Deep Fin will Advance The Phylogeny of Fishes -- A
Research Coordination Network
Participants:
Steering Committee: Guillermo ORTI (University
of Nebraska), Richard MAYDEN (Saint Louis University), William BEMIS
(University of Massachusetts), Paula MABEE (University of South Dakota),
Terry GRANDE (Loyola University Chicago), Guoqing LU (University of
Nebraska), John LUNDBERG (Academy of Natural Sciences, Philadelphia),
Gavin NAYLOR (Florida State University), Kevin TANG (American Museum
of Natural History), Peter UNMACK (Arizona State University), Ed WILEY
(University of Kansas).
Participants: Ralf BRITZ (The Natural History
Museum, London), Richard BROUGHTON (University of Oklahoma), Bruce COLLETTE
(National Marine Fisheries Service), Agnes DETTAÏ (Museum National
d’Histoire Naturelle, Paris ), Tom DOWLING (Arizona State University),
Izeni FARIAS (Universidade Federal do Amazonas), Phillip HARRIS (University
of Alabama), Shunping HE (Chinese Academy of Sciences), Tomas HRBEK
(Washington University in St Louis), Dave JOHNSON (NMNH, Smithsonian
Institution), Guillaume LECOINTRE (Museum National d’Histoire
Naturelle, Paris), Masaki MIYA (Natural History Museum & Institute,
Chiba, Japan), Randall MOOI (Milwaukee Public Museum), Mutsmi NISHIDA
(University of Tokyo, Japan), Thomas ORRELL (NMNH, Smithsonian Institution),
Lynne PARENTI (NMNH, Smithsonian Institution), Ted PIETSCH (University
of Washington), Michael SANDERSON (University of California, Davis),
Andrew SIMONS (University of Minnesota), John SPARKS (American Museum
of Natural History), Carol STEPIEN (University of Taledo), Melanie
STIASSNY (American Museum of Natural History), John SULLIVAN (Cornell
University), Richard VARI (NMNH, Smithsonian Institution), Mark WESTNEAT
(Field Museum of Natural History), Rafael ZARDOYA (Museo Nacional de
Ciencias Naturales. Madrid).
PI: Guillermo Ortí - Associate Professor
School of Biological Sciences, University of Nebraska, Lincoln.
Description of Relationship to Proposed Project and Current
Research:
In my research I use molecular genetic markers to investigate the evolutionary
history of organisms, populations and higher taxa.. Currently, one of
the main projects in the lab is to study high-level phylogenetic relationships
among major lineages of ray-finned fishes. Large-scale phylogenetic
analyses using mitochondrial and nuclear DNA sequences presently involve
hundreds of taxa representing a significant cross-section of the diversity
of living fishes. Given the ambitious scope of this research program,
extensive collaborations with other labs were initiated by this project.
The need to coordinate research teams with common interests led to the
development of the current RCN proposal.
Relevant publications
Chen, W.-J., G. Ortí, A. Meyer. 2004. Novel evolutionary relationship
among four fish model systems. Trends in Genetics 20(9):424-431.
López, A. W.-J. Chen, G. Ortí. 2004. Esociform phylogeny.
Copeia 2004:449-464.
Sivasundar, A., E. Bermingham, and G. Ortí. 2001. Population
structure and biogeography of migratory freshwater fishes (Prochilodus:
Characiformes) in major South American rivers. Molecular Ecology 10(2):
407-418.
Farias, I.P., G. Ortí, and A. Meyer. 2000. Total evidence: molecules,
morphology and the phylogenetics of cichlid fishes. J. Exp. Zool. (Mol.
Dev. Evol.) 288(1): 76-92.
Ortí, G. and A. Meyer. 1997. The radiation of characiform fishes
and the limits of resolution of mitochondrial ribosomal DNA sequences.
Systematic Biology 46:75-100.
Ortí, G. and A. Meyer. 1996. Molecular evolution of ependymin
and the phylogenetic resolution of early divergences among teleost fishes.
Molecular Biology and Evolution 13 (4): 556-573.
Ortí, G., P. Petry, J. A. Porto, M. Jegú, and A. Meyer.
1996. Patterns of nucleotide change in mitochondrial ribosomal RNA genes
and the phylogeny of piranhas. J. Mol. Evol. 42: 169-182.
Alves-Gomes, J.A., G. Ortí, et al. 1995. Phylogenetic analysis
of the South American electric fishes (order Gymnotiformes) and the
evolution of their electrogenic system: A synthesis based on morphology,
electrophysiology, and mtDNA sequence data. Mol Biol Evol 12 (2): 298-318.
William E. Bemis - Professor of Biology
University of Massachusetts, Amherst, MA 01003-0027
Description of Relationship to Proposed Project and Current
Research:
Since 1979, I have investigated phylogenetic relationships of fossil
and living fishes, especially the two extant sarcopterygians groups
(lungfishes and coelacanths) and non-teleostean actinopterygians (e.g.,
paddlefishes, sturgeons, bowfins and gars). In the last five years,
my students and I have begun to work on fossil and living lower teleosts
(e.g., osteogolossomorphs) and certain percomorphs (e.g., tetraodontiforms
and pleuronectiforms). A major research interest is the origin of teleosts,
a phrase I use to describe integrated study of actinopterygian groups
near this singularly important node in vertebrate history. Because I
include fossil taxa in my data matrices, I tend to emphasize skeletal
characters. However, I also use a variety of techniques to study neural,
developmental and other anatomical characters, and I am currently developing
large data matrices of soft-tissue characters for actinopterygians.
I also am actively collecting and studying DNA sequence data for a variety
of actinopterygian taxa, most notably non-teleostean actinopterygians.
Participation in DeepFin will help me to coordinate my group’s
research activities with those of other researchers and to identify
and tackle new opportunities for collaborative phylogenetic research
on fishes.
Relevant Publications:
Bemis, W. E. & L. Grande. 2003. Phylogenetic relationships among
the living species of gars (Acinopterygii: Lepisosteidae) inferred from
mitochondrial DNA sequences. Abstract for the annual meeting of the
Am Soc Ich Herp; Manaus, Brazil, June 2003.
Grande, L. & W. E. Bemis. 1998. A Comprehensive Phylogenetic Study
of Amiid Fishes (Amiidae) Based on Comparative Skeletal Anatomy. An
Empirical Search for Interconnected Patterns of Natural History. Soc.
Vert. Paleo, Memoir 4. Suppl, J. Vert. Paleo. 18: i-x, 1–690.
Grande, L. & W. E. Bemis. 1996. Interrelationships of Acipenseriformes,
with comments on “Chondrostei,” pp 85–115. In: Interrelationships
of Fishes. M. L. J. Stiassny, L. R. Parenti & G. D. Johnson, eds.
Academic Press, San Diego.
Grande, L. & W. E. Bemis. 1991. Osteology and phylogenetic relationships
of fossil and Recent paddlefishes (Polyodontidae) with comments on the
interrelationships of Acipenseriformes. Society of Vertebrate Paleontology,
Memoir 1, Suppl, J. Vert. Paleo. 11: i–viii, 1–121.
Liem, K. F., W. E. Bemis, W. F. Walker, Jr. & L. Grande. 2001. Functional
Anatomy of the Vertebrates. 3rd Edition. Harcourt Publishers, Philadelphia.
Ralf Britz, The Natural History Museum, London.
Description of Relationship to Proposed Project and Current
Research:
My research focuses on comparative anatomy and systematics of actinopterygian
fishes, ranging from higher level relationships and general questions
of evolutionary biology and homology to basal problems in taxonomy and
systematics of various fish groups. To date these include the most basal
actinopterygians Cladistia (bichirs and reedfish), the basal teleosts
Osteoglossomorpha and Ostariophysi, and numerous taxa from the largest
and most diverse teleost group, yAcanthomorpha, like Gasterosteiformes,
Synbranchiformes, Tetraodontiformes, and Anabantoidei, Channoidei, and
Percoidei among the Percomorpha. My approach to the study of fish phylogeny
is explicitly ontogenetic, i.e. wherever feasible I utilize characters
from the complete ontogenetic cycle, including egg and larval characters,
and developmental osteology. Looking at ontogeny in this way greatly
extends the character sources for reconstructing phylogenetic relationships.
In addition, ontogeny is also a powerful and often decisive tool to
resolve long-standing homology problems, a prerequisite for correct
character coding.
Relevant Publications:
Britz, R. & Bartsch, P. (2003). The myth of dorsal ribs in gnathostome
vertebrates. Proc. Roy. Soc. London, Biology Letters. online 30 Mai
2003 (http://www.pubs.royalsoc.ac.uk/).
Britz, R. & Johnson, G.D. (in press). On the homology of the posteriormost
gill arch in polypterids (Cladistia, Actinopterygii). Zool. J. Linn.
Soc., 9 pp.
Britz, R., Favorito-Amorim, S. & Johnson, G. D. (in press). The
hyopalatine arch of a 25 mm larva of Synbranchus and homology of the
pterygoid bone in the Synbranchidae (Teleostei: Synbranchiformes). Proc.
Biol. Soc. Wash., 4 pp.
Britz, R. (2001). The genus Betta - monophyly and intrarelationships,
with remarks on the subfamilies Macropodinae and Luciocephalinae. Ichthyol.
Explor. Freshwaters, 12: 305-318.
Britz, R. & Johnson, G. D. (2002). "Paradox Lost": Skeletal
ontogeny of Indostomus paradoxus and its significance for the phylogenetic
relationships of Indostomidae (Teleostei, Gasterosteiformes). American
Museum Novitates, 3383: 1-43.
Kullander, S. O. & Britz, R. (2002). Revision of the family Badidae
(Teleostei: Perciformes), with description of a new genus and ten new
species. Ichthyol. Explor. Freshwaters, 13: 295-372.
Britz, R. (1994). Ontogenetic features of Luciocephalus (Perciformes,
Anabantoidei), with a revised hypothesis of anabantoid intrarelationships.
Zool. J. Linn. Soc. 112: 491-508.
Britz, R. (1996). Ontogeny of the ethmoidal region and hyopalatine arch
in Macrognathus pancalus (Teleostei, Mastacembeloidei), with critical
remarks on mastacembeloid inter- and intrarelationships. Amer. Mus.
Novitates, 3181: 1-18.
Richard E. Broughton - Assistant Professor
Department of Zoology and Oklahoma Biological Survey, University of
Oklahoma
Description of Relationship to Proposed Project and Current
Research:
I am actively involved in several projects related to molecular phylogenetics
of fishes. One project involves sequencing complete mitochondrial genomes
for use in investigating the phylogeny of major groups of actinopterygian
(ray-finned) fishes. Another objective of this project is to use the
large genomic data set to examine nucleotide sampling properties and
relative information content of DNA sequences from various genes and
nucleotide sites. I am also conducting several other projects that involve
investigating relationships among genera, species, or populations of
cyprinid and poeciliid fishes. Goals of these projects include phylogeny,
biogeography, processes of speciation and population divergence, and
conservation. Nearly all of these activities involve phylogenetic analysis
and so relate directly to the proposed RCN. Such a network will fill
a vital role in the systematic community for such issues as standardizing
genes, morphological characters, and taxa. It will increase collaboration,
reduce redundant effort, ultimately, increase the efficiency by which
our understanding of fish (and basal vertebrate) evolution grows. I
anticipate contributing to and greatly benefitting from such a network.
Relevant Publications:
Broughton, R.E., L.B. Stewart and J.R. Gold. 2002. Microsatellite loci
reveal substantial gene flow among Gulf of Mexico and Atlantic Ocean
populations of king mackerel (Scomberomorus cavalla). Fisheries Research,
54: 305-316.
Broughton, R.E., J.E. Milam, and B.A. Roe. 2001. The complete sequence
of the zebrafish (Danio rerio) mitochondrial genome and evolutionary
patterns in vertebrate mitochondrial DNA. Genome Research 11: 1958-1967.
Broughton, R.E., S.E. Stanley, and R.T. Durrett. 2000. Quantification
of homoplasy for nucleotide transitions and transversions and a re-examination
of assumptions in weighted phylogenetic analysis. Systematic Biology
49:617-627.
