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36 records · Page 2Linked to original sources
USGS2022

Low levels of hybridization between sympatric cold-water-adapted Arctic cod and Polar cod in the Beaufort Sea confirm genetic distinctiveness

As marine ecosystems respond to climate change and other stressors, it is necessary to evaluate current and past hybridization events to gain insight on the outcomes and drivers of such events. Ancestral introgression within the gadids has been suggested to allow cod to inhabit a variety of habitats. Little attention has been given to contemporary hybridization, especially within cold-water-adapted cod ( Boreogadus saida Lepechin, 1774 and Arctogadus glacialis Peters, 1872). We used whole-genome, restriction-site associated, and mitochondrial sequence data to explore the degree and direction of hybridization between these species where previous hybridization had not been reported. Although nearly identical morphologically at certain life stages, we detected very distinct nuclear and mitochondrial lineages. We detected one potential hybrid with a Arctogadus mitochondrial haplotype and Boreogadus nuclear genotype, but no early generational hybrids. The presence of a late generation hybrid suggests that at least some hybrids survive to maturity and reproduce. However, a historical introgression event could not be excluded. Contemporary gene flow appears asymmetrical from Arctogadus into Boreogadus , which may be due to overlap in timing of spawning, environmental heterogeneity, or differences in population size. This study provides important baseline information for the degree of potential hybridization between these species within Alaska marine environments.

Beaufort Sea, Chukchi Sea↗
USGS2017

Acetoclastic Methanosaeta are dominant methanogens in organic-rich Antarctic marine sediments

Despite accounting for the majority of sedimentary methane, the physiology and relative abundance of subsurface methanogens remain poorly understood. We combined intact polar lipid and metagenome techniques to better constrain the presence and functions of methanogens within the highly reducing, organic-rich sediments of Antarctica’s Adélie Basin. The assembly of metagenomic sequence data identified phylogenic and functional marker genes of methanogens and generated the first Methanosaeta sp. genome from a deep subsurface sedimentary environment. Based on structural and isotopic measurements, glycerol dialkyl glycerol tetraethers with diglycosyl phosphatidylglycerol head groups were classified as biomarkers for active methanogens. The stable carbon isotope (δ 13 C) values of these biomarkers and the Methanosaeta partial genome suggest that these organisms are acetoclastic methanogens and represent a relatively small (0.2%) but active population. Metagenomic and lipid analyses suggest that Thaumarchaeota and heterotrophic bacteria co-exist with Methanosaeta and together contribute to increasing concentrations and δ 13 C values of dissolved inorganic carbon with depth. This study presents the first functional insights of deep subsurface Methanosaeta organisms and highlights their role in methane production and overall carbon cycling within sedimentary environments.

ISME Journal↗
USGS2024

Seasonal mortality of Wild Atlantic Menhaden (Brevoortia tyrannus) is caused by a virulent clone of Vibrio (Listonella) anguillarum; Implications for biosecurity along the Atlantic Coastal United States

Atlantic menhaden are a highly migratory marine species in the Eastern United States that suffer from seasonal chronic mortality. Affected fish show neurologic signs referred to as spinning disease, including circling at the surface and erratic corkscrew swimming before death. We investigated three similar menhaden mortality events consistent with spinning disease in coastal New Jersey and New York between 2020 and 2021 to understand the cause. A unique strain of Vibrio (Listonella) anguillarum (serogroup O3) was detected regularly in high loads, particularly in the brains of moribund fish, by both metagenomics and bacterial isolation. The most common histopathological changes in moribund fish were hemorrhagic meningitis, encephalitis, pyknosis, and karyorrhexis of hematopoietic tissues in the kidney and spleen. Whole genome sequencing of isolates from moribund fish representing a wide spatial and temporal range showed that they were nearly identical clones, suggesting it to be a pathogenic strain circulating in the population. Though V. anguillarum is believed to be the main pathogen associated with spinning disease and mortality, Yersinia ruckeri (serotype O1) was isolated from smaller numbers of fish. Considering the highly migratory nature of Atlantic menhaden throughout the eastern United States and their use as bait for other fisheries, these findings identify potential biosecurity challenges that should be considered in Atlantic salmon aquaculture, fisheries, and emerging marine aquaculture in the region.

