacific Northwest of North America. IHNV causes severe epidemics in young fish and can cause disease or occur asymptomatically in adults. In a broad survey of 323 IHNV field isolates, sequence analysis of a 303 nucleotide variable region within the glycoprotein gene revealed a maximum nucleotide diversity of 8·6 %, indicating low genetic diversity overall for this virus. Phylogenetic analysis revealed three major virus genogroups, designated U, M and L, which varied in topography and geographical range. Intragenogroup genetic diversity measures indicated that the M genogroup had three- to fourfold more diversity than the other genogroups and suggested relatively rapid evolution of the M genogroup and stasis within the U genogroup. We speculate that factors influencing IHNV evolution may have included ocean migration ranges of their salmonid host populations and anthropogenic effects associated with fish culture.

Journal of General Virology↗

USGS2007

In situ time-series measurements of subseafloor sediment properties

The capabilities and diversity of subsurface sediment sensors lags significantly from what is available for the water column, thereby limiting progress in understanding time-dependent seabed exchange and high-frequency acoustics. To help redress this imbalance, a new instrument, the autonomous sediment profiler (ASP), is described herein. ASP consists of a four-electrode, Wenner-type resistivity probe and a thermistor that log data at 0.1-cm vertical intervals over a 58-cm vertical profile. To avoid resampling the same spot on the seafloor, the probes are moved horizontally within a 20 times 100-cm -2 area in one of three preselected patterns. Memory and power capacities permit sampling at hourly intervals for up to 3-mo duration. The system was tested in a laboratory tank and shown to be able to resolve high-frequency sediment consolidation, as well as changes in sediment roughness. In a field test off the southern coast of France, the system collected resistivity and temperature data at hourly intervals for 16 d. Coupled with environmental data collected on waves, currents, and suspended sediment, the ASP is shown to be useful for understanding temporal evolution of subsurface sediment porosity, although no large depositional or erosional events occurred during the deployment. Following a rapid decrease in bottom-water temperature, the evolution of the subsurface temperature field was consistent with the 1-D thermal diffusion equation coupled with advection in the upper 3-4 cm. Collectively, the laboratory and field tests yielded promising results on time-dependent seabed change.

IEEE Journal of Oceanic Engineering↗

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↗