Broughton, R.E., and J.R. Gold. 2000. Phylogenetic relationships in
the North American cyprinid genus Cyprinella (Actinopterygii: Cyprinidae)
based on mitochondrial ND2 and ND4L gene sequences. Copeia 2000: 1-10.
Broughton, R.E., G.J.P. Naylor and T.E. Dowling. 1998. Conflicting phylogenetic
patterns caused by molecular mechanisms in mitochondrial DNA sequences.
Systematic Biology 47: 696-701.
Bruce Collette - Senior Systematic Zoologist,
Systematics Laboratory, National Marine Fisheries Service (NMFS)
Division of Fishes, National Museum of Natural History, Smithsonian
Institution
Description of Relationship to Proposed Project and Current Research:
In my more than 40 years of research based at the National Museum for
what is now NOAA Fisheries, I have concentrated on the anatomy, systematics,
andzoogeography of three families of fishes: needlefishes (Belonidae),
halfbeaks (Hemiramphidae), and tunas and their allies (Scombridae andScombroidei).
Recently I have added molecular data to these studies by collaborating
with three recent Ph.D. students - Heidi Banford, Nathan Lovejoy, and
Tom Orrell. I have drafted accounts for the three families for the series
of checklists being edited by Bill Eschmeyer at the California Academy
of Sciences as an outgrowth of his Catalog.
Relevant Publications:
Collette, B.B., C. Reeb, and B.A. Block. 2001. Systematics of the tunas
and mackerels (Scombridae). In: Tuna: Physiology, ecology, and evolution,
B.A. Block and E.D. Stevens, eds. Academic Press, San Diego, pp. 1-33.
Lovejoy, N.R., and B.B. Collette. 2001. Phylogenetic relationships of
New World needlefishes (Teleostei: Belonidae) and the biogeography of
transitions between marine and freshwater habitats. Copeia 2001:324-338.
Meisner, A. Downing, and B.B. Collette. 1999. Generic relationships
of the internally-fertilized southeast Asian halfbeaks (Hemiramphidae:
Zenarchopterinae). Proc. 5th Indo-Pacific Fish. Conf., Nouméa,
1997, Soc. Fr. Ichtyol.:69-76.
Banford, H.M., E. Bermingham, B.B. Collette, and S.S. McCafferty. 1999.
Phylogenetic systematics of the Scomberomorus regalis (Teleostei: Scombridae)
species group: molecules, morphology and biogeography of Spanish mackerels.
Copeia 1999:596-613.
Collette, B.B. 1999. Mackerels, molecules, and morphology. Proc. 5th
Indo-Pacific Fish. Conf., Nouméa, 1997, Soc. Fr. Ichtyol.:149-164.
Carpenter, K.E., B.B. Collette, and J.L. Russo. 1995. Unstable and stable
classifications of scombroid fishes. Bull. Mar. Sci. 56(2):379-405.
Boughton, D.A., B.B. Collette, and A.R. McCune. 1991. Heterochrony in
jaw morphology of needlefishes (Teleostei: Belonidae). Syst. Zool. 40(3):
329-354.
Collette, B.B. and J.L. Russo. 1985. Morphology, systematics, and biology
of the Spanish mackerels (Scomberomorus, Scombridae). Fish. Bull., U.S.
82(4): 545-692.
Collette, B.B., G.E. McGowen, N.V. Parin, and S. Mito. 1984. Beloniformes:
Development and relationships. In: Ontogeny and systematics of fishes,
Amer. Soc. Ich. Herp. Spec. Publ. No. 1:335-354.
Dettaï, Agnès, PhD
Muséum National d’Histoire Naturelle, département
de Systématique. Paris, France.
Description of Relationship to proposed project and current research
I have worked with molecular sequences on the phylogenetic relationships
within the wide clade of acanthomorph teleosts. For this, I have not
only completed sequences in already existing datasets, but also developed
three molecular markers new to the group (partial MLL, IRBP and C-MOS).
Due to the particular problems for the reconstruction of relationships
within this group, we have worked on the notion of reliability of the
tree reconstructions through taxonomic congruence. With such an approach,
the more datasets available the better, and an international collaboration
for data acquisition and treatment seems the best way to achieve good
results.
I have also planned and started to build a database for a better storage
and manipulation of morphological data in the group Acanthomorpha. The
group is so wide and diverse, and there are so many data sets about
it that it cannot be dealt with by a single mind, and a searchable database
that accomodates all the specificities of morphological data, is needed.
Such a database can only be completed and used on a freely available,
cooperative basis, so it is absolutely necessary to integrate it to
a network such as the one proposed in the DeepFin project.
Relevant publications
DETTAI, A. and LECOINTRE, G. Taxonomic congruence in acanthomorph relationships
inference with a new molecular marker, IRBP. in preparation.
DETTAI, A. and LECOINTRE, G. MetAcanthomorpha, essay on a phylogeny-oriented
database for morpho-anatomical data: the acanthomorph example. Accepted
in Systematic Biology.
DETTAI, A. and LANCELOT, G. Ce que les phylogénies moléculaires
et les bases de données peuvent apporter à la relance
de l’anatomie comparée : l’exemple des téléostéens.
Accepted in the Journal de la Société Française
de Biologie (non peer-reviewed scientific journal)
DETTAI, A. and LECOINTRE, G. (2004): In search of the Notothenioid relatives.
Antarctic Science. 16(1), 71-85.
DEROME, N., CHEN, W.J., DETTAI, A., BONILLO, C., and LECOINTRE, G. (2002):
Phylogeny of antarctic dragon fishes (Bathydraconidae, Notothenioidei,
Teleostei) and related families based on their anatomy and two mitochondrial
genes. Molecular Phylogenetics and Evolution 24(1), 139-152.
Tom Dowling - Associate Professor
Arizona State University
Description of Relationship to Proposed Project and Current Research:
My research program is focused on understanding the patterns of evolution
and the forces responsible for production and maintenance of biodiversity.
This requires knowledge of how evolutionary processes (e.g., drift,
selection) promote change at the population level, the role these changes
play in the origin and maintenance of species, and the persistence of
such changes over time. To address these issues, I have used morphological
and molecular methods to closely examine population genetic processes,
phylogenetic patterns, and the evolution of reproductive discontinuity
in cyprinid and catostomid fishes (minnows and suckers, respectively),
two of the most diverse freshwater groups in North America. Consideration
of phylogenetic patterns and evolutionary processes along with the evolution
of factors responsible for reproductive isolation provides the foundation
necessary for understanding the process of speciation and historical
patterns of diversity.
Relevant Publications:
Cunha, C., N. Mesquita, T. E. Dowling, A. Gilles, and M. M. Coelho.
2002. Phylogenetic relationships of Eurasian and American cyprinids
using cytochrome b sequences J. Fish Biol. 61:929-944.
Dowling, T. E., D. P. Martasian, and W. R. Jeffery. 2002. Evidence for
multiple genetic forms with similar eyeless phenotypes in the blind
cavefish, Astyanax mexicanus. Mol. Biol. Evol. 19:446-455.
Dowling, T. E., C. A. Tibbets, W. L. Minckley, and G. R. Smith. 2002.
Evolutionary
Gerber, A. S., C. A. Tibbets, and T. E. Dowling. 2001. The role of introgressive
hybridization in the evolution of the Gila robusta complex (Teleostei:
Cyprinidae). Evolution 55:2028-39.
Weibel, A. C., T. E. Dowling, and B. J. Turner. 1999. The evolution
of sexual reproduction in an hermaphroditic fish (Rivulus marmoratus):
A phylogenetic and biogeographic study. Evolution 53:1217-1225.
Broughton, R. E., G. J. P. Naylor, and T. E. Dowling. 1998. Conflicting
phylogenetic patterns caused by molecular mechanisms in mitochondrial
DNA sequences. Systematic Biology 47:696-701.
Dowling, T. E., R. E. Broughton, and B. D. DeMarais. 1997. Significant
role for historical effects in the evolution of reproductive isolation:
evidence from patterns of introgression between the cyprinid fishes,
Luxilus cornutus and Luxilus chrysocephalus. Evolution 51:1574-1583.
Dowling, T. E., and G. J. P. Naylor. 1997. Evolutionary relationships
of minnows in the genus Luxilus (Teleostei: Cyprinidae) as determined
from cytochrome b sequences. Copeia 1997:758-765.
Izeni P. Farias - Assistant Professor
Universidade Federal do Amazonas, Brasil
Description of Relationship to Proposed Project and Current
Research:
A great part of my research has concentrated on phylogenetic studies
of Neotropical fishes. My main contribution has been on molecular systematics
of the major lineages of Neotropical cichlid fishes using mitochondrial
and nuclear gene sequences. I am also interested in population-level
studies of Amazonian fishes, related to management and conservation.
Relevant Publications:
Hrbek T., Farias, I. P., Crossa, M., Sampaio,I., Porto, J.I.R., Meyer
A. 2003. Population genetics of Arapaima gigas, one of the biggest freshwater
fishes the Amazon basin: implications for its conservation. Conservation
Genetics. In press
Farias, I. P., Hrbek T., Brinkmann H., Sampaio I., Meyer A. 2003 Characterization
and isolation of DNA microsatellite primers for Arapaima gigas, an economically
important but severely over-exploited fish species of the Amazon basin.
Molecular Ecology Notes 3: 128-130.
Farias, I. P., Ortí, G., Sampaio, I., Schneider, H., Meyer, A.
2001 The cytochrome b as a phylogenetic marker: the limits of resolution
for analyzing relationships among cichlid fishes. Journal of Molecular
Evolution, v.53, p.89 - 103.
Farias I.P., A. Meyer & G. Ortí. 2000 Total evidence: molecules,
morphology, and the phylogenetics of cichlids fishes. J. Exp. Zool.
(Mol. Dev. Evol.) 288: 76-92
Farias I.P., G.Ortí, I. Sampaio, H. Schneider & A. Meyer.
1999 Mitochondrial DNA Phylogeny of the Family Cichlidae: Monophyly
and Fast Molecular Evolution of the Neotropical assemblage. J. Mol.
Evol. 48: 703-711.
Farias I.P., H. Schneider & I. Sampaio. 1998 Molecular Phylogeny
of Neotropical Cichlids: The Relationships of Cichlasomines and Heroines.
In Phylogeny and Classification of Neotropical Fishes, (eds. L. Malabarba
; R. Reis; R. P. Vari; Z. M. S. Lucena and C. A. S. Lucena) Edipucrs,
Porto Alegre, Brasil pp. 499-508.
Terry Grande - Department of Biology Loyola University, Chicago, and
Field Museum of Natural History.
Description of Relationship to Proposed Project and Current
Research:
The focus of my research is to better understand the comparative morphology,
evolutionary relationships and historical biogeography of of teleost
fishes, specifically, ostariophysan fishes, their presumed relatives
(e.g. clupeomorphs, esociformes), and the evolutionary relationships
among the Clupeocephala. An understanding of this group is central to
an understanding of fish evolution in general. My research is multifacited
in that it integrates developmental morphology, paleontology, and molecular
biology.
I currently serve as the Graduate Program Director for the Department
of Biology, Advisor for the Biological Honors Society and Director of
Loyola’s undergraduate internship program with the Field Museum
of Natural History. I also have been involved in undergraduate and graduate
training in ichthyology and systematics through individual NSF research
grants and through Loyola’s programs such as W.I.S.E.R. that targets
women in science. Loyola’s internship program with Field Museum
has trained undergraduates in ichthyology and paleoichthyology. Ninety
five percent of these undergraduates have gone on to graduate school
in fish biology.
Relevant Publications:
Grande, L. and T. Grande. 1999. A new species of †Notogoneus (Teleostei:
Gonorynchidae) from the Upper Cretaceous Two Medicine Formation of Montana,
with a discussion of the Cretaceous record of freshwater fishes of North
America.. J Vert Paleont. 19(4): 612 – 622.
Grande, T. and J. Shardo. 2002. Morphology and development of the postcranial
skeleton in the
channel catfish Ictalurus punctatus (Ostariophysi: Siluriformes). Fieldiana.
1518(99): 1-30.
De Pinna, M. and T. Grande. 2003. Ontogeny of the accessory neural arch
in Pristigasteroid clupeomorphs and its bearing on the homology of the
otophysan claustrum (Teleostei). Copeia. 2003: 838-845.
