Historical Sampling Research Articles

Multi-decadal trends in the tropical Pacific western boundary currents retrieved from historical hydrological observations

As large-scale ocean circulation is a key regulator in the redistribution of oceanic energy, evaluating the multi-decadal trends in the western Pacific Ocean circulation under global warming is essential for not only understanding the basic physical processes but also predicting future climate change in the western Pacific. Employing the hydrological observations of World Ocean Atlas 2018 (WOA18) from 1955 to 2017, this study calculated the geostrophic currents, volume transport and multi-decadal trends for the North Equatorial Current (NEC), the North Equatorial Countercurrent (NECC), the Mindanao Current (MC), the Kuroshio Current (KC) in the origin and the New Guinea Coastal Undercurrent (NGCUC) within tropical western Pacific Ocean over multi-decades. Furthermore, this study examined the contributions of temperature and salinity variations. The results showed significant strengthening trends in NEC, MC and NGCUC over the past six decades, which is mainly contributed by temperature variations and consistent with the tendency in the dynamic height pattern. Zonal wind stress averaged over the western Pacific Ocean in the same latitude of each current represents the decadal variation and multi-decadal trends in corresponding ocean currents, indicating that the trade wind forcing plays an important role in the decadal trend in the tropical western Pacific circulation. Uncertainties in the observed hydrological data and trends in the currents over the tropical western Pacific are also discussed. Given that the WOA18 dataset covers most of the historical hydrological sampling data for the tropical western Pacific, this paper provides important observational information on the multi-decadal trend of the large-scale ocean circulation in the western Pacific.

Early presence of Batrachochytrium dendrobatidis in Mexico with a contemporary dominance of the global panzootic lineage.

Chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), is a devastating infectious disease of amphibians. Retrospective studies using museum vouchers and genetic samples supported the hypothesis that Bd colonized Mexico from North America and then continued to spread into Central and South America, where it led to dramatic losses in tropical amphibian biodiversity (the epizootic wave hypothesis). While these studies suggest that Bd has been in Mexico since the 1970s, information regarding the historical and contemporary occurrence of different pathogen genetic lineages across the country is limited. In the current study, we investigated the historical and contemporary patterns of Bd in Mexico. We combined the swabbing of historical museum vouchers and sampling of wild amphibians with a custom Bd genotyping assay to assess the presence, prevalence, and genetic diversity of Bd over time in Mexico. We found Bd-positive museum specimens from the late 1800s, far earlier than previous records and well before recent amphibian declines. With Bd genotypes from samples collected between 1975-2019, we observed a contemporary dominance of the global panzootic lineage in Mexico and report four genetic subpopulations and potential for admixture among these populations. The observed genetic variation did not have a clear geographic signature or provide clear support for the epizootic wave hypothesis. These results provide a framework for testing new questions regarding Bd invasions and their temporal relationship to observed amphibian declines in the Americas.

Observations of Phytoplankton Community Composition in the Santa Barbara Channel During the Thomas Fire

AbstractThe Thomas Fire ignited on December 5, 2017 and burned nearly 300,000 acres of land in Ventura and Santa Barbara counties until January 12, 2018, making it the largest wildfire in California history at the time. During the fire, a persistent plume of ash, smoke, and soot extended up to 1,000 km offshore over the Santa Barbara Channel (SBC). The effect of this ash influx on the SBC phytoplankton community was investigated with an Imaging FlowCytobot (IFCB) onboard R/V Sally Ride during a research cruise in mid‐December 2017. Over 100,000 images of phytoplankton and nonliving particles were collected and each image was manually classified, resulting in time series of phytoplankton cells and detrital particles, including ash. Comparing the Thomas Fire conditions to historical monthly sampling in the SBC in December reveals significant differences in sea surface temperature, nutrient concentration, and phytoplankton community composition (PCC) in December 2017. During the Thomas Fire, dinoflagellates dominated the phytoplankton community (comprising up to 90% of the total phytoplankton cell biovolume per sample), while diatoms and picophytoplankton typically dominate surface ocean PCC in the SBC in December. While this study was not able to demonstrate a correlational relationship between PCC and wildfire ash concentration, the significant differences in surface ocean biogeochemistry in December 2017 compared to past winters is notable. Wildfire severity and frequency are annually increasing in California and globally with unknown impacts on the marine ecosystem; thus, this study provides an important baseline assessment for the SBC.