Transboundary and Emerging Diseases↗
USGS2018

Vibrio population dynamics in Mid-Atlantic surface waters during Saharan dust events

Vibrio is a cosmopolitan genus of marine bacteria, highly investigated in coastal and estuarine environments. Vibrio have also been isolated from pelagic waters, yet very little is known about the ecology of these oligotrophic species. In this study we examined the relative change in bacterial abundance and more specifically the dynamics of Vibrio in the tropical North Atlantic in response to the arrival of pulses of Saharan dust aerosols, a major source of biologically important nutrients for downwind marine surface waters. Aerosol and surface water samples were collected over 1 month coinciding with at least two distinct dust events. Total bacterial counts increased by 1.6-fold correlating with the arrival of Saharan dust ( r = 0.76; p = 0.001). Virus-like particles (VLP) also followed this trend and were correlated with bacterial counts ( r = 0.67; p = 0.01). Vibrio specific qPCR targeting the 16S rRNA gene ranged from below detection limits to a high of 9,145 gene copies ml −1 with the arrival of dust. This increase equated to 6.5 × 10 2 −1.5 × 10 3 individual genome equivalents ml −1 based on the known range of 16S rRNA copies among this genus. Vibrio exhibited bloom-bust cycles potentially attributed to selective viral lysis or bloom depletion of organic carbon. This work is one of the few studies to examine the open ocean ecology of Vibrio , a conditionally rare taxon, whose bloom-bust lifestyle likely is a contributing factor in the flow of nutrients and energy in pelagic ecosystems.

Frontiers in Marine Science↗
USGS2007

Chromosome painting in the manatee supports Afrotheria and Paenungulata

Background Sirenia (manatees, dugongs and Stellar's sea cow) have no evolutionary relationship with other marine mammals, despite similarities in adaptations and body shape. Recent phylogenomic results place Sirenia in Afrotheria and with elephants and rock hyraxes in Paenungulata. Sirenia and Hyracoidea are the two afrotherian orders as yet unstudied by comparative molecular cytogenetics. Here we report on the chromosome painting of the Florida manatee. Results The human autosomal and X chromosome paints delimited a total of 44 homologous segments in the manatee genome. The synteny of nine of the 22 human autosomal chromosomes (4, 5, 6, 9, 11, 14, 17, 18 and 20) and the X chromosome were found intact in the manatee. The syntenies of other human chromosomes were disrupted in the manatee genome into two to five segments. The hybridization pattern revealed that 20 (15 unique) associations of human chromosome segments are found in the manatee genome: 1/15, 1/19, 2/3 (twice), 3/7 (twice), 3/13, 3/21, 5/21, 7/16, 8/22, 10/12 (twice), 11/20, 12/22 (three times), 14/15, 16/19 and 18/19. Conclusion There are five derived chromosome traits that strongly link elephants with manatees in Tethytheria and give implicit support to Paenungulata: the associations 2/3, 3/13, 8/22, 18/19 and the loss of the ancestral eutherian 4/8 association. It would be useful to test these conclusions with chromosome painting in hyraxes. The manatee chromosome painting data confirm that the associations 1/19 and 5/21 phylogenetically link afrotherian species and show that Afrotheria is a natural clade. The association 10/12/22 is also ubiquitous in Afrotheria (clade I), present in Laurasiatheria (clade IV), only partially present in Xenarthra (10/12, clade II) and absent in Euarchontoglires (clade III). If Afrotheria is basal to eutherians, this association could be part of the ancestral eutherian karyotype. If afrotherians are not at the root of the eutherian tree, then the 10/12/22 association could be one of a suite of derived associations linking afrotherian taxa.

BMC Evolutionary Biology↗
USGS2021

Palaeoceanographic changes in the late Pliocene promoted rapid diversification in pelagic seabirds