Grande, T. and B. Young. 2004. The ontogeny and homology of the Weberian
apparatus in the zebrafish Danio rerio (Ostariophysi: Cypriniformes).
Zool Journal of the Linnean Society.
Grande, T. and De Pinna, M. 2004. The evolution of the Weberian apparatus:
a phylogenetic perspective. In: Arratia, G. and H.- P. Schultze (eds.).
Mesozoic Fishes: Systematics and Biodiversity. in press.
Phillip M. Harris - Assistant Professor and Curator
The University of Alabama
Description of Relationship to Proposed Project and Current
Research:
My research focuses on the phylogenetic relationships, biogeography
and conservation genetics of freshwater fishes. I'm currently focusing
on relationships among cypriniform fishes, with emphasis on species-level
relationships among catostomids and basal-lineage relationships among
cyprinids. Other projects include phylogenetic relationships of the
Centrarchidae (in collaboration with Dr. Richard Mayden) and atherinopsid
silversides (in collaboration with Dr. Barry Chernoff). The broad geographic
distributions of many of these taxa (e.g., Cyprinidae is distributed
throughout the northern hemisphere, southeast Asia and Africa) necessitate
finding collaborators in the global-ichthyological community. For example,
as part of my work on cypriniform relationships, I needed representatives
of several subfamilies of minnows found in India. I literally spent
close to 30 hours over several weeks searching the web and contacting
potential collaborators in India before finding a willing contact. The
coordination of research efforts provided by Deepfin to reduce project
overlap, and the ability to form collaborative working groups among
its participants, would have greatly simplified my search had the resources
of Deepfin been available at that time.
Relevant Publications:
Harris, P.M., K.J. Roe and R.L. Mayden. Submitted. Phylogenetic Relationships
of the Sunfish Genus Lepomis (Actinopterygii; Centrarchidae): Alternative
Hypotheses Derived from Complete Mitochondrial Cytochrome b Gene Sequences.
Copeia.
Harris, P.M. and D.F. Markle. In revision. Molecular Phylogenetic Relationships
of the genus Siphateles (Ostariophysi:Cyprinidae) from the Great Basin
of western North America. Copeia.
Harris, P.M., R.L. Mayden, H.S. Espinosa Pérez, and F. García
de Leon. 2002. Phylogenetic relationships of Moxostoma and Scartomyzon
(Catostomidae) based on mitochondrial cytochrome b sequence data. Journal
of Fish Biology 61:1433-1452.
Roe, K.J., P.M. Harris and R.L. Mayden. 2002. An examination of the
phylogenetic relationships of the sunfishes and basses (Percoidei: Centrarchidae)
as evidenced by the mitochondrial cytochrome b gene. Copeia 2002:897-905.
Harris, P.M. and R.L. Mayden. 2001. Phylogenetic relationships of major
clades of Catostomidae (Teleostei: Cypriniformes) as inferred from mitochondrial
SSU and LSU rDNA sequences. Molecular Phylogenetics and Evolution 20:225-237.
Shunping He, PhD and Researcher with Professorship
Laboratory of Phylogeny and Biogeography for Freshwater Fish, Institute
of Hydrobiology, Chinese Academy of Sciences
Description of Relationship to Proposed Project and Current Research:
In China there are almost 1000 species freshwater fish. Among them about
70% are cyprinid andd 80% are in Cypriniformes, while the second largest
group is Siluriformes. We have eleven families and more than 100 species
in this Order. Most of my work is concentrated on these two large groups
for which we have very rich specimen collections and detailed information
of taxonomy. For this reason I am working on the phylogeny of Cypriniformes,
especially the family Cyprinidae and Siluriformes in Asia since 1985
when I was a graduated student. I use almost all the methods. At present
time I work with the morphological characters including osteology, mitochondrial
DNA genes or genome, nuclear genes, and SINE insertion patterns.
The Laboratory of Fish systematics and biogeography is one of the 22
laboratories in the Institute of Hydrobiology CAS, Wuhan. In my lab,
there are 10 graduate student, 4 PhD and 6 MS. I also have several associated
colleagued and curatorial staff. I have an independent morphology and
molecular facility.
Currently, I am in charge of the collection of aquatic organisms, CAS.
In this collection we house the largest cyprinid fish collection of
the world. Also we have many exchange specimens and 261 type specimens.
A biodiversity information system for fish is being built in our collection.
Also a database named ChinaFishBase will be finished. We will post digital
photographies and X-rays on our homepage for each species.
Relevant Publications:
He, S. The phylogeny of the Glyptosternoid fishes, Cybium (France),
20(2): 115-159, 1996.
He, S. M. Gayet and F.Meunier Phylogeny of the Amphiliidae, Ann. Sci.
nat. _Zool_. 1999, 20(4):117-146.
He, S., Y. Chen & Y. Zhang Preliminary Study on Mitochondrial Cytochrome
b DNA Sequences and Phylogeny of Formalin Fixed Sisorid Fishes. Zool.
Res._20(2): 81-87, 1999.
He, S, Y Chen and T Nakajima 2001 Sequences of cytochrome b gene for
primitive cyprinid fishes in East Asia and their phylogenetic concerning.
Chinese Science Bulletin. 46(8): 661-665.
Peng, Z., S. He, Y. Zhang 2002 Mitochondrial cytochrome b sequence variations
and phyologeny of the East Asian bagrid catfishes. Progress in Natural
Sciences. 12(6): 421-425.
Wang, X., S. He, Y. Chen, 2002 Sequence variations of the S7 ribosomal
protein gene in primitive cyprinid fishes: implication on phylogenetic
analysis. Chinese Science Bulletin. 47 (19): 1638-1643.
Wang W., S. He, Y. Chen 2002 Mitochondrial d-loop sequence veriation
and phylogeny of gobiobotine fishes. Progress in Natural Science. 12(11):
866-868.
Son, Y. M., S. He 2001 Transfer of Cobitis laterimaculata to the Genus
Niwaella (Cobitidae). Korean J. Ichthyol. 13(1): 1-5.
Tomas Hrbek - Assistant Professor
University of Puerto Rico
Relationship to proposed project and current research
My current research would greatly benefit from as well as contribute
to the goal of reconstructing the phylogeny of fishes. My research focus
is on the order Cyprinodontiformes, one of the most diverse teleost
assemblages, comprising more than 1000 fish species with a near world-wide
distribution. They are poor dispersers, and thus their phylogenetic
relationships reflect well the geological history of the regions they
inhabit. Their phylogenetic relationships are spatially and temporally
concordant with the geological history of the areas they occupy, and
thus are ideal for the study of biogeography.
Relevant publications:
Hrbek, T., K. N. Stölting, F. Bardakçi, F. Küçük,
R. Wildekamp and A. Meyer. Plate tectonics and biogeographical patterns
of the Pseudophoxinus (Pisces: Cypriniformes) species complex of central
Anatolia, Turkey. Mol. Phylo. Evol. (submitted)
Hrbek, T., D. N. Reznick, J. Seckinger and A. Meyer. Phylogeny of the
Poeciliidae: biogeographic and life-history implications. Evolution.
(submitted)
Hrbek, T., and D. C. Taphorn. 2003. Rise of the Andes, and its implication
for speciation within the annual fish genus Austrofundulus. Biol. J.
Linn. Soc. (accepted)
Hrbek, T., I. P. Farias, M. Crossa, I. Sampaio, J. I. R. Porto and A.
Meyer. 2003. Assessing population genetic structure of Arapaima gigas:
implications for conservation of the biggest freshwater fish of South
America. Conserv. Gen. (accepted)
Hrbek, T. , and R. H. Wildekamp. 2003. Description of a new Aphanius
species (Pisces: Cyprinodontiformes) from the Sakarya River basin of
the central Anatolian plain. Ichthyol. Explor. Freshwaters. 14:137-144.
Hrbek, T., and A. Meyer. 2003. Closing of the Tethys and the phylogeny
of Eurasian killifishes (Cyprinodontiformes: Cyprinodontidae). J. Evol.
Biol. 16:17-36.
Hrbek, T., F. Küçük, T. Frickey, K. N. Stölting,
R. H. Wildekamp and A. Meyer. 2002. Molecular phylogeny and historical
biogeography of the Aphanius (Pisces, Cyprinodontiformes) species complex
of central Anatolia, Turkey. Mol. Phylo. Evol. 25:125-137.
Hrbek, T. and A. Larson. 1999. The evolution of diapause in the family
Rivulidae (Atherinomorpha: Cyprinodontiformes): A molecular phylogenetic
and biogeographic perspective. Evolution. 53:1200-1216.
David Johnson - Division of Fishes, National Museum of Natural History,
Smithsonian Institution, Washington, DC 20560. (202) 357-4140.
Description of Relationship to Proposed Project and Current
Research:
I am currently working on a number of projects which are summarized
as follows; Survey of the dorsal gill-arch musculature of actinopterygian
fishes, with Vic Springer and Karie Darrow; osteological development
and relationships of Gasterosteiformes and related groups, with Ralf
Britz of the University of Tuebingen; comparative osteology and relationships
of the pygmy sunfish, Elassoma, with Vic Springer; a molecular phylogeny
and total evidence analysis of the Scombroidei with Tom Orrell (NRC
Associate) and Bruce collete; a brief review of actinopterygian classsification
with emphasis on Teleostei for the AMNH Tree of Life Symposium with
Melanie Stiassny and Ed Wiley: galaxioid osteology and phylogeny, with
Bob McDowall; description and paleoecology of a specimen of the unusual
percoid fish Mene from the Mancora formation of Peru, with 2001 RTP
intern Matt Friedman; description of three new cepolids of the genus
Sphenanthias, with Bill Smith-Vaniz; intrarelationships of Stephanoberyciformes,
with John Paxton, concentrating this year on the relationships of the
rare mirapinnids (hairyfishes) and megalomycterids (large-nosed fishes)
to whalefishes; evidence for monophyly of the Percopsiformes, sensu
latu, a response to Murray and Wilson (1999).
Relevant Publications:
Wiley, E. O., G. D. Johnson, and W. W. Dimmick. 2000. The interrelationships
of acanthomorph fishes: A total evidence approach using molecular and
morphological data. Biochem. Syst. and Ecol. 28: 319-350.
Tang, K. L., P. B. Berendzen, E. O. Wiley, J. F. Morrissey, R. Winterbottom,
and G. D. Johnson.1999. The phylogenetic relationships of the Suborder
Acanthuroidei (Teleostei: Perciformes) based on morphological and molecular
evidence. Mol. Phylogenetics and Evol.: 415-425.
Wiley, E. O., G. D. Johnson, and W. Dimmick. 1998. The phylogenetic
relationships of lampridiform fishes (Teleostei: Acanthomorpha), based
on a total evidence analysis of morphological and molecular data. Mol.
Phylogenetics and Evol.: 417-425.
Mooi, R. D. and G. D. Johnson. 1997. Dismantling the Trachinoidei: evidence
of a scorpaenoid relationship for the Champsodontidae. Ichthyol. Res.
44:143-176.
Mooi, R. D. and G. D. Johnson. 1997. Dismantling the Trachinoidei: evidence
of a scorpaenoid relationship for the Champsodontidae. Ichthyol. Res.
44:143-176.
Johnson, G. D. 1993. Percomorph phylogeny: progress and problems. Bull.
Mar. Sci. 52 (1). 3-28.
Johnson, G. D. and C. Patterson. 1993. Percomorph phylogeny: a survey
of acanthomorphs and a new proposal. Bull. Mar. Sci. 52 (1): 554-626.
Lecointre, Guillaume - Professor.
Muséum National d’Histoire Naturelle, département
de Systématique. Paris, France.
Description of Relationship to proposed project and current
research
Molecular systematics of fishes is an important part of the scientific
activity of our lab. Our research in ichthyology is focused on two fields
of two very different taxonomic levels: first, the molecular phylogeny
of the Acanthomorpha, a teleostean radiation which contains 314 families
and represents one third of the extant vertebrates; and second, the
molecular phylogeny of the Notothenioidei, a suborder of Antarctic perciforms.
