Geology topics

Christopher Osborne

Publications and source records attributed to Christopher Osborne.

13 recordsLinked to original sources

USGS2026

Genomic structural variation rescues a classic biological invader from a population bottleneck

Invasion genetics presents a classic paradox: How do species successfully spread despite severe population bottlenecks? The brown treesnake ( Boiga irregularis ) in Guam represents a notable example of this phenomenon, having been introduced with only a handful of individuals. We show that the population endured an extreme bottleneck, with roughly half of the genome exhibiting runs of homozygosity, comparable to species of conservation concern. Despite this, we uncovered extensive diversity in the form of nearly 19,000 genomic structural variants, which affect almost eight times more of the genome than single-nucleotide variants and provide material for “rescuing” the population from inbreeding-driven declines. Structural variant density was highest in gene promoters, where recombination and DNA repair often occur, providing a mechanism for rapid evolution of gene-linked diversity. This diversity is enriched in genes vital for adaptive immunity and olfaction, suggesting genomic diversity in key chromosomal regions can rescue populations from inbreeding. This work has critical implications for invasion biology and conservation genetics practitioners.

Guam↗

USGS2026

A Lake Charr pangenome reveals highly conserved Ohnologs as drivers of phenotypic diversity

Whole-genome duplication (WGD) is hypothesized to spur evolutionary diversification by producing genome-wide duplicate gene sets (Ohnologs) that are initially functionally redundant but can diverge markedly as the effects of relaxed selection accumulate over time. However, the underlying mechanisms remain unclear, in part because genomic studies often reconstruct Ohnolog evolution over millions of years, during which subsequent mutations can obscure deep-time signals. Investigating the relationship between Ohnolog evolution and diversification on a contemporary timescale offers clearer insights. We explore this relationship in Lake Charr ( Salvelinus namaycush ), where ∼10% of genes are retained highly conserved polyploid duplicates following the Salmonid-Specific Fourth Round WGD. Using 31 chromosome-level assemblies of Lake Charr from morphologically and ecologically diverse populations, joined into a pangenome graph, we characterized 189,555 structural variants (SVs) that were significantly less likely to affect genes retained as sequence-conserved Ohnolog pairs, nuancing the hypothesis that gene redundancy, relaxed selection, and functional diversification are intertwined. However, we found that SVs affecting such conserved Ohnologs may be potent drivers of adaptive evolution. Notably, we identified a putative 938-Kb interchromosomal translocation containing 25 genes with highly conserved Ohnologs in a paralogous (but untranslocated) genomic block. This putative translocation appears to have facilitated Ohnolog divergence in ankrd11 and hp , genes putatively linked to craniofacial and lipid metabolic diversity in sympatric Lake Superior morphs. This research reveals that conserved Ohnologs previously presumed to be redundant remain a reservoir for adaptive change.

BioRxiv↗

USGS2026

Genomic structural variation rescues a classic biological invader from a population bottleneck

Invasion genetics presents a classic paradox: how do species successfully spread despite severe population bottlenecks? The brown treesnake ( Boiga irregularis ) in Guam represents a striking example of this phenomenon, having been introduced with only a handful of individuals. We show that the population endured an extreme bottleneck, with roughly half of the genome exhibiting runs of homozygosity, comparable to species of conservation concern. Despite this, we uncovered extensive diversity in the form of nearly 19,000 genomic structural variants, which affect almost eight times more of the genome than single-nucleotide variants and provide material for ‘rescuing’ the population from inbreeding-driven declines. Structural variant density was highest in gene promoters, where recombination and DNA repair often occur, providing a mechanism for rapid evolution of gene-linked diversity. This diversity is enriched in genes vital for adaptive immunity and olfaction, suggesting genomic diversity in key chromosomal regions can rescue populations from inbreeding. This work has critical implications for invasion biology and conservation genetics practitioners.