Resident vegetation modifies climate-driven elevational shift of a mountain sedge

Mountain plant species are changing their ranges in response to global warming. However, these shifts vary tremendously in rate, extent and direction. The reasons for this variation are yet poorly understood. A process potentially important for mountain plant re-distribution is a competition between colonizing species and the resident vegetation. Here, we focus on the impact of this process using the recent elevational shift of the sedge Carex humilis in the northern Italian Alps as a model system. We repeated and extended historical sampling (conducted in 1976) of the species in the study region. We used the historical distribution data and historical climatic maps to parameterize a species distribution model (SDM) and projected the potential distribution of the species under current conditions. We compared the historical and the current re-survey for the species in terms of the cover of important potential competitor species as well as in terms of the productivity of the resident vegetation indicated by the Normalized Difference Vegetation Index (NDVI). We found that Carex humilis has shifted its leading range margin upward rapidly (51.2 m per decade) but left many sites that have become climatically suitable since 1976 according to the SDM uncolonized. These suitable but uncolonized sites show significantly higher coverage of all dwarf shrub species and higher NDVI than the sites occupied by the sedge. These results suggest that resistance of the resident vegetation against colonization of migrating species can indeed play an important role in controlling the re-distribution of mountain plants under climate change.

Personal Names in the Families of Russian Germans: Challenges of Self-Identification of the Ethnic Group

The research deals with the topical issue of changing the ‘ethnolinguistic and cultural area’, a shift in the system of ethnolinguistic and cultural orientations and values of the people. The problem is discussed from the perspective of anthroponymic material in the families of ethnic Germans born in Russia, whose ancestors settled on Russian lands since the reign of Catherine II. The primary purpose of the study is to carry out a comprehensive analysis of some (often controversial) aspects of (self)identification of the linguistic personality of Russian Germans from the perspective of the corpus of personal names. Using the methods of functional historical analysis, continuous sampling, interview, systemisation, and interpretation, the authors of this study, based on the analysis of a relatively large corpus of collected personal names, as well as based on answers of 200 respondents, who are descendants of Russian Germans, attempted to determine which names are chosen for children and what language Russian Germans speak today. The problem is considered from a synergistic perspective: sociolinguistics, linguoculturology and ethnolinguistics, as well as anthroponymics. The authors conclude that the choice of names in the families of Russian Germans of German/non-German origin depends on several factors— traditions of the family; place of residence; the level of education; profession/specialisation. In the anthroponymicon of Russian Germans, under the influence of personal names of the surrounding ethnic groups, socio-cultural and historical changes result in internal changes in language units.

Spatio-temporal variation in species composition of New Zealand's whitebait fishery

ABSTRACT Whitebait comprise a culturally, commercially and recreationally important fishery in New Zealand, where post-larvae are netted while returning from their marine phase. In this study, we expanded an historical (1964) sampling programme to gain a contemporary understanding of the species composition of the whitebait fishery; 87 rivers were sampled over six months in 2015. Over the entire country, >12 species were found in samples and 87.6% of these were īnanga (Galaxias maculatus). Kōaro (G. brevipinnis) and banded kōkopu (G. fasciatus) were abundant in some rivers and regions at particular times of the year. Buller was the most variable region, spatially and temporally, for species composition; Canterbury was the least variable. Banded kōkopu whitebait migrated one month earlier north of Cook Strait than in the south. There was a positive association between the abundance of kōaro and banded kōkopu in samples and the level of indigenous forest cover in catchments. Compared to samples from 50 years ago, there was a greater proportion of kōaro and banded kōkopu whitebait throughout the country. This spatio-temporal variability requires fishery regulations to be more tailored and flexible if they are to conserve the diversity of life-histories present in the catch and sustain the whitebait fishery.