Our team has now a very good taxonomic and molecular sample of the acanthomorph
biodiversity: about 100 terminals already sequenced for five independent
nuclear and mitochondrial datasets (550 to 800 bp each) allowed to extract
a number of clades new for science. Among these datasets, two of the
nuclear markers are new for the group (IRBP and a new segment of MLL),
and we are currently working on one additional marker, also new for
the group, to improve the reliability of our phylogenetic findings,
while enlarging the taxomic sample. The presence of two automatic sequencers
in our lab is not the panacea: international coordination is necessary.
This coordination is not only important technically, but also methodologically:
the closer will be taxonomic samples of each team, the more powerful
the tests for repeatability. It is therefore our wish to coordinate
our efforts with teams within an international network; for all of us
it has common advantages: 1. To share biological samples, primers and
technical protocols; 2. To agree upon the genes to be sequenced so that
trees can be really compared and finally, all data can be gathered together
from different labs; 3. exchanging morphological expertise to fill a
database (Metacanthomorpha) we are creating for collecting knowledge
of potential synapomorphies already proposed within the acanthomorphs.
Such a database should potentially be very useful to indicate where
anatomical characters should be checked and/or investigated among this
large variety of fishes..
Relevant publications
Le, H.L.V., Lecointre, G. and Perasso, R. 1993. A 28S rRNA based phylogeny
of the gnathostomes: first steps in the analysis of conflict and congruence
with morphologically based cladograms. Mol. Phylog. Evol.. 2: 31-51.
Lecointre, G. and Nelson, G.J. 1996. Clupeomorpha, Sistergroup of Ostariophysi.
In Stiassny, M.L.J., Parenti, L., and Johnson, D. (eds): Interrelationships
of Fishes II. Academic Press. pp. 193-207.
Lavoue, S., Bigorne, R., Lecointre, G. Agnese, J.F. 2000. Phylogenetic
relationships of electric elephant-fishes (Mormyridae: Teleostei) inferred
from cytochrome b sequences. Mol. Phylog. Evol. 14: 1-10.
Derome, N., Chen, W.J., Dettai, A., Bonillo, C., G. Lecointre. 2002.
Phylogeny of antarctic dragon fishes (Bathydraconidae, Notothenioidei,
Teleostei) and related families based on their anatomy and two mitochondrial
genes. Mol. Phylog. Evol. 24 : 139-152.
Chen, W.J., Bonillo, C., Lecointre, G. 2003. Repeatability of Clades
as Criterion of Reliability: A Case Study for Molecular Phylogeny of
Acanthomorpha (Teleostei) with Larger Number of Taxa. Mol. Phylog. Evol.
26 : 262-288.
Dettai, A. and G. Lecointre. 2004. MetAcanthomorpha, essay on a phylogeny-oriented
database for morpho-anatomical data: the acanthomorph example. Accepted
in Systematic Biology
Guoqing Lu - Assistant Professor.
Department of Biology, University
of Nebraska at Omaha
Description of Relationship to Proposed Project and Current
Research:
My initial training in biology was
in ichthyology but my current research interest focuses on bioinformatics.
After obtaining my PhD in biology at University Laval (Canada), I pursued
a MS degree in Bioinformatics at Concordia University. I continued my
bioinformatics training as a postdoctoral fellow at the Center for Bioinformatics,
McGill University. From a biological perspective, I am interested in
exploring existing molecular databases to discover knowledge of species
phylogeny and molecular evolution. Regarding informatics, I am interested
in the development and implementation of computer applications to facilitate
the above research. Since August 2002, I have been involved in the DeepFin
project, working with Dr. Ortí to design and implement the DeepFin
website and databases. My future involvement is to significantly expand
this site with new functions and resources to make it a powerful tool for
the ichthyological community interested in establishing a data-rich
phylogeny for all fishes.
Relevant Publications:
Scott, M., G. Lu, M. Hallett, and D. Thomas.The Hera database and its
use in the characterization of endoplasmic reticulum proteins. Bioinformatics
(Submitted).
Lu, G., M. Hallett, S. Pollock, and D. Thomas. 2003. DePIE: Designing
Primers for Protein Interaction Experiments. Nucleic Acids Research.
In Press.
Lu, G., D.J. Basley, and L. Bernatchez. 2001. Contrasting patterns of
mitochondrial DNA and microsatellite introgressive hybridization between
lineages of lake whitefish(Coregonus clupeaformis); relevance for speciation.
Molecular Ecology 10: 965-985.
Lu, G. and L. Bernatchez. 1999. Correlated trophic specialization and
genetic divergence in symmetric whitefish ecotypes (Coregonus sp.):
support for the ecological speciation hypothesis. Evolution 53: 157-171.
Bernatchez, L., A. Chouinard, and G. Lu.1999. Integrating molecular
genetics and ecology in speciation studies: coregonid fishes as a model
system. Biol. J. Linn. Soc. 68: 173-194.
Lu, G., S.F. Li, and L. Bernatchez. 1997. Mitochondrial DNA diversity,
population structure, and conservation genetics of four native carps
within the Yangtze River, China. Can. J. Fish. Aquat. Sci.54:47-58.
John G. Lundberg - Curator and Chair
Department of Ichthyology, The Academy of Natural Sciences, Philadelphia
Description of Relationship to Proposed Project and Current
Research:
My research focuses on fish phylogenetics emphasizing catfishes world
wide and South American electric fishes. I employ morphological, paleontological
and molecular data and approaches. I have a particular interest in the
origin and diversification of modern continental fish faunas, and in
that context I use paleontological, Earth science and molecular information
to estimate the ages of clades. I also have interest in the emerging
technologies for electronically imaging, archiving and distributing
morphological data. All of my recent projects involve training and collaboration
at the national or international level.
Relevant Publications:
Lundberg, J.G., F. Mago-Leccia & P. Nass. 1991. Exallodontus aguanai,
a new genus & species of Pimelodidae (Teleostei: Siluriformes) from
deep river channels of South America & delimitation of the sub-family
Pimelodinae. Proc. Biol. Soc. Wash. 104(4):840- 869.
Lundberg, J.G., A.H. Bornbusch & F. Mago-Leccia. 1991. Gladioglanis
conquistador n. sp. from Ecuador, with diagnoses of the subfamily Rhamdiinae
Bleeker (1862) & Pseudopimelodinae n.subf. (Siluriformes: Pimelodidae).
Copeia (1991)1: 190-208.
Lundberg, J.G. 1992. The phylogeny of ictalurid catfishes. In R. Mayden
(ed.) Systematics, historical ecology and North American freshwater
fishes. Stanford University Press.
Lundberg, J.G. 1993. African-South American freshwater fish clades and
continental drift: problems with a paradigm. In Goldblatt, P. (ed.)
Biological Relationships between Africa and South America. Yale University
Press.
Lundberg, J.G. 1998. The Temporal Context for Diversification of Neotropical
Fishes. In L.R. Malabarba, et al. eds. Phylogeny & Classification
of Neotropical Fishes. Museu de Ciências e Tecnologia, PUCRS.
Porto Alegre, Brazil.
Lundberg, J.G., M. Kottelat, G.R. Smith, M. Stiassny & T. Gill.
2000. So Many Fishes, So Little Time: An Overview of Recent Ichthyological
Discoveries in Fresh Waters. Ann. Missouri Bot. Gard. 87(1)26-62.
Lundberg, J.G. & B.M. Parisi. 2002. Propimelodus, New Genus, &
Redescription of Pimelodus eigenmanni Van der Stigchel 1946, a Long-Recognized
yet Poorly-Known South American Catfish (Pimelodidae, Siluriformes).
Proc. Phila. Acad. Sci. 152(1):75-88.
Paula Mabee - Professor
Department of Biology, University of South Dakota
Description of Relationship to Proposed Project and Current
Research:
My research centers around understanding the development and evolution
of the actinopterygian skeleton from both morphological and molecular
perspectives. Ongoing morphological work in my lab includes (1) the
developmental morphology of the axial skeleton of the zebrafish, Danio
rerio using histology and whole-mount methods, (2) actinopterygian pectoral
fin development and evolution, and (3) evolution of axial skeleton “modules”
in fishes. The molecularly focused project in my lab involves determining
the evolution of the molecular developmental genetics underlying fish
median fins: we are testing the hypothesis that the developmental genetic
pathways underlying the formation of joints in tetrapods evolved from
segmentation mechanisms in fishes. The expression of gdf5, chordin,
noggin, shh, sox9, bmps and wnts are being examined in conjunction with
functional studies. Deep Fin will facilitate the collaboration among
researchers interested in the connection between morphology and genetics.
Relevant Publications:
Bird, N. and P. M. Mabee. Submitted. The developmental morphology of
the axial skeleton of the zebrafish, Danio rerio (Ostariophysi: Cyprinidae).
Mabee, P. M., P. L. Crotwell, A. C. Burke, and N. C. Bird. 2002. Evolution
of median fin modules in the axial skeleton of fishes. Journal of Experimental
Biology: Molecular and Developmental Evolution 294: 77-90.
Crotwell, P. L., T. G. Clark, and P. M. Mabee. 2001. Gdf5 is expressed
in the developing skeleton of median fins of late-stage zebrafish, Danio
rerio. Development, Genes and Evolution 211: 555-558.
Mabee, P. M. 2000. Developmental data and phylogenetic systematics:
evolution of the vertebrate limb. American Zoologist 40: 789-800.
Mabee, P. M., K. L. Olmstead, and C. C. Cubbage. 2000. An experimental
study of intraspecific variation, developmental timing and heterochrony
in fishes. Evolution 54: 201-2106.
Cubbage, C. and P. M. Mabee. 1996. Development of the cranium and paired
fins in the zebrafish Danio rerio (Ostariophysi, Cyprindae). Journal
of Morphology 229:121-160.
Mabee, P. M. and T. A. Trendler. 1996. Development of the cranium and
paired fins in Betta splendens (Teleostei: Percomorpha): Intraspecific
variation and interspecific comparisons. Journal of Morphology 227:249-287.
Collazo, A. C., S. E. Fraser and P. M. Mabee. 1994. A dual embryonic
origin for vertebrate mechanoreceptors. Science 264:426-430.
Richard L. Mayden - Professor and Chair
Department of Biology, Saint Louis University, St. Louis, MO
Description of Relationship to Proposed Project and Current Research:
My research and ongoing projects in my laboratory focus on the phylogenetic
relationships of various lineages of fishes using morphological (osteology,
myology, neurology) and molecular (nuclear and mitochondrial DNA, proteins)
characters and various methods of data analysis, including maximum parsimony,
likelihood, and Bayesian. The various studies with which I am currently
engaged include phylogenies of “Agnathan” fishes (Petromyzontiformes,
Myxiniformes), sturgeon (Acipenseriformes), Otophysi (Cypriniformes),
trout (Salmoniformes), and acanthomorph and percomorpha groups. Cypriniform
fishes are some of the most challenging taxonomic groups for revisionary
studies, largely because of their sheer diversity and the existence
of so many species that "look alike." My research efforts
with Cypriniformes has attempted
to change this perception of this group of fishes. I have examined these
fishes for a variety of topics, including systematics, taxonomy, and
biogeography, speciation and rates of evolution, and ecology, both autecology
and synecology. I have used a wide variety of morphological-types of
characters and both mtDNA and nDNA to reconstruct phylogenetic relationships
of species, genera, and higher taxa, as well as describe new species.
Most of my research has focused on Leuciscine species within Cyprinidae,
especially those from North America, and species of Catostomidae.
Relevant (Recent) Publications:
Gill, H.S., C.B. Renaud, F. Chapleau, R.L. Mayden, and I. C. Potter.
(In press). A phylogeny of living parasitic lampreys (Petromyzontiformes)
based on morphological data. Copeia (4).
Harris, P.M. and R.L. Mayden. 2001. Phylogenetic relationships of major
clades of Catostomidae (Teleostei: Cypriniformes) as inferred from mitochondrial
SSU and LSU rDNA sequences. Molecular Phylogenetics and Evolution 20:225-237.
Harris, P.M., K.J. Roe and R.L. Mayden. Submitted. Phylogenetic Relationships
of the Sunfish Genus Lepomis (Actinopterygii; Centrarchidae): Alternative
Hypotheses Derived from Complete Mitochondrial Cytochrome b Gene Sequences.
Copeia.
Harris, P.M., R.L. Mayden, H.S. Espinosa Pérez, and F. García
de Leon. 2002. Phylogenetic relationships of Moxostoma and Scartomyzon
(Catostomidae) based on mitochondrial cytochrome b sequence data. Journal
of Fish Biology 61:1433-1452.
