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Progress Report for NSF Cypriniformes Tree of Life Grant: Years 1 and 2 Contents A. USA National Science Foundation Funds Cypriniformes Tree of Life
A. USA National Science Foundation Funds Cypriniformes Tree of Life The US NSF program Assembling the Tree of Life, AToL, is a relatively newly developed programmatic area. The three-year-old programmatic research initiative in the Division of Environmental Biology is one of the newest and most innovative programmatic areas developed in the natural sciences at NSF. This program has as one of its major goals and organized efforts unveiling the evolutionary history and biological classification of all species on planet Earth. This program has an upper limit of funding of $3 million per award to a collaborative research proposal, and over 20 such awards have been funded and are well on their way to accomplishing the high goals of the program. August 2004 brought great news to a number of investigators around the world who have focused their research efforts for many years on the world’s most diverse group of freshwater fishes, the Order Cypriniformes. After submitting a Collaborative research grant to the USA NSF program in March 2004 US investigators from many collaborators from world-wide institutions received word from Program Directors at NSF that the grant had been fully funded! US investigators and non-USA collaborators currently involved in the project (identified below) are involved in many individual and collaborative projects, and many of them have a long history of cooperative and collaborative work with Cypriniformes. Most know these fishes as suckers, buffalos, carpsuckers, shiners, chubs, minnows, carps, “sharks”, loaches, and other interesting vernaculars. Regardless, of their varied names, this targeted group of fishes by this research team and others is important to our society for many reasons other than pure science. Researchers note that the knowledge gained from this AToL initiative of the diversity and evolutionary relationships of cypriniform fishes is much larger than can be seen at the “surface.” Being the most diverse group of freshwater fishes and comprising the vast majority of fish species in aquatic ecosystems the results of this study will have a profound impact on our understanding of the history and origins of freshwater ecosystems around the world, will provide independent tests for hypotheses as to the timing and connection of the numerous continental plates via plate tectonics, histories of ancestral river systems, and the longevity and quality of ecosystems. Results of this Tree of Life initiative will also provide critical information on evolutionary relationships of many important model species in the research sciences and education. This will allow researchers to better understand both the developmental and genomic research being generated today but in a comparative and evolutionary vacuum. As these fishes serve as a critically important food source in many cultures and societies, the research from this study will have profound impacts on developing better aquaculture practices. These fishes include the important model fish species “zebrafish” or Zebra Danio that is being examined worldwide in genomic research and extensive developmental biology studies. Cypriniformes also include a number of critically important fishes in aquaculture and comprise the vast majority of the biomass of most freshwater ecosystems around the world. Cypriniform fishes are found in rivers, creeks, streams, swamps, and lakes from all continents except South America, Antarctica, and Australia. These researchers predict that after this 5-year project is completed there will be an estimated 5,000 species known for the order, that several of the Earth’s most poorly explored regions will be better inventoried, and that a phylogenetic framework of over 1,000 ingroup species will be resolved and serve as a critical framework for advancing future work of these economically, scientifically, and agriculturally important fishes. Funding for this project will provide these researchers the opportunity to examine an broad array of morphological characters, sequences for four nuclear and four mitochondrial genes for over 1,000 species, complete mitogenomics for 350 species, and fully developmental series for 25 species to complement similar data for the model organism zebra Danio or zebrafish. B. Investigators and Collaborators
C. Connect with the CToL Initiative – Join the Energy of Resolving Cypriniformes! The CToL project has many long-term goals for better understanding the diversity, phylogeny, genetics, morphology, and development of all Cypriniformes fishes – and – educating the general public (K-gray) about these fishes and the collaborative international efforts at better understanding them. This cannot be accomplished for all of the predicted 5,000 species by only a few researchers currently involved in the initial CToL project – it will necessarily involve an expanding collaborative effort among scientists, laboratories, and countries to make this possible. One of the targeted discussion points at the August 2004 Investigator’s meeting in New Orleans (see below) was how to involve people from the community interested in becoming part of the initiative of the CToL. In the Policies and Procedures document accepted by investigators provides for US investigators to sponsor others interested in being involved in various aspects of CToL initiative. Obviously, the funding of the initial CToL project provided by NSF are limited and have already been committed to US laboratories and collaborators. D. Foreign Collaborative Support: Systematics and Biotic Inventories Thus far, PI Mayden has expended NSF funding for foreign participants to individuals in Brunei (1 researcher), China (3), Etheopia (1), Germany (2), India (3), Indonesia (1), Mexico (2), Pakistan (1), Poland (2), Russia (3), Thailand (1), Turkey (1), Turkmenistan (1), and UK (1) for inventory studies to acquire specimens for investigation and for the generation of data, analyses, and publications. Mayden is