Jim Bence and Travis Brenden from the QFC will be teaching an AFS continuing education course at the American Fisheries Society annual meeting on Sunday August 17, 8am-5pm. The early registration deadline is June 20. If you are interested we encourage you to sign up by the deadline to help avoid the chance of the course being cancelled due to low enrollment! The cost of the course is $150 for AFS members, $200 for non-members, $100 for AFS student members and $130 for non-AFS students. In addition the QFC offers a more extensive online R course and will offer discounts to those who take the AFS R course and then sign up for the online course in the next year. For more information on the AFS R course see http://qfc.fw.msu.edu/courses_r_workshop_AFS.asp and for more information on our online R course see http://qfc.fw.msu.edu/online_courses.asp
Also, check out this article summary on work by QFC’s Iyob Tsehaye, Michael L. Jones, Travis O. Brenden, James R. Bence while you are are registering! Boom and Bust in Lake Michigan
On May 1, Lisa Peterson successfully defended her MS thesis, titled Investigating Assumptions Made in the Assessment of Lake Erie Yellow Perch. For the first part of Lisa’s thesis research, she investigated the assumption that there was no movement of yellow perch between the four management units in Lake Erie. She used a statistical catch-at-age model that assumed movement between two of the management units to evaluate the effect this assumption had on the results of the stock assessment (e.g. abundance estimates, catchability). Lisa’s second chapter of her thesis focused on a catch-rate standardization for the Ohio trawl survey data that is used in the stock assessment as an index of yellow perch abundance. She developed a model that took into account different environmental factors to extract a standardized index. These factors included a wind component that incorporated both wind speed and direction, which are not commonly used in catch-rate standardizations. She then compared the standardized index of yellow perch with the non-standardized index to investigate the effect these factors have on catch rates in Lake Erie. Lisa has some edits to make to her thesis before she can submit a final copy to the Michigan State University Graduate School, but these should be completed in early summer. Lisa is continuing on in the Quantitative Fisheries Center as a PhD student and is in the beginning stages of her project. Congratulations Lisa!!!
Read more about her work from the Lake Erie Committee
During the first quarter of 2014 we made two important changes to the QFC computing environment which impacted our computing resource meters. We replaced two older processors running Windows XP with new equipment and Windows 7. Microsoft dropped support of Windows XP in April 2014 leaving users vulnerable to security problems. With the exception of some general use computers, all processors at the QFC are now running fully supported operating systems. In mid-March, we migrated from our hardy but aging server to a new server. The existing QFC web site and FTP hosts were successfully rebuilt on the new server with minimal disruption to online service. The replacement of these three processors by newer equipment increased the total computing resources at the QFC (http://qfc.fw.msu.edu/about.asp). The most significant increase occurred in our hard drive capacity, which increased by 50%, to allow us to keep most of our historical data files online and readily available.
QFC Co-director Mike Jones traveled to Rome, Italy in early March to attend the 2nd International Conference on Fishery Dependent Information. Aside from making the most of his first ever visit to Rome (what an amazing city!), Mike presented on the QFC work with the Lake Erie Percid Management Advisory Group (LEPMAG). One of the primary themes of the conference was developing ways to improve stakeholder involvement in the process of developing fishery harvest policy. There were many other presentations on stakeholder involvement in fishery management – there is a very high level of interest in this in Europe – and Mike came away from the meeting feeling very good about our accomplishments with LEPMAG relative to the global experience in engaged harvest policy analysis. It was really valuable to meet “kindred spirits” from Europe, Australia, and New Zealand, and learn about their experiences with similar challenges. The proceedings of the conference are expected to be published in a special issue of the ICES Journal of Marine Science.