Roe, K.J., P.M. Harris and R.L. Mayden. 2002. An examination of the
phylogenetic relationships of the sunfishes and basses (Percoidei: Centrarchidae)
as evidenced by the mitochondrial cytochrome b gene. Copeia 2002:897-905.
Simons, A. M., P. B. Berendzen, and R. L. Mayden. (In press). Molecular
Systematics of North American Phoxinin Genera (Actinopterygii: Cyprinidae)
Inferred from Mitochondrial 12S and 16S Ribosomal RNA Sequences. J.
Linnaean Soc.
Simons, A.M., R.M. Wood, L.S. Heath, B.R. Kuhajda, and R.L. Mayden.
2001. Phylogenetics of Scaphirhynchus based on mitochondrial DNA sequences.
Transactions of the American Fisheries Society. 130:359-366.
Masaki Miya
Department of Zoology, Natural History Museum & Institute, Chiba
Description of Relationship to Proposed Project and Current
Research:
Our research group has pursued the ray-finned fish relationships at
various taxonomic levels using complete mitochondrial DNA (mtDNA) sequences
from a large number of species. Recently-published papers have covered
entire diversity of the ray-finned fishes (see below). Our laboratories
will be able to provide guidelines for experiments (primer design, protocol
for long PCR, sequencing, etc.) as well as basic data for a specific
group to promote uses of long DNA sequences in phylogenetic analysis.
Relevant Publications:
Miya, M. and M. Nishida. 1999. Organization of the mitochondrial genome
of a deep-sea fish Gonostoma gracile (Teleostei: Stomiiformes): First
example of transfer RNA gene rearrangements in bony fishes. Marine Biotechnology,
1 (5): 416–426.
Miya, M. and M. Nishida. 2000. Use of mitogenomic information in teleostean
molecular phylogenetics: A tree-based exploration under the maximum-parsimony
optimality criterion. Molecular Phylogenetics and Evolution, 17 (3):
437–455.
Inoue, J. G., M. Miya, K. Tsukamoto and M. Nishida. 2001. Complete mitochondrial
DNA sequence of Conger myriaster (Teleostei: Anguilliformes): Novel
gene order for vertebrate mitochondrial genomes and the phylogenetic
implications for anguilliform families. Journal of Molecular Evolution,
52 (4): 311–320.
Inoue, J. G., M. Miya, K. Tsukamoto and M. Nishida. 2001. A mitogenomic
perspective on the basal teleostean phylogeny: Resolving higher-level
relationships with longer DNA sequences. Molecular Phylogenetics and
Evolution, 20 (2): 275–285.
Miya, M., A. Kawaguchi and M. Nishida. 2001. Mitogenomic exploration
of higher teleostean phylogenies: A case study for moderate-scale evolutionary
genomics with 38 newly-determined complete mitochondrial DNA sequences.
Molecular Biology and Evolution, 18 (11): 1993–2009.
Inoue, J. G., M. Miya, K. Tsukamoto and M. Nishida. 2003. Basal actinopterygian
relationships: A mitogenomic perspective on the phylogeny of the “ancient
fish.” Molecular Phylogenetics and Evolution, 26 (1): 110–120.
Miya, M., H. Takeshima, H. Endo, N. B. Ishiguro, J. G. Inoue, T. Mukai,
T. P. Satoh, M. Yamaguchi, A. Kawaguchi, K. Mabuchi, S. M. Shirai, and
M. Nishida. 2003. Major Patterns of higher teleostean phylogenies: A
new perspective based on 100 complete mitochondrial DNA sequences. Molecular
Phylogenetics and Evolution, 26 (1): 121–138.
Saitoh, K., M. Miya, J. G. Inoue, N. B. Ishiguro and M. Nishida. 2003.
Mitochondrial genomics of ostariophysan fish: Perspectives on phylogeny
and biogeography. Journal of Molecular Evolution, 56 (4): 464–472.
Ishiguro, N., M. Miya and M. Nishida. 2003. Basal euteleostean relationships:
A mitogenomic perspective on the phylogenetic reality of the “Protacanthopterygii.”
Molecular Phylogenetics and Evolution, 27 (3): 476–488.
Randall David Mooi - Curator of Fishes
Milwaukee Public Museum
Relationship of Current Research to Proposed Project:
My research program examines the phylogenetic relationships of acanthomorph
fishes, particularly the Perciformes, using morphology. Strengths of
the program involve investigation of novel character systems for phylogenetic
hypotheses including egg surface morphology, pterygiophore development,
paired-fin myology, and epaxial muscle systems. Some of these systems,
and others, are being applied to the perciform suborder Gobioidei, a
speciose group (over 2000 species) that is diverse in morphology and
habitat. The gobioid project is collaborative, involving morphological
and molecular workers, perhaps serving as a model for the Deep Fin initiative.
Relevant Publications:
Gill, A.C. and R.D. Mooi. 2002. Phylogeny of Fishes. Pp. 15-42, Chapter
2 in Hart, P. and J. Reynolds (eds.), Handbook of Fish and Fisheries,
Vol. 1. Blackwell Science, London.
Mooi, R.D. 2000. Review of New Zealand bullseyes (Perciformes: Pempheridae).
New Zealand Journal of Marine and Freshwater Research, 34: 87-102.
Mooi, R.D. and G.D. Johnson. 1997. Dismantling the Trachinoidei: evidence
for a scorpaeniform relationship of the Champsodontidae. Ichthyological
Research, 44(2): 143-176.
Mooi, R.D. 1996. Revision, phylogeny, and discussion of biology and
biogeography of the plesiopid fish genus Plesiops (Perciformes: Plesiopidae).
Royal Ontario Museum Life Sciences Contribution 159, iv + 108 pp.
Mooi, R.D. and A.C. Gill. 1995. Epaxial muscle associations with dorsal-fin
pterygiophores in acanthomorph fishes, with comments on phylogenetic
relationships. Bulletin of the Natural History Museum, Zoology Series,
61(2):121-137.
Gavin J. P. Naylor - Associate Professor
Dept. of Biological Sciences, Florida State University, Tallahassee,
FL 32306
Description of Relationship to Proposed Project and Current Research:
I am interested in the mechanisms underlying biological diversification
at both the organismal level and the molecular level. A major project
in my lab involves reconstructing the evolutionary tree for sharks and
rays based on DNA sequence comparisons. We have focused on sharks because
they exhibit a diverse range of traits and they have an excellent fossil
record. We have published morphometric studies of sharks teeth. We have
generated nuclear gene sequences for hundreds of shark species and sequenced
complete mitochondrial genomes for more than 20 lamniform sharks. We
are also interested in identifying “good” genes for high-order
phylogenetic analyses of vertebrates. These will be available to enrich
the current repertoire of molecular markers to study fish phylogenetics.
Relevant Publications
Naylor, G.J.P., A.P. Martin, E.G. Matisson and W.M. Brown.1997. The
inter-relationships of lamniform sharks: Testing hypotheses with sequence
data. In Molecular Systematics of fishes, T.D Kocher and C. A . Stepien,
eds. Academic Press, pp. 195-214.
Naylor, G.J.P. and L.F. Marcus.1994 Identifying isolated shark teeth
of the genus Carcharhinus to species: relevance for tracking phyletic
change through the fossil record. American Museum Novitates no. 3109
pgs 1-53.
Martin, A.P., G.J.P Naylor and S.R. Palumbi 1992. Rates of mitochondrial
DNA evolution in sharks are slow compared to mammals. Nature 357: 153-155.
Naylor, G.J.P., J.A. Ryburn, O. Fedrigo O. and A. Lopez.(in press)
Phylogenetic Relationships among the major lineages of Sharks and Rays
deduced from multiple genes. In Reproductive Biology and Phylogeny of
Chondrichthyans (Sharks, skates, stingrays and chimaeras) W. Hamlett
and B Jamieson Eds. Univ. Queensland Press.
Maisey J.G. and G.J. P. Naylor. (in press) Mesozoic elasmobranchs, neoselachian
phylogeny and the rise of modern neoselachian diversity. In Mesozoic
Fishes (Arratia G. & A. Tintori eds.) Vergal .F. Pfeil. (in Press)
Mutsumi Nishida - Professor
Department of Marine Bioscience, Ocean Research Institute, University
of Tokyo, Japan.
Description of Relationship to Proposed Project and Current
Research:
We are trying to establish comprehensive phylogenetic framework of fishes
through analysis of complete nucleotide sequence of the mitochondrial
genome. For confirming the framework, we have begun to search for useful
nuclear genes for the source of further phylogenetic information. Our
data and expertise in examining mitochondrial DNA sequences will provide
good starting point for studying phylogenies of various fish groups
by using complete mitochondrial DNA sequences.
Relevant Publications:
Ishiguro, Naoya, Masaki Miya, and Mutusmi Nishida 2003. Basal euteleostean
relationships: A mitogenomic perspective on the phylogenetic reality
of the "Protacanthopterygii". Molecular Phylogenetics and
Evolution, 27, 476-488.
Saitoh, Kenji, Masaki Miya, Jun G. Inoue, Naoya Ishiguro, and Mutsumi
Nishida 2003. Mitochondrial genomics of ostariophysan fishes: perspectives
on phylogeny and biogeography. Journal of Molecular Evolution, 56, 464-472.
Inoue, Jun G., Masaki Miya, Katsumi Tsukamoto, and Mutsumi Nishida 2003.
Basal actinopterygian relationships: a mitogenomic perspective on the
phylogeny of the "ancient fish". Molecular Phylogenetics and
Evolution, 26, 110-120.
Miya, Masaki, Hirohiko Takeshima, H. Endo, Naoya Ishiguro, Jun G.Inoue,
Takahiko Mukai, Takashi P. Satoh, Motoomi Yamaguchi, Akira Kawaguchi,
Kohji Mabuchi, Shigeru M. Shirai, and Mutsumi Nishida 2003. Major patterns
of higher teleostean phylogenies: a new perspective based on 100 complete
mitochondrial DNA sequences. Molecular Phylogenetics and Evolution,
26, 121-138.
Miya, Masaki, Akira Kawaguchi, and Mutsumi Nishida 2001. Mitogenomic
exploration of higher teleostean phylogenies: a case study for moderate-scale
evolutionary genomics with 38 newly determined complete mitochondrial
DNA sequences. Molecular Biology and Evolution, 18, 1993-2009.
Inoue, Jun G., Masaki Miya, Katsumi Tsukamoto, and Mutsumi Nishida 2001.
A mitogenomic perspective on the basal teleostean phylogeny: resolving
higher-level relationships with longer DNA sequences. Molecular Phylogenetics
and Evolution, 20, 275-285.
Kumazawa, Yoshinori and Mutsumi Nishida 2000. Molecular phylogeny of
osteoglossoids: a new model for Gondwanian origin and plate tectonic
transportation of the Asian arowana. Molecular Biology and Evolution,
17, 1869-1878.
Miya, Masaki and Mutsumi Nishida 2000. Use of mitogenomic information
in teleostean molecular phylogenetics: A tree-based exploration under
the maximum-parsimony optimality criterion. Molecular Phylogenetics
and Evolution, 17, 437-455.
Kumazawa, Yoshinori, Motoomi Yamaguchi, and Mutsumi Nishida 1999. Mitochondrial
molecular clocks and the origin of euteleostean biodiversity: Familial
radiation of perciforms may have predated the Cretaceous/Tertiary boundary.
In "The biology of biodiversity" (ed. M. Kato), Springer.
Tokyo, pp.35-52.
Thomas Orrell
NMFS Systematics Laboratory, Smithsonian Institution, Washington D.C.,
U.S.A.
Description of Relationship to Proposed Project and Current
Research:
I am interested in the evolutionary history and biogeography of fishes,
with particular emphasis on perciform relationships. I have been using
both molecular and morphological techniques to look at the relationships
of marine and freshwater species.
My current research is a molecular phylogeny of the tunas, mackerels,
billfishes and relatives. I am sequencing nuclear markers to estimate
the phylogenetic relationships within the perciform suborder Scombroidei
from the single-copy nuclear locus, TMO-4c4. To date, I have the first
nuclear phylogeny of the group, which supports a monophyletic Scombridae,
but not a monophyletic Scombroidei.