BioRxiv↗

USGS2026

Egg thiamine concentrations reflect dietary differences between four hatchery strains, including two morphotypes, of Lake Trout in Lake Ontario

Objective Test whether dietary differences among hatchery strains of Lake Trout Salvelinus namaycush were associated with variation in egg thiamine concentrations and assess the potential for using strain-specific traits to mitigate thiamine deficiency complex (TDC) in Lake Ontario restoration efforts. Methods Stomach content analysis and stable isotope mixing models were used to compare diets among four hatchery strains of Lake Trout, representing lean and humper morphotypes. Egg thiamine concentrations were measured to test whether dietary differences correlated with susceptibility to TDC. Results Significant differences in diet and egg thiamine concentrations were observed among Lake Trout strains. A humper-like morphotype strain exhibited elevated thiamine levels, which were associated with reduced consumption of prey known to degrade thiamine levels when consumed, Alewife Alosa pseudoharengus and Rainbow Smelt Osmerus mordax , and increased reliance on Round Goby Neogobius melanostomus or sculpin species (Slimy Sculpin Cottus cognatus and Deepwater Sculpin Myoxocephalus thompsonii ). These findings support the link between the consumption of Alewife and Rainbow Smelt and thiamine deficiency. Conclusions Our findings support a link between strain-specific dietary preferences and susceptibility to TDC in Lake Trout. Preferential stocking of strains less prone to TDC, such as the strain derived from a humper morph from Lake Superior, could enhance restoration success in Lake Ontario. This strategy may be especially effective given the continued dominance of Alewife in the lake's prey base and the current management priorities supporting fisheries for Pacific salmon Oncorhynchus spp.

North American Journal of Fisheries Management↗

USGS2023

Factors influencing egg thiamine concentrations of Lake Ontario lake trout: 2019–2020

In the Great Lakes region, thiamine deficiency is considered a recruitment bottleneck for lake trout Salvelinus namaycush and has been correlated with the consumption of non-native alewife Alosa pseudoharengus . While alewife, the most abundant forage fish in Lake Ontario, are the predominant prey for lake trout, they also consume benthic prey such as round goby Neogobius melanostomus . Because variation in the proportion of alewife in lake trout diets is linked to variation in egg thiamine concentrations, understanding how factors such as region of capture and hatchery-strain of lake trout influence diet, are key to understanding the patterns of variation in egg thiamine concentrations observed in this species. With recent increases in natural recruitment of lake trout being observed in the western region of the lake, understanding if egg thiamine is a potential driver is crucial to the rehabilitation of lake trout. In this study, we evaluated egg thiamine concentrations in lake trout during 2019–2020. We found no significant difference in egg thiamine concentrations among regions. However, a stocked Lake Superior deepwater morphotype (Superior Klondike Wild – SKW) showed significantly higher egg thiamine concentrations compared to the lean morphotype including Seneca (SEN) and Lake Champlain Domestic (LCD) strains. An analysis of fatty acid signatures of each hatchery-strain suggested that the SKW strain consumed a higher proportion of round goby than lean strains. Overall, these results suggest that morphotypic differences in the feeding ecology of lake trout can result in biochemical changes which may influence the effectiveness of restoration efforts.

Lake Ontario↗

USGS2023

Field and laboratory validation of new sampling gear to quantify coregonine egg deposition and larval emergence across spawning habitat gradients

The influence of habitat and environmental conditions on Great Lakes coregonine reproduction is not well described, in part, because we lack sampling gears for early life stages that are effective across habitats. We designed new egg and larval emergence traps to quantify coregonine reproductive success across variable depths and substrates and tested them in laboratory and field settings. In the laboratory, our new metal ring egg traps had greater egg retention (94–100%) and faster post-catch processing (5–7 min) relative to a commonly employed fiber mat trap (30–67% and 30–60 min). In Lake Ontario’s Chaumont Bay, egg densities for lake whitefish Coregonus clupeaformis (0–5,832 eggs m −2 ) and cisco Coregonus artedi (0–426,501 eggs m −2 ) measured with metal ring traps (n = 112) varied across habitats but were greatest between 2–5 m on rock and dreissenid mussel substrates. Emergence traps used an inverted cone, fine mesh, and a clear collection chamber to capture positively phototactic emerging larvae. In the laboratory, traps captured 69–80% of emerged larvae. In Chaumont Bay, emergence traps deployed for 21 days after ice out caught only cisco larvae. Emergence rates varied across habitats (0–118 larvae m −2 day −1 , n = 85) but were highest on dreissenid mussel reef substrate. Our samplers improved processing efficiency and facilitated large sample sizes to quantify variability in egg deposition densities and emergence rates across habitats. These methods can advance coregonine conservation by determining how anthropogenic changes to habitat and environmental conditions influence incubation success.