On March 14, Chris Vandergoot successfully defended his PhD dissertation, bringing him one step closer to officially becoming Dr. Vandergoot. The title of his dissertation is Estimation of Regional Mortality Rates for Lake Erie Walleye Sander vitreus Using Spatial Tag-Recovery Modeling. As part of Chris’ dissertation research, he analyzed recoveries from a Lake Erie walleye jaw-tagging study that started in 1990 and ran for nearly 20 years. In total, more than 100 thousand walleyes were tagged during this study. Chris used recoveries from the study to estimate regionally-varying demographic parameters for the Lake Erie walleye population that can be of great use to fishery managers (e.g., movement rates, mortality components). Chris also conducted simulations to explore how features of tagging study designs affect our ability to accurately and precisely predict parameters of interest with an eye towards providing recommendation for future tagging studies that might be conducted on the lake. Chris has some minor edits to make to his dissertation before he can submit a final copy to the Michigan State University Graduate School; Chris is diligently working towards completing those edits. While pursuing his PhD, Chris has also been full-time employee of the Ohio Department of Natural Resources Division of Wildlife at the Sandusky Fisheries Station. Chris was recently promoted to Fisheries Biology Supervisor for the research station, so he is very much relieved to have his studies wrapped up. Congratulations Chris!!!
The QFC will be migrating online services to a new server from March 14-16, 2014. Services that will be impacted during this time include the QFC web site, ftp, and listserv functions. The move to the new server will necessitate physically migrating ftp files. Please plan to complete all ftp transfers before midnight Thursday March 13th. Any ftp transfers occurring after this time and before we complete the migration, may not be copied to the new server. Web site and listserv services should experience only minimal disruption and may be inaccessible for short periods of time during the transition. We expect normal operations to resume on Monday March 17th. If you experience any difficulties after this time, please contact us at 517-355-0126.
For the past few months we’ve been busy doing housecleaning at the QFC. Our computing resources – workstations, printers, fax, and copier – were located in various places around the QFC, including our conference room. An external review of the QFC last summer noted that items for general use should not be in the conference room. We also wanted to logically arrange items, for instance, move all printers to one location. As we reorganized the equipment, we also installed two additional electrical circuits to partition mission critical equipment on separate circuits from general use equipment. We are pleased to show you the results of all our shuffling. Our conference room is more spacious, so meetings don’t feel so cramped and our common use area comfortably supports both the shared computing resources and our lunch area.
As we promised, we’ve updated the meters that track the amount of QFC computing resources we have in our office. Each quarter, we’ll mark the resource level at the beginning (gray arrow) and end of the quarter (red arrow), and provide a brief description of what’s changed in our computing environment.
At the end of 2013, our inventoried computers increased from 23 to 28. We purchased one new computer for a new QFC post-doc and recovered several unused laptops to create a loanable pool of workstations. With no equipment being retired this quarter, our meters show an increase in all computing resources – processing speed, memory, and hard drive space.
2013 proved to be another successful and busy year for the QFC. One major highlight from this year was the completion of an external review of the QFC. As part of this review, three eminent quantitative fisheries scientists (Drs. Richard Methot, Thomas Miller, and Terrance Quinn) came to MSU, reviewed QFC activities and products, met with students, staff, and members of our Board of Advisors, and provided a report describing their recommendations for how the QFC can strategically position itself to have broader (national/international) impacts. We closed out 2013 with 19 staff members, including 4 Post-Doctoral Research Associates/Visiting Scientists, 8 Ph.D. students, and 2 M.S. students. One M.S. student (Yang Li) defended her MS thesis and elected to stay at the QFC to pursue a PhD. In terms of educational opportunities, in 2013 QFC staff taught 2 workshops on the use of R, continued to host two non-credit online courses (Maximum Likelihood Estimation for Natural Resources and Ecology, R Essentials for Natural Resource Professional), and continued work on the development of two online courses and a series of video tutorials on how to use AD Model Builder. QFC staff participated in around 10 consultation/outreach projects for supporting partner agencies and were involved in 16 research projects. QFC staff authored or co-authored 20 manuscripts/completion reports/technical reports that were published or accepted for publication in 2013, including 17 peer-reviewed scientific publications. Finally, QFC staff gave presentations at a variety of professional and technical committee meetings/conferences, including a couple of presentations at the World Conference on Stock Assessment Methods held in Boston. The QFC leadership is very proud of the excellent group of researchers and academic staff assembled at MSU and we thank them for their hard work in 2013.
The QFC would like to welcome Reneé Reilly as our newest Post-Doctoral Research Associate. Reneé has a master’s degree in Ocean, Earth, and Atmospheric Science and a Ph.D. in Oceanography, with a focus in fisheries and quantitative methods from Old Dominion University. Reneé left her position as Supervisor to the Biological Sampling Program at Virginia Marine Resources Commission, and we are lucky to have her.