Future research plans are to estimate the evolutionary relationships
of the Percomorpha, the largest and most derived (crown) group of teleost
fishes, comprising over 12,800 species. I would like to research the
relationships among the five major percomorph subgroups. The enigma
of percomorph phylogeny is one of the outstanding problems remaining
in vertebrate evolution. I believe in applying various techniques to
resolving these relationships including comparative morphology and molecular
genetics. The majority of economically important fish species are percomorphs,
yet their interrelationships remain one of the major mysteries of the
vertebrate Tree of Life. A clearer understanding of the phylogeny of
the percomorphs would facilitate a more stable higher-level classification
of the Percomorpha. These data would benefit ichthyology as a whole
and would lead to better-informed conservation decisions, and a better
understanding of genome evolution. It will lay the foundation for future
investigations of macroevolutionary trends in this large group of fishes.
Relevant Publications:
Orrell, T. M., K. E. Carpenter, J. A. Musick, and J. E. Graves. 2002.A
phylogenetic and biogeographic analysis of the Sparidae (Perciformes:
Percoidei) based on cytochrome b sequences. Copeia 2002(3):618-631.
Orrell, T. M. and K. E. Carpenter. in press. A phylogeny of the Sparidae
(Perciformes: Percoidei) inferred from the mitochondrial 16S ribosomal
RNA gene. (Submitted to Molecular Phylogenetics and Evolution).
Lynne R. Parenti - Curator of Fishes and Head
Section of Vertebrate Zoology, National Museum of Natural History, Smithsonian
Institution
Description of Relationship to Proposed Project and Current
Research:
My research focuses on the comparative anatomy, phylogenetic systematics
and biogeography of fishes, in particular atherinomorphs and gobioids;
higher-level phylogenetic relationships of osteichthyans; historical
biogeography of fishes and other animals as well as plants; and the
use of new or under-studied morphological characters in systematic ichthyology.
The investigation of characters of the soft anatomy has, by necessity,
been highly collaborative; I work closely with a reproductive biologist
(Harry J. Grier) and a neuroanatomist (Jiakun Song) in order to provide
a phylogenetic interpretation of gonad and nerve characters.
Relevant publications:
Parenti, L. R. 1981. A phylogenetic and biogeographic analysis of cyprinodontiform
fishes (Teleostei, Atherinomorpha). Bull. Amer. Mus. Nat. Hist. 168(4):335-557.
Parenti, L. R.1986. The phylogenetic significance of bone types in euteleost
fishes. Zool. J. Linn. Soc. 87:37-51.
Parenti, L.R. 1989. A phylogenetic revision of the phallostethid fishes
(Atherinomorpha, Phallostethidae). Proc. Cal. Acad. Sci. 46:243-277.
Parenti, L. R. 1993. Relationships of atherinomorph fishes (Teleostei).
Bull. Mar. Sci. 52
(1): 170-196.
Grier, H. J. & L. R. Parenti. 1994. Reproductive biology and systematics
of phallostethid fishes as revealed by gonad structure. Environ. Biol.
Fishes 41:287-299.
Stiassny, M. L. J., L. R. Parenti, & G. D. Johnson (eds). 1996.
Interrelationship of Fishes.
Academic Press, San Diego. 497 pp.
Parenti, L. R. & J. Song. 1996. Phylogenetic significance of the
pectoral/pelvic fin
association in acanthomorph fishes: A reassessment using comparative
neuroanatomy. pp. 427-444, In: Interrelationships of fishes (M. L. J.
Stiassny, L. R. Parenti, and G. D. Johnson, eds.). Academic Press, San
Diego.
Parenti, L. R.& K. R. Thomas. 1998. Pharyngeal jaw morphology and
homology in sicydiine gobies (Teleostei: Gobiidae) and allies. J. Morph.
237:257-274.
Humphries, C.J. and L. R. Parenti. 1999. Cladistic biogeography: interpreting
patterns of
plant and animal distributions, Second edition. Oxford University Press.
187 pp. Claro, R., K. C. Lindeman & L. R. Parenti (eds.). 2002.
Ecology of the Marine Fishes
of Cuba. Smithsonian Institution Press, Washington, D.C. 253 pp.
Ted Pietsch - Professor
School of Aquatic and Fishery Sciences; Adjunct Professor, Department
of Zoology; Curator of Fishes, Burke Museum of Natural History and Culture:
University of Washington, Seattle.
Description of Relationship to Proposed Project and Current
Research:
Systematics of lophiiform fishes in general and ceratioid anglerfishes
in particular. As Curator of Fishes, the UW collections have been transformed
from unused and disheveled, unknown to the scientific community and
ranked last among “other collections” (Collette and Lachner,
Copeia 1976: 625-642), to a fully computerized, well-documented, archival
research facility containing 5,950,762 specimens in 91,323 lots; a first-class
working facility, with a broad constituency, that now ranks fifth among
regional fish collections in North America (Poss and Collette, Copeia,
1995: 48-70).
Relevant publications:
Shedlock, A. M., T. W. Pietsch, M. G. Haygood, P. Bentzen, and M. Hasegawa.
In Press. Molecular systematics and life history evolution of anglerfishes
(Teleostei: Lophiiformes): evidence from mitochondrial DNA. Steenstrupia,
Copenhagen, 25 ms pp., 6 figs. (likely date of publication, mid-2003).
Pietsch, T. W., and D. B. Grobecker. 1987. Frogfishes of the World:
Systematics, Zoogeography, and Behavioral Ecology. Stanford University
Press, Stanford, xxii + 420 pp.
Pietsch, T. W. 1984. Lophiiformes: Development and relationships. pp.
320-325, In: Moser, H. G., W. J. Richards, D. M. Cohen, M. P. Fahay,
A. W. Kendall, Jr., and S. L. Richardson (editors), Ontogeny and Systematics
of Fishes, Spec. Publ. No. 1, Amer. Soc. Ichthy. Herpet., ix + 760 pp.
Bertelsen, E., T. W. Pietsch, and R. J. Lavenberg. 1981. Ceratioid anglerfishes
of the family Gigantactinidae: Morphology, systematics, and distribution.
Nat. Hist. Mus. L. A. Co., Contri. Sci., 332, vi + 74 pp.
Pietsch, T. W. 1976. Dimorphism, parasitism and sex: reproductive strategies
among deep-sea ceratioid anglerfishes. Copeia, 1976(4): 781-793.
Pietsch, T. W. 1974. Osteology and relationships of ceratioid anglerfishes
of the family Oneirodidae, with a review of the genus Oneirodes Lütken.
Nat. Hist. Mus. L. A. Co., Sci. Bull., 18, 113 pp.
Michael J. Sanderson - Professor
Division of Biological Sciences; DBS Centers and Programs; Center for
Population Biology
Evolution and Ecology; University of California, Davis
Description of Relationship to Proposed Project and Current Research:
My research and teaching areas have long focused on the systematics,
phylogenetics, and evolution of flowering plants, theoretical issues
in systematic biology, macroevolution, and molecular evolution. While
I am not a systematic ichthyologist, my research expertise in phylogenetics,
data analysis, tree comparisons, and data manipulation will provide
critical information for the Deep Fin coordination project. I have long
been associated with the Deep Green project and can bring to the Deep
Fin project expertise and experience from this large-scale collaborative
networking group and the complexities that this group and other large-scale
analyses are facing with the explosion of data and taxa, and the different
types of analyses today. I also have extensive experience in coordinating
and combining different types of data, including fossil and “age
estimate” information for taxa, into single data sets. This experience
will be critical for molecular estimates of the age of different fish
lineages and the “age of fishes,” based on the assumption
of one or more molecular clocks. My experience with different genes
in plant groups with different genes show marked variation in evolutionary
rates among lineages and suggest that ages based on single genes can
be overestimations due to reliance on high-rate of some taxa and failure
to consider rate variation across sites. I, in collaboration with others,
have proposed solutions to include more fossil age constraints on nodes
and new methods that allow deviation from a clock.
Relevant Publications
Sanderson, M.J. 1995. Objections to bootstrapping phylogenies: A critique.
Syst. Biol. 44:299-320.
Sanderson, M. J. 1998. Estimating rate and time in molecular phylogenies:
beyond the molecular clock? pp. 242-264. In: Plant Molecular Systematics.
P Soltis, D Soltis, and J. Doyle (eds.). Chapman and Hall, New York.
Baldwin, B. and M. J. Sanderson. 1998. Age and rate of diversification
of the Hawaiian silversword alliance. Proc. Nat. Acad. Sci. 95:9402-9406.
Sanderson, M.J. and J.A. Doyle. 2001. Sources of error and confidence
intervals in estimating the age of angiosperms from rbcL and 18S rDNA
data. Amer. J. Bot. 88:1499-1516.
Sanderson, M.J. 2002. Estimating absolute rates of molecular evolution
and divergence times: a penalized likelihood approach. Mol. Biol. Evol.
19:101-109.
Piel, W. H., Michael J. Donoghue, and Michael J. Sanderson. 2002. "TreeBASE:
a database of phylogenetic knowledge." Pp. 41-47. In: Shimura,
J., K. L. Wilson, and D. Gordon, eds. To the interoperable "Catalog
of Life" — with partners Species 2000 Asia Oceanea . Research
Report from the National Institute for Environmental Studies No. 171,
Tsukuba, Japan.
Sanderson, M. J. 2003. r8s: inferring absolute rates of molecular evolution,
divergence times in the absence of a molecular clock. Bioinformatics
19 (2): 301-302.
Piel, W. H., Michael J. Sanderson, and Michael J. Donoghue. 2003. The
Small-World Dynamics of Tree Networks and Data Mining in Phyloinformatics.
Bioinformatics, in press
Andrew M. Simons - Assistant Professor
Department of Fisheries, Wildlife, and Conservation Biology & Bell
Museum of Natural History, University of Minnesota
Description of Relationship to Proposed Project and Current
Research:
Participation in DeepFin would greatly enhance current research in my
lab by increasing opportunities for collaboration with colleagues. In
particular, the possibility of expanding the breadth of available phylogenies
will greatly enhance our ability to examine the evolution of complex
characters in fish clades. Research in my lab examines fish phylogeny
at several levels. We are interested in phylogeography of North American
Highland fishes, examining multiple clades of highland fishes at the
population level, using mitochondrial genes to identify changes in distribution
since the Pleistocene. We also study phylogenetic relationships among
species and higher groups in acipenseriform, osteoglossomorph, otophysan,
and atherinomorph fishes. Finally we are interested in the evolution
of body size, trophic morphology, and spawning behavior. These questions
require well resolved phylogenetic hypotheses for large numbers of taxa
but we are hampered by availability of well resolved phylogenies for
most fish groups.
Relevant Publications:
Simons, A.M., and R.L. Mayden. 1997. The phylogenetic relationships
of the Creek Chubs and Spinefins: An enigmatic group of North American
cyprinid fishes (Actinopterygii: Cyprinidae). Cladistics 13(3): 187-205.
Simons, A.M., and R.L. Mayden. 1998. Phylogenetic relationships of the
western North American phoxinins (Actinopterygii: Cyprinidae) as inferred
from mitochondrial 12S and 16S ribosomal RNA sequences. Mol. Phylogenet.
Evol. 9(2):308-329.
Simons, A.M., and R.L. Mayden. 1999. Phylogenetic Relationships of North
American Cyprinids and Assessment of Homology of the Open Posterior
Myodome. Copeia 1999(1):13-21.
Simons, A.M., K.E. Knott, and R.L. Mayden. 2000. Assessment of Monophyly
of the minnow genus Pteronotropis (Teleostei: Cyprinidae). Copeia 2000:
1068-1075.
Simons, A.M., P.B. Berendzen, and R.L. Mayden. In Press. Molecular systematics
of North American phoxinin genera (Actinopterygii: Cyprinidae) inferred
from mitochondrial 12S and 16S ribosomal RNA sequences. Zool. J. Linn.
Soc.
Berendzen, P.B., A.M. Simons, and R.M. Wood. In Press. Phylogeography
of the northern hogsucker, Hypentelium nigricans (Catostomidae: Cypriniformes):
Genetic evidence for the existence of the ancient Teays River. Journal
of Biogeography.