Fish Performance Indicators Adjacent to Oil Sands Activity: Response in Performance Indicators of Slimy Sculpin in the Steepbank River, Alberta, Adjacent to Oil Sands Mining Activity

Since 2009, the Canadian and Alberta governments have been developing monitoring plans for surface water quality and quantity of the lower Athabasca River and its tributaries (2010-2013). The objectives of the present study to the fish monitoring program were to 1) assess the current status of fish in a tributary of the lower Athabasca River, 2) identify existing differences between upstream reference and within the oil sands deposit exposure sites, and 3) identify trends/changes in fish performance indicators relative to historical studies. The present study examines the fish performance indicators in slimy sculpin (Cottus cognatus) in the Steepbank River, Alberta, in terms of growth, gonad size, condition, and hepatic 7-ethoxyresorufin-O-deethylase (EROD) activity as an indicator of exposure to oil-sands-related compounds. The sampling program followed historical sampling methods (1999-2000) to provide comparable data over time with an additional upstream site (n = 2) added as development progressed. Consistent changes were documented in sculpin collected from downstream sections of the Steepbank River within the oil sands deposit (n = 2) in 2010 through 2013. Sculpin demonstrated increased liver size with corresponding induction of EROD activity consistent with historical data and reductions in energy investment relative to reproductive development and gonadal steroid production capacity. There was no consistent evidence of changes in fish performance indicators with increased surface mining development, particularly adjacent to the Steepbank River Mid site. Although physical development in the Steepbank watershed has increased over the last 15 yr, these results are consistent with historical data suggesting that the magnitude of the response in the aquatic environment adjacent to the development has not changed. Environ Toxicol Chem 2020;39:396-409. © 2019 SETAC.

Contribution of 3D coupled hydrodynamic-ecological modeling to assess the representativeness of a sampling protocol for lake water quality assessment

This study deals with the impact of spatio-temporal heterogeneities on the assessment of lake ecological status according to the European water framework directive (WFD). A method, based on three-dimensional coupled hydrodynamic and ecological modeling, is presented to assess the variability of lake ecological status, and to locate the most representative sampling station of Lake Geneva (France/Switzerland). Five variables used in the lake ecological status evaluation were simulated by using the free software Delft3D. The numerical simulation results showed that the simulated ecological status based on chlorophyll a and total phosphorus concentrations measured at the regulatory monitoring station depend on the choice of the sampling date. Results also indicated a strong spatial heterogeneity in ecological status that varies from “poor” to “good” along an East-West gradient. Finally, the numerical simulation results showed that the most representative point of a mean theoretical ecological quality for Lake Geneva would be located in the center of the upper basin, close to the historical sampling station.

Resistance of Drakensberg grasslands to compositional change depends on the influence of fire-return interval and grassland structure on richness and spatial turnover

Frequent fire is necessary for maintaining sub-tropical and tropical grassland ecosystems, without which they may transform to forest. In the biodiversity-rich Drakensberg mountains of southern Africa, a challenge for conservation is to emulate the natural fire regime driven mainly by lightning ignition which existed before human influence commenced 25,000 BP. Here, a naturally variable fire regime was replaced with a rigid, frequent fire regime about a century ago in order to maintain a vigorous grass sward for sustained water delivery. However, its impact on plant diversity is not known. We tested impacts of frequent and infrequent fire regimes established by 1957 on grassland composition and diversity at the long-term Cathedral Peak research catchments. Historic sampling of grass composition in 1980 and 1986 was repeated in 2014, at which time forbs were sampled in order to examine a potential influence of fire on diversity. Grass composition was remarkably resistant to different fire regimes over the study period, with changes in the relative abundance of individual species limited to ≤6%. Only two decades after implementing return intervals of one to eight years was a proportion of composition variance explained by the fire regime. Forbs contributed 78% of total species richness and were influenced by the effects of the fire regime on grassland structure (e.g. making space available for recruitment). Forb richness corroborated with the Intermediate Disturbance Hypothesis and was greater in areas with intermediate fire regimes. However, forb turnover was explained in part by both frequent and infrequent fire regimes. Therefore, although richness may be greater under intermediate fire regimes, to maintain unique forb assemblages or turnover, a variable fire regime, believed to reflect the historic lightning-driven fire regime, is demonstrated to be important for maintaining grassland diversity.