also currently hosting Dr. Susana Schonhuth from Madrid, Spain as a post-doctoral researcher investigating molecular systematics of cypriniformes. This post-doc is co-sponsored by the Government of Spain and the NSF AToL (CToL) funding. Post-docs Drs. David A. Neely and Wei-Jen Chen are being co-sponsored by California Academy of Sciences and NSF CToL award to Mayden (see below). Inventory studies have been supported by Mayden for Sudan, Etheopia, South Africa, India, Pakistan, China, Indonesia, Malaysia, Brunei, Turkey, Croatia, Russia, Poland, and Iran. Dr. Ralf Britz of the British Museum of Natural History is collaborating with PI Mayden in a joint funding of one of Mayden’s Ph. D. students (Kevin Conway) for various morphological studies of Cypriniformes, as well as planned inventories of species in Myamar (to be funded by Britz) and samples will be used in CToL morphological and molecular studies. An additional collaboration initiated by PI Mayden is with the California Academy of Sciences and their NSF Biotic Surveys and Inventories study (joint project with Kunming Institute, China) for rivers of Gaoligongshan region, Yunnan, China. This joint effort includes joint funding of Post-doc Dr. David Neely for inventory and taxonomic studies of species in these drainages and Post-doctoral researcher Dr. Wei-Jen Chen to provide sequences of the Cypriniformes and Siluriformes species obtained in these inventories. E. Collaborative Support Within USA Within the USA PI Mayden has provided support to US scientists to assist in the advancement of the CToL initiative. These researchers include Drs. Tom Dowling (Arizona State University), Peter Beremzdem (Central Iowa), Morgan Raley (University of North Carolina), Rex M. Strange (Southern Indiana), and Mollie Cashner (Tulane University). F. Other CToL PIs and Collaborations In addition to Mayden’s contributions to foreign participants, Dr. Phillip Harris (University of Alabama) conducted inventory work in Malasia to obtain samples and also provided support for nationals for additional inventory studies. Dr. Harris also currently hosts a former student of Dr. Abebe Getahun, Addis Ababa University, Etheopia for Ph.D. studies on molecular and morphological studies of Barbus. This student was supported in Etheopian inventory studies. Dr. Andrew Simons (University of Minnesota) provided support for inventory studies in South Africa wherein we have received important samples for CToL. G. Student Support and Education for CToL PIs Mayden and Wood have been very active in the recruitment of K-12 students and undergraduate and graduate students for education in systematics, taxonomy, biodiversity of Cypriniformes. This support has come from three sources: 1) students supported by Saint Louis University Department of Biology, 2) NSF REU, 3) US Army eCybermission program for science and technology education of high-school students, 4) working with elementary, middle and high schools in the St. Louis metropolitan area. Each of these is briefly described below. 1. Saint Louis University Students From the beginning of the CToL project (and even prior to funding) Drs. Mayden, Wood, and Aspinwall at Saint Louis University have been very active participants in the recruitment of undergraduate and graduate students in research related to the above areas in both morphology and molecular techniques. A total of 12 undergraduate students have been involved in this study, some of which are continuing as undergraduates as of July 2006, one of which went on to medical school, one of which received a research position with Monsanto Corp. (St. Louis) based on experiences in our laboratories, and one of which has gone on to graduate school at SLU in systematic biology. These students include: 2. NSF REU on Cypriniformes PIs Mayden, Wood, Harris, and Simons receive one year of a joint REU project to be coordinated between Saint Louis University, University of Alabama, and University of Minnesota. A total of 17 students were involved in this study that involved molecular and morphological training of students for taxonomic and systematic studies of Cypriniformes. Students worked independently and in groups at each institution and between institutions on a common set of taxa for phylogenetic analyses. Other activities associated with this REU project included field studies in June 2005 in Alabama and August in Minnesota to give the students experience in fieldwork, group meetings in Alabama and Minnesota that involved the PIs and students, and a symposium at the University of Minnesota in August 2005 of all studies conducted during the REU project. The details of this REU project are posted on the web, along with presentations, images of students and fieldstudies at the following url: http://wallace.slu.edu/reu/REU_project/students/REU_Symposium_2005.html 3. US Army eCybermission in Science and Technology Seven Saint Louis area high school students had an opportunity to participate in the Cypriniformes Tree of Life (CToL) project during the summer of 2006 as a direct result of the financial support of eCYBERMISSION, a science, math, and technology program administered by the U.S. Army. The eCYBERMISSION program sponsors competitions aimed at solving real-world, community-based problems using science, math, and technology. Successful competitors were then matched with local research institutions, like Saint Louis University, for lab-based research experience. The funding provided by eCYBERMISSION allowed these students to spend a month working in the Biology Department at Saint Louis University, learning the basics of molecular lab techniques and conducting basic scientific research. As part of their training, they developed many skills in molecular techniques (including DNA extraction, PCR, cycle sequencing), data analysis and management (including sequence alignment, data matrix assembly), and phylogenetic methodology/analysis (including computer applications like BioEdit, MacClade, MrBayes, PAUP, Se-Al). Their project focused on the relationships of the North American shiner genus, Luxilus, which currently has nine recognized species. The students collected sequence data from a mitochondrial locus (COI) and a nuclear locus (IRBP) for 16 representative individuals of the genus. Their research was summarized in a poster titled: “The Study of Evolutionary Relationships of Minnows in the Genus Luxilus.” The students included Carolyn Beatty, Christine Brethorst, Bretton DeLaria, Daniel Everding, Jennifer Hannon, Kyle Mayden, Kaitlin O’Brien, all of whom were either Sophomores or Juniors (as of fall 2006) in high school. 