Reneé’s research has centered around the intersection between population dynamics of various fishes, and otolith chemistry work. She looked at different ways to use the data obtained from otoliths as environmental markers. These investigations also included quite a bit of age and growth analyses of both juvenile and adult fish.
At the QFC, Reneé will be participating in work examining the movement of Chinook salmon between Lake Huron and Lake Michigan, analyzing the data collected through total phosphorus monitoring of Platte Lake in Benzie County, and the ongoing development of models for percid management in Lake Erie.
Ever wonder just how much computing power it takes to support the research done at the QFC? We did. To answer this question, we’ve installed new meters on the About the QFC web page (http://qfc.fw.msu.edu/about.asp) that track our computing resources: memory, processing power, and hard drive space. Each quarter, we’ll update the meters to reflect our current environment and help track our growth over time.
Our computing environment is highly dynamic as our personnel and computing needs grow with the research projects we engage in. Here’s a quick summary of the current computing environment at the QFC:
- 18 people support various research and support tasks at the QFC; 14 of these folks use QFC computing resources.
- Our computing resources include 23 computers in 14 different models from 2 manufacturers
- While some of the older computers are used for workshop and training activities, our research efforts are supported by 18 computers; 67% were purchased after 2011.
- Although we have an emphasis on Windows operating systems, we also have Mac and Unix operating systems in use.
- We currently have 31.55 MHz of processing power with 87.8 Gb of memory and 4.2 terrabytes of hard drive space.
A paper authored by Iyob Tsehaye (QFC), Matt Catalano (formerly QFC, now at Auburn), Greg Sass (WI-DNR), David Glover (OSU) and Brian Roth (FW-MSU) that explored the prospects for the “collapse” of Asian carp through intensive commercial exploitation in the Illinois River has been published in the October issue of Fisheries (http://www.tandfonline.com/doi/full/10.1080/03632415.2013.836501#.Ump8BlPAG2s). This paper, which was based on a meta-analysis of demographic datasets from the Illinois and middle Mississippi rivers, compared the performance of existing and alternative harvest strategies at achieving Asian carp removal targets for the Illinois River, through which these fishes are threatening to enter the Great Lakes. In light of evidences elsewhere of Asian Carp introductions leading to decreased fish diversity and abundances, an Asian Carp invasion of the Great Lakes is feared to adversely affect native populations, with potentially serious consequences for aquatic food webs and a fishing industry valued at $7 billion annually. Alongside efforts to keep Asian carp from entering Great Lakes with electric barriers, the state of Illinois implemented a fishing program aimed at reducing their densities through intensive commercial exploitation on the Illinois River. As part of this program, the state of Illinois signed an agreement in 2010 to export 13.6-22.7 million kg of Asian carp annually to China, where they are considered a delicacy. Based on simulation results, the paper argues that it may be possible to achieve fishing effort targets required to collapse the Asian Carp populations in the Illinois River if efforts to expand commercial fishing are combined with economic incentives to improve size selectivity and species targeting.
Each fall (during October and early November) the Ohio Department of Natural Resources (ODNR), Division of Wildlife, Lake Erie Fisheries Research Stations in Fairport Harbor (east of Cleveland) and Sandusky (west of Cleveland) conduct a gill net survey in Ohio waters of Lake Erie. This year three of our QFC members, Chris V, Matt and Jie, were able to join and assist with the survey. The intent of the survey is to collect biological information pertaining to the ecologically and economically important fish populations that reside in this ecosystem. In addition to determining the status of stocks within Ohio’s portion of Lake Erie, the information is used for managing these populations on a lakewide basis. As a member of the Lake Erie Committee, the ODNR works in conjunction with the Ontario Ministry of Natural Resources, the New York State Department of Environmental Conservation, the Pennsylvania Fish and Boat Commission and the Michigan Department of Natural Resources to assess the status of fish stocks and set sustainable harvest levels. Demographic information such as length, weight and sexual maturity at age and diet information is recorded during these surveys and once synthesized, the information is used in lakewide stock assessment models for yellow perch (Perca flavescens) and walleye (Sander vitreus).
