Upper Mississippi River fish population monitoring and sport fish assessment in west-central Illinois, 2019

This report presents a summary of data collected during segment 06 (2019-2020) of the Upper Mississippi River fish population monitoring and sport fish assessment in west-central Illinois, an annual survey by staff of the Illinois Natural History Survey, with funds administered by the U.S. Fish and Wildlife Service and the Illinois Department of Natural Resources. Sampling for the program was conducted on 6 navigational pools of the Upper Mississippi River. All fishes collected were accurately identified, counted, measured, and weighed. The catch rates of several key species were calculated as the number of individuals collected per hour (CPUE ± standard error). Proportional size distribution (PSD) was also calculated for several key species. Catch rates and species varied among all sampling locations and sampling periods. Emerald Shiner and Gizzard Shad comprised most the individuals caught, and Common Carp and Smallmouth Buffalo accounted for the greatest proportion of the biomass collected. Sportfish Catch rates and sizes of popular sportfish species varied greatly among the navigation pools sampled during 2019. Bluegill and Channel Catfish were the most-abundantly collected sportfish species in nearly all areas along the Upper Mississippi River, although Largemouth Bass and Smallmouth Bass also appear to have robust populations. The slow but steady increase in White Bass CPUE since 2012 may warrant further investigation. Our long-term datasets allow us to observe substantial annual variations in the relative abundance and size distribution of many sportfish species, like Smallmouth Bass and White Bass. These observations could serve as a catalyst for future research investigating the effects environmental changes and management policies on the sustainability of Illinois’ sportfish populations. Invasive Species Although the main focus of the F-193-R project is to conduct monitoring to improve our understanding of population dynamics, life histories, and habitat requirements of sportfishes, the program’s sampling strategies are also useful for documenting trends in the relative abundance of non-native species occupying Illinois’ large river ecosystems. Our surveys suggest Common Carp populations are declining across the region since 2009, which may be the harbinger of good things to come for native fish populations that have been negatively affected by Common Carp. Alternatively, Silver Carp populations (below L&D 19) appear to be increasing since 2012, which may counteract any benefits native fish populations may have gained as a consequence of declining Common Carp populations. We advise that researchers be aware that our sampling protocols (e.g., restriction to main-channel habitats) may limit our probability of encountering the greatest densities of invasive species.Illinois Department of Natural Resources, Division of FIsheriesU.S. Fish and Wildlife Service Project F-193-R Segment 06unpublishednot peer reviewedOpe

Transcriptomic comparison of invasive bigheaded carps (\u3ci\u3eHypophthalmichthys nobilis\u3c/i\u3e and \u3ci\u3eHypophthalmichthys molitrix\u3c/i\u3e) and their hybrids

Bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix), collectively called bigheaded carps, are invasive species in the Mississippi River Basin (MRB). Interspecific hybridization between bigheaded carps has been considered rare within their native rivers in China; however, it is prevalent in the MRB. We conducted de novo transcriptome analysis of pure and hybrid bigheaded carps and obtained 40,759 to 51,706 transcripts for pure, F1 hybrid, and backcross bigheaded carps. The search against protein databases resulted in 20,336–28,133 annotated transcripts (over 50% of the transcriptome) with over 13,000 transcripts mapped to 23 Gene Ontology biological processes and 127 KEGG metabolic pathways. More transcripts were detected in silver carp than in bighead carp; however, comparable numbers of transcripts were annotated. Transcriptomic variation detected between two F1 hybrids may indicate a potential loss of fitness in hybrids. The neighbor-joining distance tree constructed using over 2,500 one-to-one orthologous sequences suggests transcriptomes could be used to infer the history of introgression and hybridization. Moreover, we detected 24,792 candidate SNPs that can be used to identify different species. The transcriptomes, orthologous sequences, and candidate SNPs obtained in this study should provide further knowledge of interspecific hybridization and introgression

Status, trends, and population demographics of selected sportfish species in the La Grange Reach of the Illinois River

Sportfish species, specifically Yellow Bass Morone mississippiensis, White Bass Morone chrysops, Largemouth Bass Micropterus salmoides, Bluegill Lepomis macrochirus, Black Crappie Pomoxis nigromaculatus, and White Crappie P. annularis, often drive economically valuable fisheries in large river systems, including the Upper Mississippi River System (UMRS). Within the Illinois River, part of the UMRS, these species are routinely sampled by an ongoing long-term fisheries monitoring program. Through this program, we investigated long-term trends (1993-2017) in catch rates and relative weights and quantified demographic rates from 2012-2016. We found all six species, with the exception of Yellow Bass, to have declining catch rates with this decline being most stark in larger, older fishes. Population demographics for Yellow Bass, White Bass, Bluegill, and Black Crappie suggest populations are dominated by younger individuals, with only Black Crappie regularly living to age 3 and older, which may be driving population declines. There are many environmental stressors acting on the Illinois River that could be contributing to the lack of older and larger fishes, including, but not limited to, navigation efforts, altered hydrology, pollution, sedimentation, lack of overwintering habitat, and introduction of invasive species. Results of this study demonstrate that additional research to understand mechanisms driving reduced abundance and stunted age structure are needed to identify effective management actions that would benefit populations of recreationally valuable sportfish species.is peer reviewedOpe