4. St. Louis Metro K-12 Education Initiated in the summer 2004, PI Mayden has worked with the Parkway West School District (Public) and the John F. Kennedy Catholic High School (private) on one main project that is educational for the students and beneficial for the developmental biology components of the CToL project. In elementary, middle and high schools Mayden has purchased aquaria and obtain specific species for the students to maintain in the classroom and to raise them to breeding condition (males and females in separate aquaria). Once the species are in breeding condition the sexes are combined in a tank with spawning materials and containers to catch fertilized eggs and protect them from predation by adults. Once the species have spawned over a 2-3 day period the adults are separated and the fertilized eggs are removed from the containers and reared separately. During the development of the fertilized eggs (up to a 90-day period) the students are mentored weekly or biweekly by Mayden and/or Biology teachers at the schools as to the developmental process and are allowed to remove subsamples of the developing eggs or larvae for observations under a dissection microscope to see the various stages of organ, skeletal, and behavioral development up to several weeks of free-swimming larvae. Following observations and discussions among the students, some of subsample of specimens is frozen and placed in formalin. The frozen materials will be used later by other laboratories associated with ZFIN to examine gene expression that accompanies the developmental process that is examined for the same hatch via the formalin preserved materials. While the CToL initiative maintains its own private and protected portal for researchers to work and share information, we have developed and maintained a collaboratory on the DeepFin website for sharing information with participants, organizing papers and projects, and recruiting collaborators from around the world. DeepFin is an initiative originally developed by PI Mayden and DeepFin PI Guillermo Orti at the Unviersity of Nebraska. It was funded by NSF as an RCN (Research Coordination Network), of which PI Mayden is one of the Steering Committee members. 1. First PI Meeting, New Orleans, Louisiana (1) general overview of project From this meeting the PIs generated a 12 page document outlining the initial understanding of the CToL project, incorporation of collaborators in the project, timing of future meetings and workshops, methods to be used in morphological and molecular studies, sharing specimens and data, authorship and publication development, portal development to accommodate the various types of information and data, and many other basic policies for the future years of the project. In addition to this document the PIs met with educational and development officers of the Aquarium of the Americas to discuss the development of outreach and other educational efforts for K-Gray on both the importance of Cypriniformes diversity and developing a tree of life. 2. CToL has its initial kickoff in European Congress Meeting and Special Symposium Following the announcement of receipt of funding from USA NSF, many of the CToL group members and other colleagues from around the world met in Tallinn, Estonia in September 2004 for the European Congress of Ichthyology. At this meeting the group of researchers held a symposium on Cypriniformes systematics and biodiversity where 27 papers were presented. During the ECI meeting, which is only held every three years, CToL researchers also met in formal and informal environments to discuss the plans of this newly funded initiative. A listing of the papers presented at the meetings is presented below. Presentations (presenting author indicated by *) 1. Arratia G. Ontogeny and phylogeny of teleosts with special reference to cypriniforms. 2. Mayden R. L. Systematics of Cypriniformes (Actinoptery GII, Ostariophysi)—an international National Science Foundation Tree of Life initiative. 3. Chang M. M. Fossil Cyprinoformes from China and its adjacent areas and their paleobiogeographical implications. 4. Arratia G.*, Mayden R. L. Implications for the phylogenetic reconstruction of relationships of cypriniformes using combined fossil and recent evidence. 5. Mayden R. L.The evolution of the Retractor Pharyngeus muscle system in cypriniformes. 6. Mabee P. M. Development and evolution of skeletal development in Zebrafish. 7. Miya M. *, Nishida M. Limits, inter- and intrarelationships of the otocephala (Clupeomorpha + Ostariophysi): a mitogenomic perspective. 8. Saitoh K. *, Miya M., Hanzawa N., Nakamura K., Nishida M. Mitogenomic exploration of familial or or subfamilial phylogenetic interrelationships among cypriniform fishes. 9. Clements M. D., Bart H. L. *, Doosey M. H., Hurley D. L. Utility of the growth hormone gene for estimating phylogenetic relationships among cypriniform fishes. 10. Liu H. Major groups of cypriniforms in East Asia and their relationships revealed by molecular data. (not able to attend) 11. Bogutskaya N. G. *, Naseka A. M.Vertebral structure in cyprinidae with special reference to leuciscinae: phylogenetic trends and ecological adaptations. 12. Coburn M. M. The Weberian Apparatus, a source of phylogenetic characters for the cypriniformes Tree of Life project. (presentation read by Paula Mabee*) 13. Mayden R. L., Harris P. M., Kuhajda B. R., Simons A. M., Wood R. M. * Phylogenetic relationships of the Shiner Clade: a species rich clade in the North American Phoxinin fauna. 14. Harris P. M. *, Mayden R. L. Interspecific phylogenetic and evolutionary relationships of the catostomidae, with comments on the sister group relationships of the family. 