The QFC welcomes Matt to our team as a new PhD student. Matt grew up in Rochester NY and went to Coastal Carolina University in Myrtle Beach South Carolina, where he earned a dual B.S. in Marine Science and Biology and a Minor in Mathematics. He then pursued a M.S. in Fish and Wildlife Conservation at Virginia Tech, where he studied natural mortality estimation within a statistical catch-at-age model. Matt will be studying the impact of movement of fish between management boundaries on the assessment of fished stocks and is excited to learn a lot of new fisheries science techniques and potential develop a few of his own while at MSU. In his spare time, Matt enjoys playing soccer, scuba diving, kayaking, and hunting, all of which he can enjoy while at MSU.
The Lake Michigan Red Flags Analysis (RFA) was developed in the 1990s by the Salmonid Working Group (SWG) under the Lake Michigan Technical Committee (LMTC). Both of these groups are part of the Lake Committee structure of the Great Lakes Fishery Commission (GLFC). The RFA was designed to help monitor the performance of the lake-wide, salmon-trout stocking plan, but it focuses primarily on Chinook salmon because they are the primary consumers of forage fishes in the lake. The RFA was a way to assemble and organize field data collected from creel surveys, weir returns, and other biological studies and to analyze them from a lake-wide perspective. Results helped managers keep track of these fisheries and helped them explain what was happening to interested anglers and the general public. A review of the biological and statistical components of the RFA was conducted in 2011. It concluded that the procedure had a number of analytical and structural problems and recommended specific improvements. Recently, two workshops were held to consider these recommendations and to solicit additional ideas from the participants to improve the analysis. The workshops were led by scientists from the Quantitative Fisheries Center, Michigan State University and were funded by a GLFC Science Transfer Grant. The workshops were attended by SWG members and other experts in Chinook-alewife biology. Some of the experts were biologists with data and knowledge from the Chinook-alewife fishery collapse in Lake Huron, a situation the RFA was designed to help avoid in Lake Michigan. The most significant result of the workshops was a decision to include an estimate of the Chinook-alewife predator-prey ratio as the primary biological indicator in the analysis. In addition, biological data from the collapse of the Lake Huron Chinook-alewife fishery will be used to help managers judge the seriousness of future changes in biological indicators in Lake Michigan. For example, these data include the average condition (weight at a given length) of Chinook salmon in Lake Huron immediately prior to the collapse. As might be expected, these fish were extremely thin and in poor condition due to their overabundance in relation to their food supply (alewives). These data from Lake Huron will help managers identify when the condition of Chinook salmon in Lake Michigan is getting low enough to be a problem. With these improvements, the new RFA should help provide better feedback on the success of the lake-wide stocking plan, including helping to determine when it is advisable to increase or decrease the number of fish stocked. The new procedure will be finalize and tested this fall. Pending formal approval of the Lake Michigan Committee, SWG would begin using the new procedure in 2014.
Dr. Mike Jones and QFC Master’s student Lisa Peterson are co-instructing an introduction to R course at the 2013 American Fisheries Society annual meeting in Little Rock, AR. Continuing the six year tradition, this one day course will teach participants the basics of R, from script writing and importing data to plotting and statistical functions. With R becoming the go-to program for ecological statistics, this course offers professionals and students alike a chance to lay the foundation for understanding and utilizing this free software. It is also a great recruiting tool for the more extensive online R course offered by the QFC, which offers participants a way to continue learning the applications of R from the comfort of their own home. Mike and Lisa are teaching this course Sunday, September 8th from 8 am to 5 pm. To sign up, go to http://afs2013.com/registration/ and fill out the Continuing Education Registration Form.
Jie Xu, an MS graduate research assistant in the College of Marine Science at Shanghai Ocean University (SHOU), is participating in an exchange program between SHOU and Michigan State University and will be visiting the QFC during the fall and spring semester. Jie hails originally from Tongxiang City, Zhejiang Province, China. Jie’s research topic at SHOU concerns assessment and management of the red-flying squid (Ommastrephes bartramii) and other short life-cycle species. She is also interested in the general area of fish population dynamics and modeling and computer simulation to inform fisheries management. While at MSU, Jie plans to enroll in two courses (Advanced Fish Ecology, Fish Population Dynamics), take the Introduction to R and Maximum Likelihood Estimation online courses offered by the QFC, and finish writing her MS thesis. Time permitting, she also hopes to engage in some ongoing QFC research projects. Jie is looking forward to perhaps getting out on the Great Lakes on sampling cruises or to fish and simply experiencing life in the US.