Journal of Great Lakes Research↗

USGS2022

Lake trout (Salvelinus namaycush) rehabilitation in Lake Ontario, 2021

Each year we report on the progress toward rehabilitation of the Lake Ontario lake trout ( Salvelinus namaycush ) population, including the results of stocking, annual assessment surveys, creel surveys, and evidence of natural reproduction observed from standard surveys performed by U.S. Geological Survey (USGS) and New York State Department of Environmental Conservation (NYSDEC). The catch per unit effort (CPUE) of adult lake trout in gill nets increased each year from 2008-2014, recovering from historic lows recorded during 2005-2007. Adult abundances declined each year from 2015 to 2017; and in 2017 were about 35% below the 2014 peak and 17% below the 1999-2004 mean. Adult abundance increased in 2018 by 51% over the 2017 value and remained nearly stable between 2018 and 2021. The 2020 rate of wounding by sea lamprey ( Petromyzon marinus ) on lake trout caught in gill nets was 1.68 A1 wounds (fresh wound) per 100 lake trout and was near target (2 wounds per 100 lake trout). Condition values for adult lake trout, indexed in September from the predicted weight for a 700 mm lake trout from annual length-weight regressions and Fulton’s K for age-6 males, were among the highest levels observed for the 1983-2021 time series. Reproductive potential for the adult stock indexed from the CPUE of mature females ≥ 4000 g was again above the target in 2021 continuing a trend observed in ten of the last eleven years. The 2021 catch of young wild lake trout marked the 27th observation in the last 28 years, however only two sites off the mouth of the Niagara River were surveyed.

Lake Ontario↗

USGS2021

Accuracy and precision of otolith-derived age Interpretations for known-age lake trout

Catch-at-age data are used to inform important management decisions for recovering populations of Lake Trout Salvelinus namaycush . Age data for Lake Trout are commonly derived from interpretation of annual growth marks (annuli) on the fish’s otoliths. Due to the tendency for annuli to vary in appearance and the subjectivity that is inherent to any age interpretation method, it is important that the common sources of interpretation error be well understood for any aging method used to inform management plans. In this study, coded wire tags were used to establish true ages for 153 Lake Trout to measure the precision and accuracy of age interpretations made from transverse-sectioned otoliths and to identify sources of potential age interpretation error that researchers and managers may encounter when using this method. Precision of age interpretations, as measured by average coefficient of variation, ranged from 7.9% to 9.2%. Accuracy of age interpretations varied among readers, with exact matches ranging from 41.8% to 53.6% and accuracy within ±1 year ranging from 81.0% to 83.0%. Age interpretation errors were more likely to be overestimates of true age for Lake Trout under age 7 and underestimates for Lake Trout over age 13. However, only reader 1 exhibited significant systematic bias in their age interpretations. Poor clarity of the first annuli, growth checks resembling annuli, and faintness of narrow annuli near otolith margins in older fish were identified as likely sources of interpretation error in this study. A digital reference collection of known-age Lake Trout otoliths is provided as supplemental material in the online version of this article. This collection can be used for training new readers, measuring the accuracy of age interpretations, and monitoring for aging bias by anyone using otoliths to obtain age data for Lake Trout.