Resolving the genetic paradox of invasions: Preadapted genomes and postintroduction hybridization of bigheaded carps in the Mississippi River Basin

The genetic paradox of biological invasions is complex and multifaceted. In particular, the relative role of disparate propagule sources and genetic adaptation through postintroduction hybridization has remained largely unexplored. To add resolution to this paradox, we investigate the genetic architecture responsible for the invasion of two invasive Asian carp species, bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) (bigheaded carps) that experience extensive hybridization in the Mississippi River Basin (MRB). We sequenced the genomes of bighead and silver carps (~1.08G bp and ~1.15G bp, respectively) and their hybrids collected from the MRB. We found moderate‐to‐high heterozygosity in bighead (0.0021) and silver (0.0036) carps, detected significantly higher dN/dS ratios of single‐copy orthologous genes in bigheaded carps versus 10 other species of fish, and identified genes in both species potentially associated with environmental adaptation and other invasion‐related traits. Additionally, we observed a high genomic similarity (96.3% in all syntenic blocks) between bighead and silver carps and over 90% embryonic viability in their experimentally induced hybrids. Our results suggest intrinsic genomic features of bigheaded carps, likely associated with life history traits that presumably evolved within their native ranges, might have facilitated their initial establishment of invasion, whereas ex-situ interspecific hybridization between the carps might have promoted their range expansion. This study reveals an alternative mechanism that could resolve one of the genetic paradoxes in biological invasions and provides invaluable genomic resources for applied research involving bigheaded carps

The XMM Cluster Survey: X-ray analysis methodology

The XMM Cluster Survey (XCS) is a serendipitous search for galaxy clusters using all publicly available data in the XMM-Newton Science Archive. Its main aims are to measure cosmological parameters and trace the evolution of X-ray scaling relations. In this paper we describe the data processing methodology applied to the 5,776 XMM observations used to construct the current XCS source catalogue. A total of 3,675 > 4-sigma cluster candidates with > 50 background-subtracted X-ray counts are extracted from a total non-overlapping area suitable for cluster searching of 410 deg^2. Of these, 993 candidates are detected with > 300 background-subtracted X-ray photon counts, and we demonstrate that robust temperature measurements can be obtained down to this count limit. We describe in detail the automated pipelines used to perform the spectral and surface brightness fitting for these candidates, as well as to estimate redshifts from the X-ray data alone. A total of 587 (122) X-ray temperatures to a typical accuracy of < 40 (< 10) per cent have been measured to date. We also present the methodology adopted for determining the selection function of the survey, and show that the extended source detection algorithm is robust to a range of cluster morphologies by inserting mock clusters derived from hydrodynamical simulations into real XMM images. These tests show that the simple isothermal beta-profiles is sufficient to capture the essential details of the cluster population detected in the archival XMM observations. The redshift follow-up of the XCS cluster sample is presented in a companion paper, together with a first data release of 503 optically-confirmed clusters.Comment: MNRAS accepted, 45 pages, 38 figures. Our companion paper describing our optical analysis methodology and presenting a first set of confirmed clusters has now been submitted to MNRA

Observations on Morgan County wetland restoration, 2005 results

Electronic copy lacks figures 1-6; report not numbered.Prepared for Morgan County Highway Department, Jacksonville, I

Growth Rates of Non-Native Bighead and Silver Carp in the Upper Mississippi River

Fish age and growth analyses can be used to infer spawning success, recruitment, and population age structure. Understanding these dynamics is important when assessing the impacts of invasive species, such as bighead carp, Hypophthalmichthys nobilis, and silver carp, H. molitrix, (bigheaded carp). These species have established throughout much of the Mississippi River Basin; however, Lock and Dam 19 (LD19) has slowed their establishment in the Upper Mississippi River, resulting in low-density populations with limited reproduction upstream. The age and growth of Bigheaded Carp in recently established populations, especially in this region, are poorly characterized. Therefore, we compared the age and growth of bigheaded carp for four low-density navigation pools of the Mississippi River near the invasion front with one long-established high-density population, separated by LD19. To assess growth rates and age at maturity, we estimated consensus age from pectoral spines, postcleithra, and vertebrae from 1229 bigheaded carp, 30 fish per 50 mm size class. Length at age of capture and back-calculated length-at-age were used to create growth curves using VBGC analysis. The analysis indicated higher growth rates of bighead carp and silver carp upstream of Lock and Dam 19 than downstream. Comparison of growth models with a likelihood ratio test indicated differences in length at time zero between the pools for bighead carp but not for silver carp. However, maximum length and growth rates were significantly different for silver carp upstream and downstream of the dam but not for bighead carp. These results will be used to better understand the population dynamics of this emerging population to inform control and containment actions