Three undergraduate students (Hongxuan Kang, Lulu Ma, Xiang Li) from Shanghai Ocean University are visiting the QFC this summer. The students are part of a larger contingent of students visiting the Department of Fisheries and Wildlife getting experience in different research laboratories as part of a visitation program between MSU and SHOU. The students arrived in Michigan on July 18 and will be here until August 15. Hongxuan’s interests are in physical oceanography and environmental impacts. Lulu’s interests are in marine resources and biology. Xiang’s interests are in marine management, policy, and assessment. While at the QFC, the students will primarily being learning how to use the R by working on the Introduction to R online course. As part of learning R, the students will be helping to develop graphs and figures in R for summarizing simulation results from Lisa Peterson’s thesis and Chris Vandergoot’s dissertation research.
As you may already be aware, the International Association for Great Lakes Research (IAGLR) will be holding its 56th Annual Conference on Great Lakes Research from June 2 – 6, 2013 in West Lafayette, IN, under the theme, Great Lakes Restoration and Resiliency. As part of this conference, the QFC is organizing a scientific session on Salmonine sustainability in the Great lakes, and we thought that you might be interested in knowing about it. The QFC session, which will be co-chaired by QFC Co-Director Mike Jones and Research Associate Iyob Tsehaye, is scheduled to take place on Thursday, June 6, in the morning. The goal of this session is to highlight contemporary analytical approaches to improving understanding of the dynamics of salmonine communities across the Great Lakes. In view of the substantial changes in the salmonine communities across the Great Lakes over the last half century, with some key fisheries experiencing drastic declines, understanding the dynamics of the salmonine communities is a prerequisite for successful management of these fisheries. Several of the talks during this session will present results from studies employing single and multispecies assessment methods to explore possible mechanisms underlying some of the recent changes in Great Lakes salmonine populations. Some of the presentations will also focus on comparisons of the dynamics of salmonine communities across the lakes, while others will describe state-of-the-art field and laboratory techniques for the estimation of Chinook salmon natural reproduction and migration as well as the study of their feeding habits. For a full list of presentations during this session, please visit the conference website (http://www.iaglr.org/conference/sessions.php).
<FONT SIZE=”3″>Master’s student Lisa Peterson received the Janice Lee Fenske Excellence in Fisheries Management Fellowship for 2012-2013. Jan Fenske was the first female biologist for the Fisheries Division of the Michigan Department of Natural Resources and this fellowship seeks to honor her legacy. This award provides financial assistance and pairs a student with an agency mentor to develop a project for the mentoring agency. Lisa is working with John Dettmers, a Senior Fisheries Biologist of the Great Lakes Fishery Commission, to develop a structured decision making (SDM) framework for riverine barrier decisions. The purpose of this framework is to guide managers through SDM to make decisions about dams in a transparent and organized way. She presented her work to the Council of Lake Committees (CLC) at the beginning of May and received positive feedback. The final product will be distributed to the CLC during the summer, which will also conclude the fellowship.
This fellowship has been a great experience for Lisa. She has been working at the GLFC secretariat office in Ann Arbor throughout her fellowship year, which has allowed her to network and get a glimpse of what it is like to work for an agency such as the GLFC. The fellowship is a great opportunity to form relationships with policy makers and witness how an agency works, which tends to be outside the normal work of a graduate student. Lisa has found all these experiences to be very valuable and knows they will help her in her future endeavors. She looks forward to seeing her finished work and continuing to interact with past (and future!) Fenske Fellows.
For more information on the Fenske Fellowship and to follow the progress of the current Fenske Fellow, see the Fenske Fellows’ Blog
For more information on how to apply, click here
Wildlife-Fisheries connections at the QFC. While the focus of the QFC work is on fisheries and especially applications to the Great Lakes, the QFC has recently been providing valuable support for wildlife applications, and the QFC fishery work is enriched by what we learn from this involvement.