John S. Sparks - Assistant Curator of Ichthyology,
Division of Vertebrate Zoology, American Museum of Natural History,
NY
Description of Relationship to Proposed Project and Current
Research:
My research focuses on the systematics and biogeography of recent fishes.
I use both morphological and nucleotide characters to reconstruct phylogenetic
relationships, and have increasingly been using features of soft anatomy
to resolve relationships within groups that exhibit little osteological
variation. We are currently working on several projects that focus on
reconstructing the phylogenetic relationships of freshwater and nearshore
marine fish assemblages that occur throughout the Mascarene region.
In conjunction with paleogeographic data, the recovered phylogenies
will be used to make inferences regarding Gondwanan vicariance and the
current distributions of these organisms. In particular, we are interested
in investigating relationships among Malagasy, Seychellian, and South
Asian ichthyofaunas. These higher-level phylogenetic studies could benefit
substantially from interaction and coordination with other groups working
on related lineages of fishes elsewhere in the world, particularly Africa,
Australia, and the Neotropics.
Relevant Publications
Sparks, J. S., and P. N. Reinthal. 2001. A new species of Ptychochromoides
from southeastern Madagascar (Teleostei: Cichlidae), with comments on
monophyly and relationships of the ptychochromine cichlids. Ichthyological
Exploration of Freshwaters 12: 115-132.
Sparks, J. S. 2002. Ptychochromis inornatus, a new cichlid (Teleostei:
Cichlidae) from northwestern Madagascar, with a discussion of intrageneric
variation in Ptychochromis. Copeia 2002 (1): 120-130.
Sparks, J. S., and M. L. J. Stiassny. 2003. Introduction to the freshwater
fishes of Madagascar. Pp. 849-863 in: S. M. Goodman and J. P. Benstead
(eds.), The natural history of Madagascar. University of Chicago Press,
Chicago.
Sparks, J. S. 2003. Molecular phylogeny and biogeography of the Malagasy
and South Asian cichlid fishes. Molecular Phylogenetics and Evolution,
in press.
Ng, Heok Hee, and J. S. Sparks. 2003. The ariid catfishes (Teleostei:
Siluriformes: Ariidae) of Madagascar, with the description of two new
species. Occasional Papers of the Museum of Zoology, University of Michigan,
1-27.
Benstead, J. P., J-L Gattolliat, F-M Gibon, P. V. Loiselle, M. Sartori,
J. S. Sparks, M. L. J. Stiassny, and P. H. de Rham. 2003. Conservation
of Madagascar’s freshwater biodiversity. Bioscience, in press.
Sparks, J. S. 2003. Taxonomic status of the Malagasy cichlid Ptychochromis
grandidieri Sauvage 1882 (Teleostei: Cichlidae), including a molecular
phylogenetic analysis of the ptychochromine cichlids. Ichthyological
Exploration of Freshwaters, in press.
Carol Stepien - Director, the Lake Erie Research Center and Department of Earth, Ecological and Environmental Sciences,
University of Taledo, Taledo, Ohio.
Description of Relationship to Proposed Project and Current Research:
Dr. Stepien is an environmental scientist who specializes in molecular
population genetics, systematics, and phylogeography of fishes and invertebrates
in the Great Lakes region, specifically anthropogenically impacted populations
and nonindigenous species. Recently funded research focuses on walleye
and smallmouth bass populations in Lake Erie. Previous work on molecular
systematics of fishes focused on blennoids and percids. An edited volume
(with T.D. Kocher) was published in 1997 (Molecular Systematics of Fishes).
Relevant Publications
Dillon, A.K. and C.A. Stepien. 2001. Genetic and biogeographic relationships
of the invasive round (Neogobius melanostomus) and tubenose (Proterorhinus
marmoratus) gobies in the Great Lakes versus Eurasian populations. J.
Great Lakes Research 27(3):267-280
Muss, A., D. R. Robertson, C.A. Stepien, P. Wirtz, and B.W. Bowen. 2001.
Phylogeography of Ophioblennius (Blenniidae): the role of Ocean currents
and geography in reef fish evolution. Evolution 55(3):561-572.
Stepien, C.A., A. K. Dillon, and A.K. Patterson. 2000. Population genetics,
phylogeography, and systematics of the thornyhead rockfishes (Sebastolobus)
along the deep continental slopes of the North Pacific Ocean. Canadian
Journal of Fisheries and Aquatic Sciences 57:1701-1717.
Stepien, C.A., A.K. Dillon, M.L. Brooks, K.L. Chase, and A.N. Hubers.
1997. The evolution of blennioid fishes based on an analysis of mitochondrial
12S rDNA sequences data. Ch. 15, pp. 245-270. In: Kocher, T.D. and C.A.
Stepien (eds.) Molecular Systematics of Fishes. Academic Press, San
Diego.
Faber, J. E. and C. A. Stepien. 1997. The utility of mitochondrial DNA
control region sequences for analyzing phylogenetic relationships among
populations, species, and genera of the Percidae. Ch. 9, pp. 129-143
In: Kocher, T.D. and C.A. Stepien (eds.) Molecular Systematics of Fishes.
Academic Press, San Diego.
Kocher, TDK and C.A. Stepien (Eds) 1997. Molecular Systematics of Fishes.
Academic Press. Reprinted in 2002.
Melanie Stiassny - Axelrod Research Curatrix
Department of Ichthyology, American Museum of Natural History
Description of Relationship to Proposed Project and Current
Research:
My interests in fish systematics are quite wide-ranging but center mainly
on the resolution of relationships amongst ctenosquamate clades with
a particular emphasis on the families Cichlidae and Bedotiidae (Atherinidae).
My expertise to date is almost exclusively morphological and I am currently
working on a text in which I aim to summarize, in an accessible form,
the basics of the musculo-skeletal anatomy of fishes. No small task…
but hopefully one that will be of interest to all members of Deep Fin
when it is finally completed. Additionally I am the lead author on a
chapter summarizing the “state-of-the-art” on the phylogenetics
of “gnathostome fishes”. This chapter is to appear in an
upcoming volume entitled “Assembling the Tree of Life” (eds.
Cracraft and Donaghue, Oxford University Press, 2004).
Relevant Publications:
Stiassny, M.L.J. 1986. The limits and relationships of the acanthomorph
teleosts. J. Zool. Lond., (B), 1: 411-460.
Stiassny, M.L.J. and J. S. Jensen. 1987. Labroid intrarelationships
revisited: morphological complexity, key innovations, and the study
of comparative diversity. Bull. Mus. Comp. Zool., 151(5): 269-319.
Stiassny, M.L.J. and J.A. Moore. 1992A review of the pelvic girdle of
acanthomorph fishes, with comments on hypotheses of acanthomorph intrarelationships.
Zool. J. Linn. Soc. 104: 209-242.
Stiassny, M.L.J. 1996Basal ctenosquamate relationships and the intrarelationships
of myctophiform(scopelomorph) fishes. : 405-426. In: Stiassny et al.
(Eds) Interrelationships of Fishes, Academic Press, San Diego.
Lundberg, J.G., Kottelat, M., Smith, G.R., Stiassny, M.L.J. and Gill,
A.C. 2000. So many fishes, so little time: an overview of recent ichthyological
discoveries in freshwaters. Annls. Miss. Bot. Gdns., 87(1): 26-62.
Stiassny, M.L.J. 2002 Bony Fishes. In: Eldredge, N. (ed.). Life on Earth:
An
Encyclopedia of Biodiversity, Ecology, and Evolution. Pp. 192-197. ABI-CLIO
Press, Santa Barbara, CA.
Stiassny, M.L.J., Wiley, E.O., G.D. Johnson and M.R. de Carvahlo. 2004
Gnathostome fishes. In: J.C. Cracraft & M. Donaghue (eds). Assembling
the Tree of Life. Oxford University Press (2004). in press
John P. Sullivan - Postdoctoral Associate
Cornell University
Description of Relationship to Proposed Project and Current Research:
Electrogenesis for the purposes of electrolocation and communication
has evolved twice in modern teleost fishes: once in the osteoglossomorph
mormyroids and again in the ostariophysan gymnotoids. My research is
focused on the phylogenetic systematics, evolution and biogeography
of both of these groups of fishes and of their relatives. I use molecular
as well morphological approaches and am interested in reconstructing
phylogeny at different hierarchical levels. My work is collections-based
and to date has included significant field work in South American and
in Central Africa.
Current projects include: (1) phylogenetic interrelationships of mormyrid
genera and species using nuclear and mt markers; (2) use of AFLP data
for phylogeny reconstruction within species flock of mormyrid genus
Brienomyrus; (3) higher level relationships and monophyly of extant
osteoglossomorph lineages using nuclear and mt markers; (4) interrelationships
of gymnotiform genera and species using nuclear and mt markers.
All projects stand to benefit from Deep Fin-generated dialogue with
other workers. Of particular interest to me is coordinating my gymnotiform
research with that of others working on other otophysan groups so that
datasets may be pooled in the future.
Relevant Publications:
Sullivan, J. P., S. Lavoué, and C. D. Hopkins. 2000. Molecular
systematics of the African electric fishes (Mormyroidea: Teleostei)
and a model for the evolution of their electric organs. Journal of Experimental
Biology 203:665-683.
Sullivan, J. P., S. Lavoué, and C. D. Hopkins. 2002. Discovery
and phylogenetic analysis of a riverine species flock of African electric
fishes (Mormyridae: Teleostei). Evolution 56:597-616.
Lavoué, S., J. P. Sullivan, and C. D. Hopkins. 2003. Phylogenetic
utility of the first two introns of the S7 ribosomal protein gene in
African electric fishes (Mormyroidea:Teleostei) and congruence with
other molecular markers. Biological Journal of the Linnean Society 78:273-292.
Kevin L. Tang - Lerner-Gray Postdoctoral Research Fellow
Department of Ichthyology, American Museum of Natural History, NY
Description of Relationship to Proposed Project and Current
Research:
My research focuses on the phylogenetic relationships of the family
Pomacentridae using morphological and molecular data. My efforts are
aimed at producing a phylogeny of the generic relationships within the
family, as well as including as many of the more than 340 species of
damselfishes as possible. As part of this research, I am interested
in the subfamily Amphiprioninae, where I am interested in the evolution
of their symbiotic relationships with sea anemones and the changes in
their biology that have occurred in unison with this symbiotic lifestyle.
Participation in Deep Fin would be an excellent opportunity to expand
on my damselfish work, not only within the damselfishes but also to
determine where they occur in the context of the Perciformes.
Publications
Tang, K. L., K. M. McNyset, and N. I. Holcroft. In press. The phylogenetic
position of five genera (Acanthochromis, Azurina, Chrysiptera, Dischistodus,
and Neopomacentrus) of damselfishes (Perciformes: Pomacentridae). Molecular
Phylogenetics and Evolution.
Jang-Liaw, N.-H., K. L. Tang, C.-F. Hui, and K.-T. Shao. 2002. Molecular
phylogeny of 48 species of damselfishes (Perciformes: Pomacentridae)
using 12S mtDNA sequences. Molecular Phylogenetics and Evolution 25:
445-454.
Tang, K. L. 2001. Phylogenetic relationships among damselfishes (Teleostei:
Pomacentridae) as determined by mitochondrial DNA data. Copeia 2001:
591-601
Tang, K. L., P. B. Berendzen, E. O. Wiley, J. F. Morrissey, R. Winterbottom,
and G. D. Johnson. 1999. The phylogenetic relationships of the suborder
Acanthuroidei (Teleostei: Perciformes) based on molecular and morphological
evidence. Molecular Phylogenetics and Evolution 11: 415-425.
Peter Unmack - PhD student
School of Life Sciences, Arizona State University
The purpose of this letter is to document my interest in participating
in RCN: Deep Fin – A coordinated Network of Scientists Assembled
to Advance The Phylogeny of “Fishes” (www.deepfin.org).
I am committed to putting in the time and effort required to make this
collabaorative project successful.
I am presently a PhD student at Arizona State University working under
Dr Tom Dowling on the biogeography of Australian freshwater fishes.
This research has led me to begin broader phylogenetic work investing
various biogeographic scales that are centered around unravelling the
biogeographic history of Australian fishes. This includes determining
the family level relationships (to understand the origins of the fauna),
the relationships among the species and the within species biogeographic
patterns. The first portion of my research program, determining family
level relationships, fits into the goals of the DeepFin project the
best.