15. Fang F. *, Norén M., Kallersjo M. Kullander S. Phylogenetic relationship of the Danionin species (Cyprinidae: Rasborinae) inferred by morphological and molecular characters. 16. Bart H. L. *, Clements M. D., Blanton R. E., Doosey M. H., Piller K. R., Hurley D. L. Patterns of variation and relationships of living ictiobines (Cyrpiniformes: Catostomidae) based on mitochondrial and nuclear genes. 17. Neely D. A. *, Blum M. J., Harris P. M., Mayden R. L. Phylogeography and molecular systematics of the cyprinid genus Campostoma. 18. Rabova M., Ráb P. *, Kotlik P., Bogutskya N.G. Cytotaxonomy of European cyprinid fish Pelecus Cultratus, with comments to concept of Howes’ subfamily Alburninae. 19. Golubtsov A. S. *, Skelton P. H., Shidlovsky K. M., Swartz E. R., Krysanov E. Yu. The discovery of a Pseudobarbus-like barb in the Bale Mountain Region, Ethiopia: an ancient trace of endemic South-African Cyprinids in the horn of Africa? 20. Getahun A. *, Stiassny M. L. J. Diversity and distribution of the African species of Garra (Pisces: Cyprinidae) and the monophyly of the genus. 21. Szlachciak J. *, Boron A. Comparative morphological characteristics of the species from the genus Leuciscus distributed in Poland. 22. Zardoya R., Doadrio I. Testing freshwater Lago Mare Dispersal Theory using cypriniform molecular phylogenies. (not able to attend) 23. Kottelat M. Brief overview of Cobitoid diversity. 24. Bohlen J. *, Perdices A., Doadrio I., Economidis P.S. Vicariance in Asia Minor and the Balkans as revealed by the phylogenetic history of spined loaches (Osteichthyes; Cobitidae). 25. Slechtova V. *, Bohlen J. Freyhof J. Extracting clades from the “Loach Bush”: Botiidae (Teleostei: Cobitoidea). 26. Vasil’ev V. P., Vasil’eva E. D. * Distribution patterns of diploid spined loach species (Cobitis, Cobitidae, Cypriniformes) and polyploid forms in FSU countries: the latest data. 27. Mayden, R.L. Cypriniformes Tree of Life – where do we go from here? 3. DNA Barcoding of Fishes, Conference in Guelph, Ontario, June 2005 In June, 2005 PI Mayden was invited (and given support) to the initial three-day meeting of the DNA Barcoding of Life meeting for fishes held in Guelph, Ontario. At this conference PI Mayden provided an oral and digital presentation on the CToL project, status of molecular work, and diversity being covered in the project. At this meeting PI Mayden was elected to be the coordinator of North American freshwater fishes barcoding initiative and Drs. Shunping He (CToL collaborator in China) and Masaki Miya (CToL collaborator in Japan) were elected to be the coordinators for freshwater fishes in southeast Asia. 4. Third CToL PI Meeting and American Society of Ichthyologists and Herpetologists Meeting 2005 During the 2005 ASIH meetings held in Tampa, Florida various PIs and collaborators within and outside of the US met together for a two-day workshop on CToL progress, coordination, collaboration, data standards, specimen acquisition, and future of the project. During this meeting all PIs, collaborators, and students provided oral presentations of their progress on CToL to date and exchanged specimens, data, and ideas. Following this workshop PIs Mayden and Mabee (Univ. South Dakota) provided oral and digital presentations at the ATOL workshop organized for all fish and herp projects funded by NSF ATOL as to different aspects of the CToL initiative and current progress. This workshop was entitled Workshop/forum: Assembling the Tree of Life (AToL) and was organized by James Hanken, Paula M. Mabee, and Maureen Kearney During the normal meetings members of CToL also provided meeting contributions in both oral and poster format. Contributions from PI Mayden and Wood labs are listed below. List of presentations for ASIH 2005 (high school or college students indicated with *)
5. Fourth CToL PI Meeting and American Society of Ichthyologists and Herpetologists Meeting 2006 During the 2006 ASIH meetings held in New Orleans, Lousiana various PIs and collaborators within and outside of the US met together for a three-day workshop on CToL progress, coordination, collaboration, data standards, specimen acquisition, and future of the project. During this meeting all PIs, collaborators, and students provided oral presentations or posters of their progress on CToL to date and exchanged specimens, data, and ideas. During the normal meetings members of CToL also provided meeting contributions in both oral and poster format. Contributions from PI Mayden and Wood labs are listed below. List of presentations (high school or college students indicated with *) 1. Reconstruction of phylogenetic relationships of the Cypriniformes (Actinopterygii: Teleostei) using the nuclear rhodopsin gene. 2006. Mary Agnew*. ASIH Poster. 2. Molecular phylogenetics of the minnow genus Pteronotropis (Teleostei: Cyprinidae). 2006. Jason Allen*. ASIH Talk. 3. Utility of GIS information and GARP modeling in detecting and predicting critical habitat: Examples from the diverse ichthyofauna of Alabama. 2006. Karl Anderson*. ASIH Poster. 4. Osteology of the genus Paedocypris comprising some of the smallest vertebrates (Cyprinidae, Teleostei). 2006. Ralf Britz, Kevin Conway*, Maurice Kottelat, and Heok Hui Tan. ASIH Talk. 5. The Cypriniformes Tree of Life (CToL) Initiative: A progress report on the phylogeny of the order Cypriniformes. 2006. Sarah Chamberlain*, Leah Schneider*, Mitchell Sudkamp*, Kevin L. Tang, Robert M. Wood, and Richard L. Mayden. ASIH Poster. 6. A phylogenomic perspective on the new era of ichthyology. 2006. Wei-Jen Chen, Robert Wood, and Richard Mayden. ASIH Poster. 7. The systematic position of Psilorhynchus (Ostariophysi: Cyprinidae): Evidence from gill-arch characters. 2006. Kevin Conway*. ASIH Talk. 8. A wee croaker: Sexual dimorphism in the weberian apparatus of Sundadanio axelrodi (Ostariophysi: Cyprinidae). 2006. Kevin Conway*, Ralf Britz, and Richard Mayden. ASIH Poster. 9. The utility of cytochrome c oxidase subunit I (COI) for species identification and phylogeny reconstruction within Cypriniformes (Actinopterygii; Teleostei). 