Aim Palaeoceanographic changes can act as drivers of diversification and speciation, even in highly mobile marine organisms. Shearwaters are a group of globally distributed and highly mobile pelagic seabirds. Despite a recent well-resolved phylogeny, shearwaters have controversial species limits, and show periods of both slow and rapid diversification. Here, we explore the role of palaeoceanographic changes on shearwaters' diversification and speciation. We investigate shearwater biogeography and the evolution of a key phenotypic trait, body size, and we assess the validity of their current taxonomy. Location Worldwide. Taxa Shearwaters (Order Procellariiformes, Family Procellariidae, Genera Ardenna , Calonectris and Puffinus ). Methods We generated genomic (ddRAD) data to infer a time-calibrated species tree for the shearwaters. We estimated ancestral ranges and evaluated the roles of founder events, vicariance and surface ocean currents in driving diversification. We performed phylogenetic generalised least squares to identify potential predictors of variability in body size along the phylogeny. To assess the validity of the current taxonomy, we analysed genomic patterns of recent shared ancestry and differentiation among shearwater taxa. Results We identified a period of high dispersal and rapid speciation during the Late Pliocene–early Pleistocene. Species dispersal appears to be favoured by surface ocean currents, and founder events are supported as the main mode of speciation in these highly mobile pelagic seabirds. Body mass shows significant associations with life strategies and local conditions. The current taxonomy shows some incongruences with the patterns of genomic divergence. Main Conclusions A reduction of neritic areas during the Pliocene seems to have driven global extinctions of shearwater species, followed by a subsequent burst of speciation and dispersal probably promoted by Plio-Pleistocene climatic shifts. Our findings extend our understanding on the drivers of speciation and dispersal of highly mobile pelagic seabirds and shed new light on the important role of palaeoceanographic events.

Journal of Biogeography↗
USGS2017

Detection of diazotrophy in the acetylene-fermenting anaerobe Pelobacter sp. strain SFB93

Acetylene (C2H2) is a trace constituent of the present Earth's oxidizing atmosphere, reflecting a mixture of terrestrial and marine emissions from anthropogenic, biomass-burning, and unidentified biogenic sources. Fermentation of acetylene was serendipitously discovered during C2H2 block assays of N2O reductase, and Pelobacter acetylenicus was shown to grow on C2H2 via acetylene hydratase (AH). AH is a W-containing, catabolic, low-redox-potential enzyme that, unlike nitrogenase (N2ase), is specific for acetylene. Acetylene fermentation is a rare metabolic process that is well characterized only in P. acetylenicus DSM3246 and DSM3247 and Pelobacter sp. strain SFB93. To better understand the genetic controls for AH activity, we sequenced the genomes of the three acetylene-fermenting Pelobacter strains. Genome assembly and annotation produced three novel genomes containing gene sequences for AH, with two copies being present in SFB93. In addition, gene sequences for all five compulsory genes for iron-molybdenum N2ase were also present in the three genomes, indicating the cooccurrence of two acetylene transformation pathways. Nitrogen fixation growth assays showed that DSM3426 could ferment acetylene in the absence of ammonium, but no ethylene was produced. However, SFB93 degraded acetylene and, in the absence of ammonium, produced ethylene, indicating an active N2ase. Diazotrophic growth was observed under N2 but not in experimental controls incubated under argon. SFB93 exhibits acetylene fermentation and nitrogen fixation, the only known biochemical mechanisms for acetylene transformation. Our results indicate complex interactions between N2ase and AH and suggest novel evolutionary pathways for these relic enzymes from early Earth to modern days.

Applied and Environmental Microbiology↗
USGS1989

Isolation of a reovirus from coho salmon ( Oncorhynchus kisutch ) in Oregon, USA

Reoviruses isolated from aquatic animals share certain common characteristics: (1) a typical reovirus-like morphology which shows an icosahedral particle with a double capsid that is approximately 75 nm in diameter; (2) a genome with eleven segments of double-stranded RNA (dsRNA) distributed as three large, three medium and five small segments with a total molecular weight of approximately 15 x 106; (3) a virion composed of five major and several minor structural proteins that range in molecular weight from 32,000 to 137,000; and (4) form plaque-like syncytia in monolayer cultures of fish cells. Intact virus particles have buoyant densities in CsCl of 1.34 to 1.36 g/ml. The viruses have been isolated from fish and shellfish collected in both the marine and freshwater environments and will replicate in several fish cell lines (Plumb et al., 1979; Meyers and Hirai, 1980; Winton et al., 1981; Nagabayashi and Mori, 1983; Hedrick et al., 1984; Chen and Jiang, 1984). The original four aquatic reovirus isolates have been compared by Winton et al., 1987.