The Nature Conservancy's Emiquon Preserve Fish and Aquatic Vegetation Monitoring 12-Year (2007-2018) Field Report

Since 2007, The Emiquon Preserve (Emiquon) has been monitored using Key Ecological Attributes (KEA) to determine the success of restoration on the vegetation and fish communities. The indicators outlined in the KEA’s are used to determine if the desired ranges are being met to provide an overall healthy ecosystem. From 2016-2018, Emiquon experienced fluctuating stages of water level management and in 2018, water reduction occurred during most of the sampling season and during the peak of the growing season (July/August). The impacts of the drawdown on flora and fauna are still being evaluated as restoration efforts continue in the future. Emiquon continues to maintain a robust population of fish, maintaining a dominance of primarily native fish over time (98%). Additionally, native submersed aquatic vegetation (SAV) abundance and richness continue to be the dominant macrophyte communities. Submersed aquatic vegetation species diversity has remained stable and native species dominate the community composition. However, the abundance of non-native eurasian watermilfoil (Myriophyllum spicatum) has increased until 2018, when water levels were reduced over the growing period. This drawdown reduced abundance and composition of native SAV present but also reduced the detections of non-native eurasian watermilfoil. The number of fish species found continues to grow and the number and biomass of native species remains above the desired range. Largemouth bass (Micropterus salmoides) abundance threshold greater than 100 fish/hr wasn’t attained in most years; however, Emiquon remains a popular destination for anglers. Although the goal of 100 fish/hr has not been achieved in most years, the random and fixed site design of the U.S. Army Corps of Engineers’ Upper Mississippi River Restoration (UMRR) Program’s Long-Term Resource Monitoring element (LTRM) does not target sites based on habitat that would possibly increase catch rates of largemouth bass, thus preventing this goal from being achieved. The native fish population dominates in both abundance and composition. The success of adult fish and presence of young-of-year (YOY) fish indicate Emiquon is providing abundant spawning, nursery, and over-wintering habitat for fish. Several species (~12 of 32)of stocked fish have not been detected since being introduced by the Illinois Department of Natural Resources. Additionally, a limited connection to the Illinois River in 2013 likely introduced several riverine fish including species initially stocked but not detected until after being inundated. Water clarity decreased over the last 12 years. Secchi disc transparency (Fig 24) has decreased since 2009, dropped substantially in 2012 (drought year) and 2018 (which mimicked a drought year due to drawdown), and conductivity increased (Fig 23). Dissolved oxygen levels throughout the seasons are within their respective ranges (Tables 2, 3, & 4). Anecdotally, in 2016, it was common to find softball size and larger bryozoan communities; however, in 2018 they were largely absent except for small communities observed on vegetation samples. The presence of bryozoans often indicates good water quality.The Nature Conservancyunpublishednot peer reviewedLimitedStandard 2 year embarg

Complex to simple: Fish growth along the Illinois River network

Fish growth in river ecosystems is influenced by a multitude of environmental drivers, including the heterogeneity of these drivers. Globally, river ecosystems are subject to anthropogenic stressors that can simplify riverine landscapes, homogenize riverine communities, and favor nonnative fishes. Yet, how anthropogenically driven simplification of riverine landscapes affects fish life-history traits remains largely unknown. The aim of this study was to examine the character of fish growth along the entire main channel of an Anthropocene River. We collected four species of potamodromous fish from different functional feeding guilds, from each of six functional process zones (FPZs) – unique large-scale hydrogeomorphic patches – along the entire length of the Illinois River (Illinois, USA), and calculated three growth metrics: growth rate (k), maximum size (L∞), and a relative growth index. The majority (7 of 12) of species-growth metric combinations did not differ among FPZs. Of the five species-growth metric combinations that were different, none exhibited more than three distinct groups of values. The limited difference in growth along the main channel of the Illinois River reflects a homogenization of ecosystem function, and is associated with the systemic simplification of physical heterogeneity of the river channel. The fishes studied from the Illinois River also tended to have faster growth rates (k) and smaller maximum sizes (L∞) relative to other North American freshwater ecosystems. Our results reveal spatial constraints to life-history traits and changes to ecosystem interactions, which are evidence of being in a new regime or state. This has implications for the reproductive output and resilience of native fishes in Anthropocene Rivers