2006. Miranda Haskins*. ASIH Talk. 10. Phylogenetic inference of relationships of Cypriniformes (Actinopterygii; Teleostei) diversity using cytochrome b sequences: Evaluating standard methods versus insight from substitution stationarity. 2006. Richard Mayden, Casey Dillman*, Kyle Mayden* and Theresa Clouse*. ASIH Poster. 11. Phylogenetic relationships of Danio within the order Cypriniformes: A framework for comparative and evolutionary studies of a model species. 2006. Richard L. Mayden, Kevin L. Tang, Robert M. Wood, Masaki Miya, Kevin Conway*, Sarah J. Chamberlain*, Miranda Haskins*, Leah Schneider* and Mitchell Sudkamp*. ASIH Talk. 12. Molecular systematics and phylogeography of the Mexican stoneroller, Campostoma ornatum. 2006. David Neely, Michael Blum, Francisco Garcia de Leon, Hector Espinosa-Perez, Alejandro Varela Romero*, and Richard Mayden. ASIH Talk. 13. Ichthyofauna of the Gaoligongshan region, Yunnan, China. 2006. David Neely, David Catania, Xiao-Yong Chen. ASIH Poster. 14. Comparison of evolutionary rates in the mitochondrial DNA cytochrome b gene and control region and their implications for phylogeny of the Cobitoidea (Teleostei: Cypriniformes). 2006. Qiongying Tang*, Huanzhang Liu, Richard Mayden, and Bangxi Xiong*. ASIH Talk. 15. Speciation in the North American genus Dionda (Actinopterygii, Cyprinidae) (II). 2006. Susana Schönhuth, Ignacio Doadrio, and Richard Mayden. ASIH Poster. 16. The Cypriniformes Tree of Life (CToL) Initiative: A progress report on the phylogeny of the order Cypriniformes. 2006. Sarah Chamberlain*, Leah Schneider*, Mitchell Sudkamp*, Kevin L. Tang, Robert M. Wood, and Richard L. Mayden. ASIH Poster. 6. CToL and Evolutionary Synthesis Center: Duke University Working Group on Towards an integrated database for fish evolution. Dr. Paula Mabee, CToL PI at University of South Dakota, proposed and was awarded three workshops through the NSF NESCent to bring together a group of scientists studying morphology and working with CToL, AllCatfish (NSF PBI), or ZFIN (Zebrafish Information Network) to investigate the development and deployment of ontologies for morphologies of Ostariophysian fishes, specifically the Order Cypriniformes. 2005. Participant in “Towards an integrated database for fish evolution”. First working group meeting at the National Evolutionary Synthesis Center (NESCent) in Durham, NC, November 4-7, 2005. 2006. Participant in “Towards an integrated database for fish evolution”. Second working group meeting at the National Evolutionary Synthesis Center (NESCent) in Durham, NC, April 8-11, 2006. The result of two of the three working groups included the following manuscript submitted for publication. Mabee, P. M., G. Arratia, M. Coburn, M. Haendel, E. J. Hilton, J. G. Lundburg, R. L. Mayden, N. Rios, and M. Westerfield. In press. Connecting evolutionary morphology to genomics using ontologies: A case study from Cypriniformes including zebrafish. J. Exp. Zool. Part B: Molecular and Developmental Evolution. The following poster was presented by PI Mabee at the First International Biocurator’s meeting (Asilomar, CA, Dec. 8-11, 2005). 2005. Mabee P., M. Westerfield, M. Haendel, G. Arratia, M. Coburn, E. Hilton, J. Lundberg, C. Lushbough, R. Mayden, N. Rios. Relating evolutionary and model organism phenotypes using ontologies. 7. Special Symposium at Society of Integrative and Comparative Biology, Tampa, Florida. January 4-8, 2006. Zebrafish in a Comparative Context Dr. Jacqueline F. Webb, Department of Biology, University of Rhode Island, in collaboration with CToL, organized a special symposium held at the 2006 SICB meetings entitled "Zebrafish in Comparative Context". This symposium was being sponsored in collaboration with the NSF CToL initiative and is aimed at providing a better comparative framework for researchers working across many disciplinary boundaries but employing Danio rerio as the model organism. Dr. Webb is a CToL collaborator, specializing in morphology and development of the lateralis system, and did an excellent and expedient job in organizing this symposium and is very supportive of the mission of the CToL initiative. The 2006 meeting of the Society for Integrative and Comparative Biology (SICB) took take place January 4-8, 2006 in Orlando, Florida. The symposium extended for two days plus contributed sessions which extend the event for a third day. This symposium was highly successful in bringing these two communities together for discussions and future collaborative studies. Drs. Mabee, Mayden, and Webb also contributed significantly to the open discussions of on the various topics for discussion. Our works, as presented in these talks, were discussed in Science by Pennisi (2006). More detailed information about the symposium can be found at www.sicb.org. Publications from conference: (students indicated by *) PI Mayden presented the following talk at the conference. 2006. Mayden, R. L., K. W. Conway*, K. Tang, J. Freyhof, S. Chamberlain*, M. Haskins*, L. Schneider*, M. Sudkamp*, R. M. Wood, M. Agnew*, A. Bufalino*, Z. Sulaiman, M. Miya, K. Saitoh, S. He. Phylogenetic Relationships of Danio within the Order Cypriniformes: A Framework for Comparative and Evolutionary Studies of a Model Species. Journal of Experimental Zoology, Part B - Molecular Development and Evolution. PI Mabee presented the following talk at the conference. 2006. Mabee P., M. Westerfield, M. Haendel, G. Arratia, M. Coburn, E. Hilton, J. Lundberg, C. Lushbough, R. Mayden, N. Rios “Integrating CToL-related studies with available phenotype & genomics databases for the zebrafish”. Invited talk in Zebrafish Symposium. Society of Integrative and Comparative Biology meeting. Pennisi E. 2006. Fishing for common ground. Science 311: 766-767. 8. 2006 AAAS Symposium on Assembling the Tree of Life, St. Louis, MO Symposium Description. The 2006 AAAS meetings were held in St. Louis, MO. This provided a great opportunity for PI Mayden (also in St. Louis) to organize a symposium on the ATOL program and bring specialists together to explain the aims of the ATOL program at NSF. Mayden was the convener of the symposium that included the following presentations by the following individuals.