North American Journal of Fisheries Management↗

USGS2021

Lake trout rehabilitation in Lake Ontario, 2020

Each year we report on the progress toward rehabilitation of the Lake Ontario lake trout (Salvelinus namaycush) population, including the results of stocking, annual assessment surveys, creel surveys, and evidence of natural reproduction observed from standard surveys performed by USGS and NYSDEC. Response to the COVID-19 pandemic limited survey effort such that spring and summer bottom trawl surveys and the creel survey were not completed in 2020, and sites sampled during the fall gillnet survey were limited to those east of Rochester, NY. The catch per unit effort of adult lake trout in gill nets increased each year from 2008-2014, recovering from historic lows recorded during 2005-2007. Adult abundances declined each year from 2015 to 2017; and in 2017 were about 35% below the 2014 peak and 17% below the 1999-2004 mean. Adult abundance increased in 2018 by 51% over the 2017 value and remained nearly stable between 2018 and 2020. The 2020 rate of wounding by sea lamprey (Petromyzon marinus) on lake trout caught in gill nets was 2.27 A1 wounds (fresh wound) per 100 lake trout and was near target (2 wounds per 100 lake trout). Condition values for adult lake trout, indexed in September from the predicted weight for a 700 mm lake trout from annual length-weight regressions and Fulton’s K for age-6 males, were among the highest levels observed for the 1983-2020 time series. Reproductive potential for the adult stock indexed from the CPUE of mature females ≥ 4000 g was again above the target in 2020 continuing a trend observed in nine of the last ten years. The 2020 catch of young wild lake trout marked the 26th observation in the last 27 years, however the low numbers of native adults observed during that time period continues to indicate substantial restoration impediments still exist.

Lake Ontario↗

USGS2021

Angler-caught salmonid diets illustrate Lake Ontario Alewife population and predator-prey dynamics

Lake Ontario fisheries decision makers use information about the status and trajectory of prey fish populations, such as alewife, for salmonid sport fish management. In 2020, the April bottom trawl survey, typically used to assess alewife, was canceled the day after it began due to Coronavirus health concerns. This prompted NYSDEC and USGS science teams to initiate a diet study using angler-collected samples to provide information on the alewife population in 2020. Over 800 salmonid diets were collected from across Lake Ontario southern shore from May through September. Past diet studies illustrated alewife size distribution in piscivore diets overlapped April trawl survey-based distributions (proportion overlap = 0.51- 0.81, n = 5). In 2020 few age-1 sized alewife (40 - 140 mm) were observed in salmonid diets, suggesting that 2019 alewife reproduction was below average. Given that alewife reproductive success from 2017 and 2018 were also below average, the 2021 Lake Ontario adult alewife population will likely be at a record low for the 43-year time series. For all years and piscivore species, adult-sized Alewife ( total length > 140 mm) were the predominate size consumed by piscivores greater than 400 mm (~ 16 inches). Sizes of alewife in the diet were positively related to piscivore size. Diet composition, by dry weight, indicated alewife remain the dominant prey supporting salmonids and diets were generally similar to trawl-based estimates of prey fish community composition. The most notable deviation from this pattern included round goby, which comprised substantial portions of brown trout and lake trout diets in 2013 and 2020. These results inform decision making related to Lake Ontario salmonid stocking and predator prey dynamics and highlight the utility of angler-caught piscivore diets for indicating alewife population status.

Lake Ontario↗

USGS2020

Bottom trawl assessment of Lake Ontario prey fishes, 2019

Multi-agency, collaborative Lake Ontario bottom trawl surveys provide information for decision making related to Fish Community Objectives including predator-prey balance and understanding prey fish community diversity. In 2019, bottom trawl surveys in April (n = 252 tows) and October (n = 160 tows) sampled main lake and embayments at depths from 5–226 m. Combined, the surveys captured 283,383 fish from 39 species. Alewife were 67% of the total catch by number while round goby, deepwater sculpin, and rainbow smelt comprised 13, 10, and 4% of the catch, respectively. In 2019, the lake-wide adult alewife biomass index declined from 2018 and age-1 biomass, a measure of reproductive success the previous year, was low. Year-class catch curve models identified years where estimates from surveys conducted only in U.S. waters were biased, potentially due to a greater portion of the alewife population inhabiting unsampled Canadian waters. Accounting for spatial survey bias, these model estimates indicated the 2019 adult alewife biomass was the lowest value in the 42-year time series. Models also identified the extent to which age-1 alewife biomass was historically underestimated, however lake-wide results from 2016-2019 appear less biased. If below-average year-class estimates from 2017 and 2018 are accurate, adult alewife biomass will continue to decline in 2020. Abundance indices for other pelagic prey fishes such as rainbow smelt, threespine stickleback, emerald shiner, and cisco were low and similar to 2018 values. Pelagic prey fish diversity is low because a single species, alewife, dominates the community. Deepwater sculpin and round goby were the most abundant demersal (bottom-oriented) prey fishes in 2019. Despite declines in slimy sculpin and other nearshore prey fishes, demersal prey fish community diversity has increased as deepwater sculpin and round goby comprise more even portions of the community. New experimental trawl sites in embayment habitats generally captured more species, a higher proportion of native species, and higher densities relative to main lake habitats. In 2019, a western tubenose goby (Proterorhinus semilunaris) was captured for the first time in the trawl surveys.