Bryan Stevens is a PhD student working jointly through the QFC and Quantitative Wildlife Laboratory run by Dr. Bill Porter, Boone and Crockett Professor of Wildlife in the MSU Department of Fisheries and Wildlife. His work is focusing on: 1) developing demographic models to evaluate density dependence in wild turkey population dynamics, and 2) using these models to inform harvest policy simulations and evaluate management trade-offs in turkey harvest management. This work will link demographic modeling and harvest simulations using ideas from structured decision making (SDM), specifically management strategy evaluation (MSE) techniques developed for applications in commercial fisheries management. The link to QFC expertise lies in using MSE and SDM techniques commonly used in Great Lakes fisheries management to an application in terrestrial wildlife harvest management. The work is focused on improving understanding of density dependence in turkey population dynamics, and how stochastic density-dependent and density-independent dynamics interact to affect sustainability of turkey harvests. Heather Porter is an MS student also jointly working with the QFC and the Quantitative Wildlife Laboratory. Her research is focused on adaptive management of sharp-tailed grouse in the Upper Peninsula of Michigan. She is creating a linked population and landscape model that will examine how sharp-tailed grouse respond to varying harvest and habitat management scenarios. This relates to fisheries work at the QFC that also involves adaptive management and structured decision making. Sarah Mayhew is a PhD student at the QFC and also a full-time biometrician with the Wildlife Division of the Michigan Department of Natural Resources. Sarah is working on statistical population reconstruction for black bear populations in Michigan. Statistical population reconstruction methods originated in fisheries, re extensively used at the QFC, have emerged as alternative approaches to capture-recapture or other intensive survey techniques for assessing wildlife populations. Sarah is exploring the use of this assessment approach for black bears using age-at-harvest data collected during mandatory registration of harvested bears. The situation with bears differ from most assessed fish populations in that the populations are much smaller and a larger fraction of the harvest is evaluated for sex and age. Nevertheless, the modeling strategies are similar and the experience of the QFC will be a tremendous asset for this project.
In January of this year, Sharon Reasoner began working part time at the QFC as an Administrative Assistant. Sharon is originally from Holt, Michigan but considers Tucson, Arizona her second home as that is where many of her immediate family members live, including her daughter and two granddaughters. Sharon began her employment at Michigan State University in 2000 working in the field of student services. She has worked in Judicial Affairs, The Resources Center for Persons with Disabilities (RCPD), and the Counseling Center. While working with the RCPD, she was involved in arranging the Adaptive Sports Festival, which demonstrated athletic opportunities for all abilities. Sharon considers this to be one of the most rewarding events she has been involved in while at MSU. In 2008, Sharon transferred to the Department of Fisheries and Wildlife, where she currently serves as Administrative Assistant for the Department Chair, Mike Jones. In her spare time, Sharon enjoys golfing, gardening, traveling, and puppeteering for her church’s children’s program. For the QFC, Sharon will be involved primarily in bookkeeping, including balancing project accounts and keeping the QFC leadership appraised of the overall fiscal health of the center.
QFC researchers are in the final stages of developing new stock assessment tools to understand Saginaw Bay walleyes. Since returning to recovery targets, the assessment needs for this stock of walleyes in Lake Huron has been elevated. In the past, the Michigan DNR relied on a tag return Brownie style model to indicate mortality and exploitation metrics. The analysis was largely unchanged in 30 years and concern was expressed that those methods only reflected the recreational fishery and possibly omitted other sources of extraction and mortality. This project has developed a statistical catch at age (SCAA) model to take an entirely new approach to estimating the same metrics. SCAA methods have the advantage of being age specific and more easily account for other fisheries exploiting this same stock from around Lake Huron. Graduate Student Dave Fielder along with QFC faculty Jim Bence are comparing the estimates of the two models and evaluating integrated versions that utilize some of the predictive capacity of the tag returns in with the SCAA model as an integrated version option. Estimates of key metrics resulting from this analysis allow the evaluation of the sustainability of the collective fisheries. Estimates of population size is another resultant that is being used in a bioenergetics model for Lake Huron evaluating the predation consequences of the recovered walleye population on the lake’s prey resources. Still planned is further modeling to apply what is learned to an evaluation of management options and forecasting tools to aid the Michigan DNR in its future management efforts.