9. 3rd International Conference Loaches of the genus Cobitis and Related Genera: Biology, Systematics, Genetics, Distribution, Ecology, and Conservation - Sibnick, Croatia. September 2006 This conference is being held for presentations, discussions, and actions on the Biology, Systematics, Genetics, Distribution, Ecology, and Conservation of loaches worldwide. At this conference PI Mayden will provide an overall presentation of the status and goals of CToL, discuss collaborations with experts in other countries, and will present a research paper on the evolutionary rates of gene evolution and classification in loaches of the Cobitoidea. 10. Special Symposium on Biology of Cypriniformes, 12-15 September 2006, Wuhan, China. PI Mayden and Chinese collaborator Dr. Shunping He (Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan) have organized an international symposium to be held at the Institute of Hydrobiology. The symposium is expected to have excellent attendance based on feedback that Mayden has received from the webpages developed for the symposium (http://bio.slu.edu/mayden/conferences/CToLSyposium/). This conference will also include workshops and special topics for contributions that include the following areas: Oral and Poster Presentation Contribution Topics
Workshop topics include:
11. European Ichthyological Congress, Croatia The 2007 European Ichthyological Congress will be held in Croatia. PI Mayden has arranged for and agreed to convene the second Symposium on the Systematics, Taxonomy, Ecology, and Biology of Cypriniformes at this congress meeting. Colleagues from around the world will be in attendance at this congress and participate in the symposium. The previous symposium held in Tallinn, Estonia, in 2004 was extremely successful for CToL through the incorporation of ideas and collaborators from around the globe. 12. 2008 Japanese Ichthyological Society Meeting. In collaboration with Drs. Kenji Saitoh and Masaki Miya, PI Mayden is assisting in the organization of a symposium on Cypriniformes fishes at the 2008 Japanese Ichthyological Society meetings. 1. Official Website for Cyriniformes Tree of Life Initiative Following the initial notification of award for this international collaboration focusing on the phylogenetics, biodiversity and biogeography of cypriniform fishes an official url was purchased by PI Mayden— www.cypriniformes.org. 2. Logo for Cypriniformes Tree of Life Initiative Following the initial notification of award for this international collaboration a generalized logo and a letterhead were developed for use for official correspondence, presentations, and other materials associated with this NSF project. These images are presented below and are available at www.cypriniformes.org. 1. CToL Initiative Introduced at International Zoological Congress, Beijing In August 2004 PI Mayden presented “Systematics of Cypriniformes (Actinopterygii, Ostariophysi) – An International National Science Foundation Tree of Life Initiative” at the International Zoological Congress held in Beijing, China. The presentation provided a general overview of the objectives of this international study, the participants of the project, the framework of how the collaborative effort will be achieved, the possibilities of involving additional collaborators, and the importance of cypriniform fishes worldwide. The presentation was warmly received and generated considerable discussion and attention from a broad audience. From this introduction to the CToL project additional discussion at the meetings followed that involved the establishment of collaborative efforts and a possible internationally funded ATOL initiative via separate countries and their equivalent agencies for research funding. CToL Collaborators from China (Shunping He) and Japan (Masaki Miya) both submitted proposals to their funding agencies and obtain funding to support collaborative and complimentary studies. Additional researchers interested in joining the project at some level included two researchers from India, three researchers from China, one from Germany, and one from Borneo. 2. Mayden visits China with CToL Tour While attending the International Zoological Congress in Beijing in August 2004, PI Mayden traveled also traveled Wuhan, China, to visit the Institute of Hydrobiology to present seminars and work with CToL collaborators Shunping He and Huanzhang Lui, as well as other experts with Cypriniformes systematics. While in Wuhan, Mayden presented three semiars to an audience of students and Professors at the Institute of Hydrobiology. Drs. Shunping He, Huanzhang Liu, and their students and postdocs are all located at the Institute of Hydrobiology, a part of the Chinese Academy of Sciences, in Wuhan, and are specialists in Cypriniformes systematics using both molecular and morphological characters. Currently, Drs. He and Lui are collaborators with the CToL project focusing their efforts on molecular sequencing of both nuclear and mitochondrial genes. 3. CToL Establishes Critical Working Groups to Achieve Goals During the first CToL workshop held at the European Congress of Ichthyology collaborators discussed many pertinent issues regarding the launching of this Tree of Life project. One of the critical agenda items was the determination of appropriate working groups to advance critical activities that will help to ensure the success of this project. In the initial pass, it was decided that at least nine different areas were in need of active working groups for programmatic coordination. Additional groups may eventually need to be formulated in future months. These are identified below along with the proposed charge of each group and members (listed alphabetically). Each group was immediately charged with identifying a working group leader or chair to facilitate coordination among members of the group and with other working group leaders. a. Databasing/Database Development This working group is charged with researcher, developing, and maintaining a functional system for the CToL initiative that will host all of the perceived needs of the project for collaborators around the world, including hosting varied forms of data necessary to complete outlined objects (images, DNA sequence files, tree files, Nexus files, citations, etc.). Members: Hank Bart, Paula Mabee, Rick Mayden, and Nelson Rios. b. Specimens and Inventory This working group is charged with maintaining the current taxonomy of Cypriniformes, maintaining the target list of species to be examined in the Tree of Life project, keeping project members appraised of critical species and necessary areas for inventory work, and the proper curation of museum specimens, tissues, and DNA used in this project. Members: Nina Bogutskaya, Hank Bart, Phil Harris, Alexander Naseka, Richard Mayden, Nelson Rios. c. Phylogenetic Analysis This working group is charged