Lake Ontario↗

USGS2020

Lake trout rehabilitation in Lake Ontario, 2019

Each year we report on the progress toward rehabilitation of the Lake Ontario lake trout ( Salvelinus namaycush ) population, including the results of stocking, annual assessment surveys, creel surveys, and evidence of natural reproduction observed from all standard surveys performed by USGS and NYSDEC. The catch per unit effort of adult lake trout in gill nets increased each year from 2008-2014, recovering from historic lows recorded during 2005-2007. Adult abundances declined each year from 2015 to 2017; and in 2017 were about 35% below the 2014 peak and 17% below the 1999-2004 mean. Adult abundance increased in 2018 by 51% over the 2017 value and increased and addition 16% in 2019. The 2019 rate of wounding by sea lamprey (Petromyzon marinus) on lake trout caught in gill nets (0.53 A1 wounds (fresh wound) per 100 lake trout) was below target (2 wounds per 100 lake trout). Estimates from the NYSDEC fishing boat survey indicated angler catch rate of lake trout was low in 2019 and among the lowest recorded for the time series. Condition values for an adult lake trout, indexed in September from the predicted weight for a 700mm lake trout from annual length-weight regressions and Fulton’s K for age-6 males, were among the highest levels observed for the 1983-2019 time series. Predicted weight for a 400mm lake trout from July 2019 bottom trawl catches was near the long-term average while age-2 K was among the lowest for the time series. Reproductive potential for the adult stock indexed from the CPUE of mature females ≥ 4000g was again above the target in 2019 continuing a trend observed in nine of the last ten years. The 2019 catch of young native lake trout marked the 25th observation in the last 26 years, however the low numbers of native adults observed during that time period continues to indicate substantial restoration impediments still exist.

Lake Ontario↗

USGS2020

Lake trout spawning studies: Updates, new survey, and comparison to standard September gillnet survey

In Lake Ontario, lake trout restoration efforts have not established a self-sustaining population. Herein we describe efforts to evaluate standard and new surveys, and to estimate dispersal from stocking locations, to better understand impediments to natural reproduction. In 2019, lake trout egg deposition was sampled at two locations, Stony Island Reef, and Ford Shoals. No eggs were collected at either site. Egg deposition rates at Stony Island Reef, expressed in eggs/net/day, were lower in 2019 (0) and 2017 (0.0004) than in 1987 and 1989 (1.27 and 0.27, respectively). Spawning lake trout were indexed using standard gillnets set at six locations along the southern shore. Sites were fished overnight with two nets, except Youngstown where only one net was set. When comparing the standard September gillnet survey to the spawning survey, the spawning survey caught more and older fish, but had a similar representation of strains. Both gillnet surveys revealed that, during the early to late fall, most lake trout (>72%) are caught as adults near where they were stocked as juveniles. This spawning survey demonstrated that lake trout in spawning condition are aggregating near possible spawning habitat, but the presence of adults alone cannot identify the specific spawning habitat. Egg deposition results suggest lake trout may be depositing eggs in different habitats then they have in the past. Alternatively, our egg collection methods may not be effective when egg abundance is low. Lake Ontario lake trout restoration would benefit from survey approaches that identify specific spawning habitat.

Lake Ontario↗