Book chapter↗
USGS2023

Coupling large-spatial scale larval dispersal modelling with barcoding to refine the amphi-Atlantic connectivity hypothesis in deep-sea seep mussels

In highly fragmented and relatively stable cold-seep ecosystems, species are expected to exhibit high migration rates and long-distance dispersal of long-lived pelagic larvae to maintain genetic integrity over their range. Accordingly, several species inhabiting cold seeps are widely distributed across the whole Atlantic Ocean, with low genetic divergence between metapopulations on both sides of the Atlantic Equatorial Belt (AEB, i.e. Barbados and African/European margins). Two hypotheses may explain such patterns: (i) the occurrence of present-day gene flow or (ii) incomplete lineage sorting due to large population sizes and low mutation rates. Here, we evaluated the first hypothesis using the cold seep mussels Gigantidas childressi, G. mauritanicus, Bathymodiolus heckerae and B. boomerang . We combined COI barcoding of 763 individuals with VIKING20X larval dispersal modelling at a large spatial scale not previously investigated. Population genetics supported the parallel evolution of Gigantidas and Bathymodiolus genera in the Atlantic Ocean and the occurrence of a 1-3 Million-year-old vicariance effect that isolated populations across the Caribbean Sea. Both population genetics and larval dispersal modelling suggested that contemporary gene flow and larval exchanges are possible across the AEB and the Caribbean Sea, although probably rare. When occurring, larval flow was eastward (AEB - only for B. boomerang ) or northward (Caribbean Sea - only for G. mauritanicus ). Caution is nevertheless required since we focused on only one mitochondrial gene, which may underestimate gene flow if a genetic barrier exists. Non-negligible genetic differentiation occurred between Barbados and African populations, so we could not discount the incomplete lineage sorting hypothesis. Larval dispersal modelling simulations supported the genetic findings along the American coast with high amounts of larval flow between the Gulf of Mexico (GoM) and the US Atlantic Margin, although the Blake Ridge population of B. heckerae appeared genetically differentiated. Overall, our results suggest that additional studies using nuclear genetic markers and population genomics approaches are needed to clarify the evolutionary history of the Atlantic bathymodioline mussels and to distinguish between ongoing and past processes.

Frontiers in Marine Science↗
USGS2014

Molecular identification of erythrocytic necrosis virus (ENV) from the blood of Pacific herring ( Clupea pallasii )

Viral erythrocytic necrosis (VEN) is a condition affecting the red blood cells of more than 20 species of marine and anadromous fishes in the North Atlantic and North Pacific Oceans. Among populations of Pacific herring ( Clupea pallasii ) on the west coast of North America the disease causes anemia and elevated mortality in periodic epizootics. Presently, VEN is diagnosed by observation of typical cytoplasmic inclusion bodies in stained blood smears from infected fish. The causative agent, erythrocytic necrosis virus (ENV), is unculturable and a presumed iridovirus by electron microscopy. In vivo amplification of the virus in pathogen-free laboratory stocks of Pacific herring with subsequent virus concentration, purification, DNA extraction, and high-throughput sequencing were used to obtain genomic ENV sequences. Fragments with the highest sequence identity to the family Iridoviridae were used to design four sets of ENV-specific polymerase chain reaction (PCR) primers. Testing of blood and tissue samples from experimentally and wild infected Pacific herring as well as DNA extracted from other amphibian and piscine iridoviruses verified the assays were specific to ENV with a limit of detection of 0.0003 ng. Preliminary phylogenetic analyses of a 1448 bp fragment of the putative DNA polymerase gene supported inclusion of ENV in a proposed sixth genus of the family Iridoviridae that contains other erythrocytic viruses from ectothermic hosts. This study provides the first molecular evidence of ENV's inclusion within the Iridoviridae family and offers conventional PCR assays as a means of rapidly surveying the ENV-status of wild and propagated Pacific herring stocks.

Veterinary Microbiology↗
USGS2010

Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear

The polar bear has become the flagship species in the climate-change discussion. However, little is known about how past climate impacted its evolution and persistence, given an extremely poor fossil record. Although it is undisputed from analyses of mitochondrial (mt) DNA that polar bears constitute a lineage within the genetic diversity of brown bears, timing estimates of their divergence have differed considerably. Using next-generation sequencing technology, we have generated a complete, high-quality mt genome from a stratigraphically validated 130,000- to 110,000-year-old polar bear jawbone. In addition, six mt genomes were generated of extant polar bears from Alaska and brown bears from the Admiralty and Baranof islands of the Alexander Archipelago of southeastern Alaska and Kodiak Island. We show that the phylogenetic position of the ancient polar bear lies almost directly at the branching point between polar bears and brown bears, elucidating a unique morphologically and molecularly documented fossil link between living mammal species. Molecular dating and stable isotope analyses also show that by very early in their evolutionary history, polar bears were already inhabitants of the Artic sea ice and had adapted very rapidly to their current and unique ecology at the top of the Arctic marine food chain. As such, polar bears provide an excellent example of evolutionary opportunism within a widespread mammalian lineage.