with researching and providing advise to the CToL community as to issues associated with development of efficient and effective databases for phylogenetic analysis and best methods for the analysis of data files that are both very large and diverse in character types. Members: Wei-Jen Chen, Phil Harris, Paula Mabee, Richard Mayden, Misaki Miya, Andrew Simons, Kevin Tang, Rob Wood d. Development A major component of the CToL initiative includes the study of the developmental biology of 30 different species of Cypriniformes as comparative studies with the zebrafish (Danio rerio), a model organism species. The examination of these species requires detailed studies of spawning, rearing of young, preservation of critical comparative stages, examination of specimens for osteological features, and placement of the comparative osteologies on the CToL portal for public use. Another critical stage of this component of CToL is the linkage of the developmental stages of these species with the comparable stages of Danio rerio with ZFIN. The synchronization of this information, in conjunction with the phylogenetic relationships of D. rerio relative to other Cypriniformes will provide a world-wide audience with a comparative perspective to the development of this model species. In order for this synchronization to occur an anatomical ontology is required and is being developed by the working group with the NESCent working group Towards an integrated database for fish evolution (see above). PIs Mayden and Mabee have spearheaded major publications from the SICB symposium entitled Zebrafish in a Comparative Context (see above) that provides the fundamental components, developed out of the NESCent working group for this synchronization to occur. Members: Gloria Arratia, Nevin Aspinwall, Nina Bogutskaya, Miles Coburn, Paula Mabee, Richard Mayden e. Paleontology: The Cypriniformes contains many different fossil taxa that are critical to understanding the evolutionary relationships of these fishes, dating the molecular evolution of the speciation events in the group, and understanding some aspects of homology. Members: Gloria Arratia, Hank Bart, Meemann Chang, Miles Coburn, Richard Mayden f. Molecular: Members: Hank Bart, Wei-Jen Chen, Phil Harris, Richard Mayden, Misaki Miya, Kenji Saitoh, Andrew Simons, Kevin Tang, Rob Wood g. Morphology One of two major components to resolving the phylogenetic relationships of Cypriniformes is the use of morphological characters. The members of this working group are working in collaboration to evaluate morphological character complexes useful in generating characters for the Cypriniformes. Members of this group and the development group are also working in collaboration with Paula Mabee’s working group at NESCent group focusing on integrating morphology and genomics with an anatomical ontology. Members: Gloria Arratia, Nina Bogutskaya, Miles Coburn, Kevin Conway, Paula Mabee, Rick Mayden, and Alexander Naseka. h. Bulletin This group is responsible for producing biannual issues of The Cypriniformes Tree of Life Bulletin. This newsletter is one of the official publications produced by the group to not only keep members of the initiative informed of activities associated with the project but also serves to inform the general public (science and non-science) as to the numerous activities of the CToL project. Members: Hank Bart, Miles Coburn, and Rick Mayden i. Outreach/Education This group is charged with developing outreach information on a variety of subjects that will help to educate the public as to systematics, evolution, and Cypriniformes fishes. These include web interfaces, publications, podcasts, and movies. Members: Hank Bart, Rick Mayden, Nelson Rios, and Andrew Simons. 4. CToL Bulletin, Instructions to Contributors The Cypriniformes Tree of Life Bulletin is a quarterly journal produced by the CToL group for communication purposes. It is an open access publication that is available electronically from www.cypriniformes.org free of charge. The Bulletin offers a venue for publication of short contributions, news items, planned activities, methods, and any other activities related to furthering the Assembling the Tree of Life initiative. Contributions should be submitted directly to the Mayden at cypriniformes@gmail.com. 5. CToL Joins with California Academy of Sciences and Kunming Institute of Zoology to Advance Biodiversity and Systematics of Cypriniformes. In Summer 2005 CToL researchers from Saint Louis University joined an ongoing USA NSF-BSI-Funded project with researchers at The California Academy of Sciences and The Kunming Institute of Zoology to collaborate on A Survey of the Biological Diversity of the Gaoligongshan of Western Yunnan, China. The Gaoligongshan (Gaoligong Mountains, hereafter GLGS) is a long and narrow mountain range which stretches some 600 km from near the border with Xizang Autonomous Region (Tibet) south to where the Nujiang (Salween) River makes an abrupt bend westward toward Myanmar. Its ridgeline forms the border between Myanmar and China for several hundred kilometers. The GLGS is the southernmost extension of the Hengduan Mountains (literally, "transverse mountains"), a range that is drained by most of the great rivers of Asia, including the Irrawaddy, the Nujiang, and Lancanjiang (Mekong). Together, these rivers traverse the region from north to south through spectacularly narrow parallel gorges. All three rivers head in glacial snowfields on the Himalayan Plateau, and the combination of glacial melt and summer monsoons result in extreme seasonal fluctuations in flow and a generally high sediment load. The GLGS fauna is characterized by striking biodiversity and endemism. Because of both the high level of diversity and a high level of threats, the overall region has been ranked as a global conservation priority by multiple conservation groups. The area is remote, relatively undeveloped, and supports a generally low human density, factors which have contributed to its intact forests. These same factors, together with political sensitivities that resulted in the GLGS being closed to foreigners from 1937-1996, have also resulted in a poor knowledge of the diversity of the region. Despite sporadic investigations by the Kunming Institute of Botany (KIB) and Kunming Institute of Zoology (KIZ) of the Chinese Academy of Sciences, few biological specimens from the region were available to non-Chinese scientists. Only in the past decade have we begun to scratch the surface of biological diversity in the region, a process that was enabled by support (to the California Academy of Sciences) from NSF and the MacArthur Foundation. The construction of new roads in the region and a new openness to foreigners have together allowed scientific survey to progress at an unprecedented pace. Dr. David Neely joined this project in a joint Post-Doctoral appointment in 2005, and is participating in ongoing studies on the ichthyofauna of the GLGS. Our principal goals for this project are to identify what fishes occur in the Gaoligongshan region, how they are distributed across the landscape, and what factors are responsible for the observed patterns. Preliminary data suggest that the fishes of the Gaoligongshan are represented by roughly 60 native species, predominantly from three families; the Cyprinidae (~22 spp), Sisoridae (~16 spp) and Balitoridae (~9spp). Cypriniform tissues from this project are being used in molecular analyses at both SLU (CToL) and CAS. 6. Publications with the CToL 2004-present (high school or college students = *) 1. Blum, M. J., D. A. Neely, P. M. Harris, and R. L. Mayden. In press. Molecular systematics of the cyprinid genus Campostoma (Actinopterygii: Cypriniformes). Molecular Phylogenetics and Evolution. 