A perfect storm for mammalogy: declining sample availability in a period of rapid environmental degradation

Natural history collections have stimulated insights into systematics and evolution, but the extensive biodiversity sampling held in museums is increasingly employed to address other critical societal concerns, especially those related to changing environmental conditions on our planet. Due to large-scale digitization efforts in the last decade, specimen information can now be collated across natural history museums. Here, we leverage the availability of digital records of specimens in the United States that span the past ∼135 years to explore the vitality of this resource. Using mammals as an example, we document a significant decline in recent specimen acquisition at a time of extreme environmental degradation and loss of mammalian populations. To stimulate rigorous assessments of the impacts of changing conditions and future-proof this basic infrastructure for mammalogy, we recommend a renewed effort to build temporally deep, geographically extensive, and site-intensive collections of holistic specimens. Targeted fieldwork should be designed to leverage historic sampling to enable retrospective environmental analyses and derive more complete perspectives of change.

Amphibians and reptiles of C. E. Miller Ranch and the Sierra Vieja, Chihuahuan Desert, Texas, USA.

We report the occurrence of 50 species of amphibians and reptiles recently collected on C. E. Miller Ranch and the Sierra Vieja in the Chihuahuan Desert of Texas, USA and describe their perceived distribution and abundance across various habitat associations of the region. Our recent surveys follow intense, historic sampling of amphibians and reptiles from this region in 1948. Of the 50 species detected in recent surveys, six were not collected in 1948 and an additional three species documented in 1948 have yet to be detected in a 14-year period of recent surveys. Combining data from both historic and recent surveys, a total of 53 species of amphibians and reptiles are known from the ranch (11 amphibians, 42 reptiles). Land stewardship and conservation practices have likely contributed to the persistence of the majority of these species through time. Additionally, we discuss the status of amphibians and reptiles not collected during recent surveys and comment on potential species that have not yet been detected.

Assessing temporal shifts in lotic fish community structure in the upper Red River basin, Oklahoma

ABSTRACTA long-term fish community monitoring program was established by the Oklahoma Department of Wildlife Conservation Streams Program in 2016. One of the primary goals of this program is to evaluate contemporary fish species distributions in Oklahoma and draw inferences regarding changes in those distributions over time. In 2016, fish community surveys took place from late June to early August at a total of 48 sites within the upper Red River basin. Compared to the most comprehensive historical sampling effort within the basin, contemporary surveys detected an additional eight species while three species historically present were not detected in 2016. Multivariate generalized linear model results indicated significant differences in community structure between historical and contemporary surveys. Univariate testing paired with Sum-of-LR analyses revealed differences in community structure were largely driven by increases in generalist fish species (e.g. Green Sunfish and Common Carp) and decreases in small-bodied specialist cyprinids (e.g. Chub Shiner). Although changes in species occurrences may be partially driven by differences in sampling methodology and effort, changes across multiple stream reaches likely reveal real trends.

Spatiotemporal modeling and prediction of soil heavy metals based on spatiotemporal cokriging

Soil heavy metals exhibit significant spatiotemporal variability and are strongly correlated with other soil heavy metals. Thus, other heavy metals can be used to improve the accuracy of predictions when performing spatiotemporal predictions of soil heavy metals within a given area. In this study, we propose the spatiotemporal cokriging (STCK) method to enable the use of historical sampling points and co-variables in the spatial prediction of soil heavy metals. Moreover, experimental spatiotemporal (ST) semivariogram and ST cross-semivariogram computational methods, a fitting strategy to the ST semivariogram and ST cross-semivariogram models based on the Bilonick model, and the STCK interpolation algorithm are introduced; these methods are based on spatiotemporal kriging (STK) and cokriging (CK). The data used in this study consist of measurements of soil heavy metals from 2010 to 2014 in Wuhan City, China. The results show that the behavior of predictions of the concentrations of heavy metals in soils is physically more realistic, and the prediction uncertainties are slightly smaller, when STCK is used with greater numbers of co-variables and neighboring points.