PNAS↗
USGS2005

Ichthyophonus in Puget Sound rockfish from the San Juan Islands archipelago and Puget Sound, Washington, USA

In vitro explant cultures identified Ichthyophonus in 10.9% of 302 Puget Sound rockfish Sebastes emphaeus sampled from five sites in the San Juan Islands archipelago and Puget Sound, Washington, in 2003. None of the infected fish exhibited visible lesions and only a single fish was histologically positive. Significantly more females were infected (12.4%) than males (6.8%), and while infected males were only detected at two of the five sites, infected females were identified at all sites, with no significant differences in infection prevalence. Genomic sequences of Ichthyophonus isolates obtained from Puget Sound rockfish, Pacific herring Clupea pallasii, and Yukon River Chinook salmon Oncorhynchus tshawytscha were identical in both the A and B regions of the small subunit 18S ribosomal DNA but were different from Ichthyophonus sequences previously isolated from four different species of rockfish from the northeastern Pacific Ocean. Ichthyophonus in Puget Sound rockfish may not have been previously detected because the infection is subclinical in this species and earlier investigators did not utilize in vitro techniques for diagnosis of ichthyophoniasis. However, since clinical ichthyophoniasis has recently been identified in several other species of northeast Pacific rockfishes, it is hypothesized that this either is an emerging disease resulting from changing marine conditions or the result of introduction by infected southern species that appear during periodic El Nin??o events. ?? Copyright by the American Fisheries Society 2005.

Washiginton↗
USGS2014

Molecular epidemiology and evolution of fish Novirhabdoviruses

The genus Novirhabdoviridae contains several of the important rhabdoviruses that infect fish hosts. There are four established virus species: Infectious hematopoietic necrosis virus (IHNV), Viral hemorrhagic septicemia virus (VHSV), Hirame rhabdovirus (HIRRV), and Snakehead rhabdovirus (SHRV). Viruses of these species vary in host and geographic range, and they have all been studied at the molecular and genomic level. As globally significant pathogens of cultured fish, IHNV and VHSV have been particularly well studied in terms of molecular epidemiology and evolution. Phylogenic analyses of hundreds of field isolates have defined five major genogroups of IHNV and four major genotypes of VHSV worldwide. These phylogenies are informed by the known histories of IHNV and VHSV, each involving a series of viral emergence events that are sometimes associated with host switches, most often into cultured rainbow trout. In general, IHNV has relatively low genetic diversity and a narrow host range, and has been spread from its endemic source in North American to Europe and Asia due to aquaculture activities. In contrast, VHSV has broad host range and high genetic diversity, and the source of emergence events is virus in widespread marine fish reservoirs in the northern Atlantic and Pacific Oceans. Common mechanisms of emergence and host switch events include use of raw feed, proximity to wild fish reservoirs of virus, and geographic translocations of virus or naive fish hosts associated with aquaculture.

Book chapter↗
USGS2013

Smolt physiology and endocrinology

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↗
USGS2018

Rapid discovery of SNPs differentiating hatchery steelhead trout from ESA-listed natural-origin steelhead trout using a 57K SNP array

Natural-origin steelhead trout ( Oncorhynchus mykiss (Walbaum, 1792)) in the Pacific Northwest, USA, are threatened by a number of factors including habitat destruction, disease, decline in marine survival, and a potential erosion of genetic viability due to introgression from hatchery strains. Our major goal was to use a recently developed SNP array containing ∼57 000 SNPs to identify a subset of SNPs that differentiate hatchery and natural-origin populations. We analyzed 35 765 polymorphic SNPs in nine populations of steelhead trout sampled from Puget Sound, Washington, USA. We then conducted two outlier tests and found 360 loci that were candidates for divergent selection between hatchery and natural-origin populations (mean F CT = 0.29, maximum = 0.65) and 595 SNPs that were candidates for selection among natural-origin populations (mean F ST = 0.25, maximum = 0.51). Comparisons with a linkage map revealed that two chromosomes (Omy05 and Omy25) contained significantly more outliers than other chromosomes, suggesting that regions on Omy05 and Omy25 may be of adaptive significance. Our results highlight several advantages of the 57 000 SNP array as a tool for population and conservation genomics studies.