2. Bohlen, J. Freyhof, and C. Wolter. 2005. First records of Cobitis elongatoides and Sabanejewia baltica (Cobitidae) for Germany. Cybium 29(1): 103-104. 3. Conway, K. *, and R. L. Mayden. In press. The Phylogenetic Significance of the Gill Arches of Fishes of the Order Cypriniformes (Actinopterygii: Ostariophysi). Copeia. 4. Freyhof, J. & A. M. Naseka, 2005. Gobio delyamurei, a new gudgeon from Crimean Peninsular (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters 16, 331-338. 5. Freyhof, J. and E. Korte, 2005. The first record of Misgurnus anguillicaudatus in Germany. Journal of Fish Biology 66 (2): 568-571. 6. Freyhof, J., D. Lieckfeldt, C. Pitra, & A. Ludwig. 2005. Molecules and morphology: evidence for introgression of mitochondrial DNA in Dalmatian cyprinids. Molecular Phylogenetics and Evolution 37: 347-354. 7. George, A. L. *, and R. L. Mayden. 2005. Species Concepts and the Endangered Species Act: How a Valid Biological Definition of Species Enhances the Legal Protection of Biodiversity. Natural Resources Law Journal 45:367-407. (under Legislation section) 8. He, S. R. L. Mayden, X. Wang, W. Wang, and Y. Chen. In preparation. Molecular Phylogenetics of the Family Cyprinidae (Actinopterygii: Cypriniformes) as Evidenced by S7 Ribosomal Gene Sequences: The First Nuclear Gene Evidence for the Evolution and Classification of This Diverse Family of Fishes. 9. Mabee, P. M., G. Arratia, M. Coburn, M. Haendel, E. J. Hilton, J. G. Lundburg, R. L. Mayden, N. Rios, and M. Westerfield. In press. Connecting evolutionary morphology to genomics using ontologies: A case study from Cypriniformes including zebrafish. J. Exp. Zool. Part B: Molecular and Developmental Evolution. 10. Mayden, R. L., A. M. Simons, R. M. Wood, P. M. Harris, and B. R. Kuhajda. 2006. Molecular Systematics and classification of North American Notropin shiners and minnows (Cypriniformes: Cyprinidae), p. 000-000. In: Ma. De Lourdes Lozano-Vilano and Armando J. Contreras-Balderas (Eds.). Studies of North American Desert Fishes in Honor of E. P. (Phil) Pister, Conservationist. Universidad Autonoma de Nuevo Leon, Mexico. 11. Mayden, R. L., K. W. Conway*, K. Tang, J. Freyhof, S. Chamberlain*, M. Haskins*, L. Schneider*, M. Sudkamp*, R. M. Wood, M. Agnew*, A. Bufalino*, Z. Sulaiman, M. Miya, K. Saitoh, S. He. In press. Phylogenetic Relationships of Danio within the Order Cypriniformes: A Framework for Comparative and Evolutionary Studies of a Model Species. Journal of Experimental Zoology, Part B - Molecular Development and Evolution. 12. Miya, M., K. Saitoh, R. Wood, M. Nishida & R. L. Mayden. 2006. New primers for amplifying and sequencing the mitochondrial ND4/ND5 gene region of the Cypriniformes (Actinopterygii: Ostariophysi). Ichthyological Research. 13. Saitoh, K., T. Sado, R. L. Mayden, N. Hanzawa, K. Nakamura, M. Nishida & M. Miya. 2007. Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): The first evidence towards resolution of higher-level relationships of the World’s largest freshwater-fish clade based on 59 whole mitogenome sequences. Molecular Phylogenetics and Evolution. 14. Schönhuth, S., I. Doadrio, and R. L. Mayden. 2006. A biogeographic perspective on the phylogeny of Mexican cyprinids (Actinopterygii, Cyprinidae), p. 000-000. In: Ma. De Lourdes Lozano-Vilano and Armando J. Contreras-Balderas (Eds.). Studies of North American Desert Fishes in Honor of E. P. (Phil) Pister, Conservationist. Universidad Autonoma de Nuevo Leon, Mexico. 15. Tang, Q. *, H. Liu, R. L. Mayden, and B. Xiong*. 2006. Comparison of evolutionary rates in the mitochondrial DNA cytochrome b gene and control region and their implications for phylogeny of the Cobitoidea (Teleostei: Cypriniformes). Mol. Phy. Evol. 39 (2006):347-357. 16. X. Gu, R. L. Mayden, and Y. Chen. In preparation. Mitochondrial Genome Phylogeny joins Psilorhynchidae with Cyprinidae：Relationship and divergence time estimation within Order Cypriniformes. 7. Expeditions for Cypriniformes Biodiversity Expeditions were conducted to obtain materials for CToL to the following Countries or river basins since funding of the project. Expeditions were either by PI and associates, by collaborators in different countries, or by ALLCatfish project. China (collaborators and CAS), Congo Basin, Africa (collaborators), Croatia (CToL and collaborators), Estonia (collaborators), Etheopia: (collaborator), Japan: (collaborator), Malaysia: (CToL and AllCatfish), Mexico: (CToL), Mongolia: (CToL and AllCatfish), Nepal: (collaborator), Pakistan (collaborator), Poland (collaborators), Russia (collaborators), Slovenia (collaborator), South Africa (collaborator), Sudan (collaborator), Sulawasia (ALLCatfish), Taiwan (CToL and collaborators), Thailand (collaborators), Turkey (collaborators), and Ukraine (collaborators) 8. Planned Expeditions for sampling in the next three years India, North Vietman, Tanzania, Thailand, Borneo, Laos, Mayamar. Since the beginning of this project the CToL team has amassed materials for over 2,100 specimens representing 685 species fixed in EtOH for DNA analysis and over 4000 specimens fixed in formalin for clearing and staining for osteological studies. To date the morphological comparisons have included multiple labs working in concert with pharyngeal arches, caudal skeleton, and the hyomandibular region. These data are uploaded with images and character codes to the Cypriniformes portal where all parties can view characters hypothesized and coded into a character matrix. To date the molecular portion of the project is sequencing whole mitogenomes (122 species), mitochondrial genes cyt b, CO1, ND4, ND5, tRNA-His, tRNA-Leu, and tRNA-Ser for those taxa not being sequenced for whole mitogenomes, and the nuclear genes Rag-1, Rag-2, S7, Rhodopsin, GH, EGR2B, and IRBP. The laboratories for PIs Mayden and Wood have been examined amplified, and sequenced over 350 taxa (over 1/3 of total taxa to be examined in 5-year project). |
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