Optimal PID controller tuning using stochastic programming techniques

We argue that stochastic programming provides a powerful framework to tune and analyze the performance limits of controllers. In particular, stochastic programming formulations can be used to identify controller settings that remain robust across diverse scenarios (disturbances, set‐points, and modeling errors) observed in real‐time operations. We also discuss how to use historical data and sampling techniques to construct operational scenarios and inference analysis techniques to provide statistical guarantees on limiting controller performance. Under the proposed framework, it is also possible to use risk metrics to handle extreme (rare) events and stochastic dominance concepts to conduct systematic benchmarking studies. We provide numerical studies to illustrate the concepts and to demonstrate that modern modeling and local/global optimization tools can tackle large‐scale applications. The proposed work also opens the door to data‐based controller tuning strategies that can be implemented in real‐time operations. © 2017 American Institute of Chemical Engineers AIChE J, 64: 2997–3010, 2018

Riparian and landscape disturbance effects on stream fish community composition in an agriculturally-dominated drainage

We compared historical stream fish community sampling and remote sensing data from 1993–2011 in an agriculturally-dominated drainage basin to determine the effects of varying levels of riparian and landscape disturbances on fish communities. Stream fish guilds were analyzed with National Land Cover Database and aerial imagery products to quantify disturbance levels at a local and watershed scale. Insectivores and benthic insectivores were associated with intact riparian areas, whereas environmentally tolerant and omnivorous species were found in environments with degraded riparian areas. Riparian disturbances had the greatest effect near the stream (0–10 m), and the effects diminished with increasing distance from the stream. This spatial scale corresponds with those reported in the literature whereby allocthonous inputs and riparian filtering influenced stream fish communities and water quality. The landscape disturbance was not a strong predictor for any fish guild, indicating that local riparian condit...

Detecting spatial patterns of rivermouth processes using a geostatistical framework for near-real-time analysis

This paper proposes a geospatial analysis framework and software to interpret water-quality sampling data from towed undulating vehicles in near-real time. The framework includes data quality assurance and quality control processes, automated kriging interpolation along undulating paths, and local hotspot and cluster analyses. These methods are implemented in an interactive Web application developed using the Shiny package in the R programming environment to support near-real time analysis along with 2- and 3-D visualizations. The approach is demonstrated using historical sampling data from an undulating vehicle deployed at three rivermouth sites in Lake Michigan during 2011. The normalized root-mean-square error (NRMSE) of the interpolation averages approximately 10% in 3-fold cross validation. The results show that the framework can be used to track river plume dynamics and provide insights on mixing, which could be related to wind and seiche events.

Genomic and phenotypic analysis of Vavilov\u2019s historic landraces reveals the impact of environment and genomic islands of agronomic traits

The Vavilov Institute of Plant Genetic Resources (VIR), in St. Petersburg, Russia, houses a unique genebank, with historical collections of landraces. When they were collected, the geographical distribution and genetic diversity of most crops closely reflected their historical patterns of cultivation established over the preceding millennia. We employed a combination of genomics, computational biology and phenotyping to characterize VIR’s 147 chickpea accessions from Turkey and Ethiopia, representing chickpea’s center of origin and a major location of secondary diversity. Genotyping by sequencing identified 14,059 segregating polymorphisms and genome-wide association studies revealed 28 GWAS hits in potential candidate genes likely to affect traits of agricultural importance. The proportion of polymorphisms shared among accessions is a strong predictor of phenotypic resemblance, and of environmental similarity between historical sampling sites. We found that 20 out of 28 polymorphisms, associated with multiple traits, including days to maturity, plant phenology, and yield-related traits such as pod number, localized to chromosome 4. We hypothesize that selection and introgression via inadvertent hybridization between more and less advanced morphotypes might have resulted in agricultural improvement genes being aggregated to genomic ‘agro islands’, and in genotype-to-phenotype relationships resembling widespread pleiotropy.