British Columbia, Washington↗
USGS2017

Molecular characterization of a novel orthomyxovirus from rainbow and steelhead trout ( Oncorhynchus mykiss )

A novel virus, rainbow trout orthomyxovirus (RbtOV), was isolated in 1997 and again in 2000 from commercially-reared rainbow trout ( Oncorhynchus mykiss ) in Idaho, USA. The virus grew optimally in the CHSE-214 cell line at 15°C producing a diffuse cytopathic effect; however, juvenile rainbow trout exposed to cell culture-grown virus showed no mortality or gross pathology. Electron microscopy of preparations from infected cell cultures revealed the presence of typical orthomyxovirus particles. The complete genome of RbtOV is comprised of eight linear segments of single-stranded, negative-sense RNA having highly conserved 5′ and 3′-terminal nucleotide sequences. Another virus isolated in 2014 from steelhead trout (also O. mykiss ) in Wisconsin, USA, and designated SttOV was found to have eight genome segments with high amino acid sequence identities (89–99%) to the corresponding genes of RbtOV, suggesting these new viruses are isolates of the same virus species and may be more widespread than currently realized. The new isolates had the same genome segment order and the closest pairwise amino acid sequence identities of 16–42% with Infectious salmon anemia virus (ISAV), the type species and currently only member of the genus Isavirus in the family Orthomyxoviridae . However, pairwise comparisons of the predicted amino acid sequences of the 10 RbtOV and SttOV proteins with orthologs from representatives of the established orthomyxoviral genera and a phylogenetic analysis using the PB1 protein showed that while RbtOV and SttOV clustered most closely with ISAV, they diverged sufficiently to merit consideration as representatives of a novel genus. A set of PCR primers was designed using conserved regions of the PB1 gene to produce amplicons that may be sequenced for identification of similar fish orthomyxoviruses in the future.

Virus Research↗
USGS2013

Worldwide phylogenetic relationship of avian poxviruses

Poxvirus infections have been found in 230 species of wild and domestic birds worldwide in both terrestrial and marine environments. This ubiquity raises the question of how infection has been transmitted and globally dispersed. We present a comprehensive global phylogeny of 111 novel poxvirus isolates in addition to all available sequences from GenBank. Phylogenetic analysis of the Avipoxvirus genus has traditionally relied on one gene region (4b core protein). In this study we expanded the analyses to include a second locus (DNA polymerase gene), allowing for a more robust phylogenetic framework, finer genetic resolution within specific groups, and the detection of potential recombination. Our phylogenetic results reveal several major features of avipoxvirus evolution and ecology and propose an updated avipoxvirus taxonomy, including three novel subclades. The characterization of poxviruses from 57 species of birds in this study extends the current knowledge of their host range and provides the first evidence of the phylogenetic effect of genetic recombination of avipoxviruses. The repeated occurrence of avian family or order-specific grouping within certain clades (e.g., starling poxvirus, falcon poxvirus, raptor poxvirus, etc.) indicates a marked role of host adaptation, while the sharing of poxvirus species within prey-predator systems emphasizes the capacity for cross-species infection and limited host adaptation. Our study provides a broad and comprehensive phylogenetic analysis of the Avipoxvirus genus, an ecologically and environmentally important viral group, to formulate a genome sequencing strategy that will clarify avipoxvirus taxonomy.

Journal of Virology↗
USGS2021

Stock composition of the historical New York Bight Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) intercept fishery revealed through microsatellite analysis of archived spines

A targeted commercial fishery for Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus once operated in the New York Bight, where it was assumed that most harvested Atlantic Sturgeon were natal to the Hudson River population. However, more recent evidence suggests that the fishery may have been targeting a mixed-stock aggregation, in which case harvested Atlantic Sturgeon could have been comprised of individuals from multiple populations throughout the species’ range. Although there is now a moratorium on Atlantic Sturgeon harvest in the New York Bight, modern molecular approaches provide an opportunity to use archived tissues to perform a retrospective mixed-stock analysis on the fishery. Genomic DNA extracted from archived fin spines from 80 Atlantic Sturgeon collected nearly 30 years ago suggests that the fishery primarily harvested individuals from the Hudson River population. However, based on individual-based assignment tests, our results indicate that the fishery also harvested individuals from at least eight other populations located throughout the species’ range. This study highlights how archival hard parts that were previously used for age and growth analyses can be employed for retrospective genetic analyses. Further, because the New York Bight harbors relatively high concentrations of Atlantic Sturgeon, the study shows how localized management decisions can influence Atlantic Sturgeon conservation at rangewide scales. When integrated with more recent knowledge of species ecology, these analyses can be used to evaluate the efficacy of previous management strategies and understand the effects of historical processes on contemporary demography.

New York↗