Temporal genetic dynamics of reintroduced and translocated populations of the endangered golden lion tamarin (Leontopithecus rosalia)

Reintroductions—captive-born animals introduced into the species’ original distribution area—and translocations—free-living animals transferred to another location within the historical distribution area—are important conservation strategies for endangered species. Genetic analyses of 239 individuals from unmanaged, translocated and reintroduced populations of Leontopithecus rosalia were performed using 14 microsatellites. These samples were collected during two periods: (a) 1996–1997 (historic), when individuals were translocated and reintroduced into forest fragments in the lowland Atlantic Forest, and (b) 2007–09 (recent). We hypothesized that effective population size and genetic diversity would increase over time and that these management strategies would affect the resulting population genetic structure. We found trends indicating that the effective population size at the translocation site increased while that at the reintroduction sites diminished over time. The inbreeding coefficient of the translocated population diminished over time (from 0.38 to 0.03) and was much lower than that of the native (0.29) and reintroduced (0.13) recent populations. We observed a greater genetic admixture among the reintroduced sites on the historic sampling, as well as a strong genetic structure at the translocation site. In the recent sampling, the population structuring became more site-related suggesting low or inconsistent gene flow between sampling sites. This research highlights how conservation management decisions have an important influence on the genetic outcome of translocations and reintroductions. Future conservation planning should consider population genetic monitoring before and after management measures and maintain population connectivity thereafter to avoid the negative effects of a population size reduction.

Tropical fish community does not recover 45years after predator introduction.

Predation is considered to be an important factor structuring natural communities. However, it is often difficult to determine how it may influence long-term, broad-scale, diversity patterns, particularly in diverse tropical systems. Biological introductions can provide powerful insight to test the sustained consequences of predation in natural communities, if pre-introduction data are available. Half a century ago, Zaret and Paine demonstrated strong and immediate community-level effects following the introduction of a novel apex predator (peacock bass, Cichla monoculus) into Lake Gatun, Panama. To test for long-term changes associated with this predator introduction, we followed up on their classic study by replicating historical sampling methods and examining changes in the littoral fish community at two sites in Lake Gatun 45years post-introduction. To broaden our inference, we complemented this temporal comparison with a spatial analysis, wherein we compared the fish communities from two lakes with and one lake without peacock bass. Comparisons with historical data revealed that the peacock bass remains the most abundant predator in Lake Gatun. Furthermore, the collapse of the littoral prey community observed immediately following the invasion has been sustained over the past 45years. The mean abundance of native littoral fish is now 96% lower than it was prior to the introduction. Diversity (rarefied species richness) declined by 64% post-introduction, and some native species appear to have been locally extirpated. We observed a similar pattern across invaded and uninvaded lakes: the mean abundance of native fishes was 5-40 times lower in lakes with (Gatun, Alajuela) relative to the lake without peacock bass (Bayano). In particular, small-bodied native fishes (Characidae, Peociliidae), which are common prey of the peacock bass, were more than two orders of magnitude (307 times) less abundant in Gatun and one order of magnitude (28 times) less abundant in Alajuela than in Bayano. However, total native fish diversity did not differ significantly across lakes, suggesting that while many native species have declined in abundance, few have been completely extirpated. Introduced predators can have strong effects on community structure and functional diversity, even in highly diverse tropical communities, and these effects can persist over multiple decades.

Hedera caerulescens (Alcyonacea : Alcyoniidae), a new genus and species of soft coral from the temperate North Atlantic: invasive in its known range?

We describe a novel alcyoniid species of stoloniferous octocoral found off the coast of North Carolina, USA. Colonies have an encrusting morphology with pale to bright blue monomorphic polyps connected by spongy, sclerite-dense stolons that often form mats. Sclerites are colourless and sparsely tubercled. Sclerites of the stolons are predominantly spindles and rods with rare irregular fused forms, butterflies, and crosses. Polyps have a crown and points formation that consists of rods and spindles that can be curved or irregularly branched. Tentacles contain short flattened rods and rare crosses. Both the mitochondria-encoded COI-5P and mtMutS were sequenced and BLAST searches revealed no close homology with any previously sequenced species. Phylogenetic analyses of the sequence data suggested a closest relationship with species of Alcyonium Linnaeus, 1758 (Alcyoniidae) and Gersemia Marenzeller, 1877 (Nephtheidae) and supported the recognition of a new genus. This species was not previously reported in the Carolinas region despite extensive historical sampling and a recently published key to octocorals of the South Atlantic Bight. Reports and photographs from local divers suggest that this species may have been introduced in North Carolina waters ~2002–04, where it has been found on both shipwrecks and hard bottom ledges, at 13–34m depth.