Relevant publications
Dubut, V., Unmack, P.J., Salducci, M. & Gilles, A. in prep. Molecular
phylogeny and biogeography of Retropinna semoni (Teleostei: Retropinnidae,
Weber 1895) in southeastern Australia: evidence for multiple species.
Thacker, C. & Unmack, P.J. submitted. Phylogeny and biogeography
of the eleotrid genus Hypseleotris (Teleostei: Gobioidei: Eleotridae),
with redescription of H. agilis and H. cyprinoides. Records of the Australian
Museum.
Unmack, P. J. 2001. Biogeography of Australian freshwater fishes. Journal
of Biogeography. 28: 1053-1089.
Unmack, P. J. 2001. Designation of a lectotype for Porochilus argenteus
(Zietz 1896) (Osteichthyes: Plotosidae). Records of the South Australian
Museum. 34: 57-59.
Unmack, P. J. 1999. Biogeography of Australian freshwater fishes. MSc.
Thesis, Biology Department, Arizona State University.
Ivantsoff, W., Unmack, P., Saeed, B. & Crowley, L. E. L. M. 1991.
A redfinned blue-eye, a new species and genus of the family Pseudomugilidae
from central Western Queensland. Fishes of Sahul. 6(4): 277-282.
Richard P. Vari
Division of Fishes, National Museum of Natural History, Washington,
DC
Description of Relationship to Proposed Project and Current
Research:
Participant. Research in press, in manuscript, or in progress pertinent
to project includes phylogenetic studies of various groups of South
American and African characiforms (Prochilodontidae, with R.M.C. Castro,
Universidade de São Paulo (USP); Alestidae, with A. Zanata, former
Smithsonian Postdoctoral Fellow and now Museu de Zoologia, USP; Anostomidae,
with B. Sidlauskas, University of Chicago) and South American siluriforms
(Cetopsidae, with M.C.C. de Pinna, Museu de Zoologia, USP and C.Ferraris,
Jr., California Academy of Sciences). During the upcoming years I will
continue my phylogenetic studies on characiforms and siluriforms, largely
with collaborators. Projects include phylogenetic studies of components
of the African characiform family Distichodontidae using morphological
data; analysis of suprageneric relationships within the characiform
family Characidae (with Brazilian collaborators R.M.C. Castro, F. Bockmann,
and C. Oliveira) using both morphological and molecular data; and phylogenetic
studies of Neotropical siluriforms (with M.C.C. de Pinna and C. Feraris,
Jr.)
Relevant Publications
Vari, R.P. 1979. Anatomy, Relationships and Classification of the families
Citharinidae and Distichodontidae (Pisces, Characoidea). Bulletin of
the British Museum (Natural History), Zoology, 36(5):261-344.
Vari, R.P. 1983. Phylogenetic Relationships of the Families Curimatidae,
Prochilodontidae, Anostomidae and Chilodontidae (Pisces, Characiformes).
Smithsonian Contributions to Zoology, 378:iii+1-60, figs. 1-41.
Vari, R.P. 1989. A Phylogenetic Study of the Neotropical Characiform
Family Curimatidae (Pisces, Ostariophysi). Smithsonian Contributions
to Zoology, 471:iv+1-71, figs. 1-45.
Vari, R.P. 1989. Systematics of the Neotropical Characiform Genus Pseudocurimata
(Pisces, Ostariophysi). Smithsonian Contributions to Zoology, 490:iii+1-28,
figs 1-18.
Vari, R.P. 1991. Systematics of the Neotropical Characiform Genus Steindachnerina
Fowler (Pisces, Ostariophysi). Smithsonian Contributions to Zoology,
507:iii+118, figs. 1-80.
Vari, R.P. 1995. The Neotropical Characiform Fish Family Ctenoluciidae
(Teleostei, Ostariophysi): Supra and Intrafamilial Phylogenetic Relationships,
with a Revisionary Study. Smithsonian Contributions to Zoology, 564:1-97.
de Pinna, M.C.C., and R.P. Vari. 1995. Monophyly and Phylogenetic Diagnosis
of the Cetopsidae, with Synonymization of the Helogenidae (Teleostei,
Siluriformes). Smithsonian Contributions to Zoology, 571:1-26.
Vari, R.P., and A.S. Harold. 2001. Phylogenetic Study of the Neotropical
Fish Genera Creagrutus Günther and Piabina Reinhardt (Teleostei:
Ostariophysi: Characiformes), with a Revision of the Cis-Andean Species.
Smithsonian Contributions to Zoology, 613:1-239.
Castro, R.M.C. and R.P. Vari. In press. The South American Characiform
Family Prochilodontidae (Ostariophysi: Characiformes): A Phylogenetic
and Revisionary Study. Smithsonian Contributions to Zoology.
Mark Westneat - Associate Curator,
Department of Zoology, Field Museum of Natural History, Chicago
Description of Relationship to Proposed Project and Current
Research:
My research is focused on combining phylogenetics and biomechanics.
A major goal of the lab is to generate phylogenies for a number of large
coral reef fish groups, including labrids, scarids, damselfishes, and
butterflyfishes. Recent NSF funding enabled us to produce the first
higher-level tree for the family Labridae, a group of nearly 600 species.
We are also interested in higher-level relationships among reef fish
families. Phylogenetics provides a valuable framework for analysis of
biomechanics; we are studyiong the evolution of feeding and locomotion
in large clades of fishes. The DeepFin proposal is of great significance
to our shared goal of better phylogenetics of large species groups,
and will also aid our ability to interpret our work on functional morphology.
Relevant Publications
Streelman, J.T., M. Alfaro, M.W. Westneat, D.R. Bellwood and S.A. Karl.
2002. Evolutionary history of the parrotfishes: biogeography, ecology
and comparative diversity. Evolution 56: 961-971.
Hanel, R., M. W. Westneat and C. Sturmbauer. 2002. Phylogenetic relationships,
evolution of broodcare behaviour, and geographic speciation in the wrasse
tribe Labrini. J. Molec. Evol. 55, 776-789.
Hale, M. E., J. H. Long Jr, M. J. McHenry, and M. W. Westneat. 2002.
Evolution of behavior and neural control of the fast-start escape response.
Evolution 56: 993-1007.
Westneat, M. W. 1999. The Living Marine Resources of the Western Central
Pacific: FAO species identification sheets for fishery purposes. Family
Labridae. Food and Agriculture Organization of the United Nations. Vol.
6: 3381-3467.
Westneat, M.W. 1995. Feeding, function, and phylogeny: Analysis of historical
biomechanics and ecology in labrid fishes using comparative methods.
Syst. Biol. 44: 361-383.
Westneat, M. W. 1995. Systematics and biomechanics in ecomorphology.
Env. Biol. Fishes 44:263-283.
Edward O. Wiley - Curator and Professor
Natural History Museum and Biodiversity Research Center, University
of Kansas, Lawrence, KS
Description of Relationship to Proposed Project and Current
Research:
I have both theoretical and empirical research programs. My theoretical
program is centered in phylogenetic systematics and evolution. My empirical
program is centered in three areas, speciation, phylogenetic relationships
of higher taxa of fishes, and predictive niche modeling and biogeography
using genetic algorithms. My work on speciation seeks a reproach between
population genetic phenomena and macroevolutionary phenomena. Several
of my former students were actively engaged in studies of the phylogenetic
relationships among species (M.J. Ghedotti, C. Fielitz, M.J. Grose,
and K. Tang), a precursor of detailed work at finer levels using such
tools as DNA sequencing. My work on the phylogenetic relationships among
higher taxa of fishes has shifted from being primarily morphologically
based to being based on both morphology and DNA sequence data. We (W.
Dimmick, myself and G. David Johnson of the Smithsonian), plus several
graduate students (M.J. Grose, K. Tang, P.B. Berendzen, and N. Holcroft
Benson) work on the relationships of the higher teleosts (the acanthomorphs).
Expasion of this effort to study the broader relationships of acanthomorphs
with other fishes will be well-served by initiatives like Deep Fin.
Relevant publications:
Wiley, E.O., G.D. Johnson, and W.W. Dimmick. 2000. The relationships
of acanthomorph fishes: A total evidence approach using molecular and
morphological data. Biochemical Systematics and Ecology 28:319-350.
Shaw, K., A. Simons, and E.O. Wiley. 1999. Reexamination of the phylogenetic
relationships of the sand darters (Teleostei: Percidae). Sci. Pap. Mus.
Nat. Hist. Univ. Kansas No. 12:1-16.
Tang, K., P.B. Berendzen, E.O. Wiley, J.F. Morrissey, R. Winterbottom,
and G.D. Johnson.1999. The phylogenetic relationships of the Suborder
Acanthuroidei (Teleostei: Perciformes) based on morphological and molecular
evidence. Mol. Phylog. Evol 11(3):415-425.
Wiley, E. O., and R. H. Hagen. 1997. Mitochondrial DNA sequence variation
among the sand darters (Percidae: Teleostei). In: Molecular Evolution
of Fishes (T. Kocher and C. Stepien, eds.) Academic Press, New York:
75-96.
Wiley, E. O., G. D. Johnson, and W. W. Dimmick. 1998. The phylogenetic
relationships of lampridiform fishes (Teleostei: Acanthomorpha), based
on a total evidence analysis of morphological and molecular data. Mol.
Phylogenetics and Evolution 10(3): 417-425.
Rafael Zardoya
Museo Nacional de Ciencias Naturales. Madrid (Spain)
Description of Relationship to Proposed project and Current
Research:
I am interested in resolving phylogenetic relationships among fishes
at different taxonomic levels. In each case study, I want to establish
a robust phylogenetic framework onto which discuss morphological and
behavioral adaptation, as well as the historical generation of current
biogeographical patterns. My ongoing projects are: 1) The relative phylogenetic
position of lobe-finned fishes (lungfishes and coelacanths); 2) Rapid
radiation events in the family Gobiidae; 3) Brood-care behavior in the
genus Betta; 4) Molecular systematics of the suborder Labroidei; 5)
Phylogenetic relationships of antarctic fishes (Notothenioidei); 6)
Population genetics of commercial marine fish species (mackerel, tuna,
sardine). To infer deep phylogenetic relationships, I use complete mitochondrial
genomes and nuclear genes such as RAG1. To assess population structure
I used microsatellites.
Relevant Publications:
R. Zardoya, A. Garrido-Pertierra, and J.M. Bautista (1995) The complete
nucleotide sequence of the mitochondrial DNA of the Rainbow trout, Oncorhynchus
mykiss. J. Mol. Evol. 41: 942- 951
R. Zardoya y A. Meyer (1996) The complete nucleotide sequence of the
mitochondrial genome of the lungfish (Protopterus dolloi), supports
its phylogenetic position as a close relative of land vertebrates. Genetics
142: 1249-1263
R. Zardoya y A. Meyer (1996) Evolutionary relationships of the coelacanth,
lungfishes, and tetrapods based on the 28S ribosomal RNA gene. Proc.
Natl. Acad. Sci. USA 93: 5449-5454
R. Zardoya , E. Abouheif y A. Meyer (1996) Evolutionary analyses of
the hedgehog and Hoxd-10 genes in fish species closely related to the
zebrafish. Proc. Natl. Acad. Sci. USA 93: 13036-13041
R. Zardoya , D. Vollmer, C. Craddock, T. Streelman, S. Karl y A. Meyer
(1996) Evolutionary conservation of microsatellite flanking regions
and the phylogeny of cichlid fishes (Pisces: Perciformes). Proc. R.
Soc. Lond. 263: 1611-1618
R. Zardoya y A. Meyer (1997) The complete DNA sequence of the mitochondrial
genome of a “living fossil”, the coelacanth (Latimeria chalumnae).
Genetics 146: 995-1010
R. Zardoya, Y. Cao, M. Hasegawa y A. Meyer (1998) Searching for the
Closest Living Relative(s) of Tetrapods through evolutionary analyses
of mitochondrial and nuclear data. Mol. Biol. Evol. 15: 506-517
R. Zardoya, e I. Doadrio (1999) Molecular evidence on the evolutionary
and biogeographical patterns of European cyprinids. J. Mol. Evol. 49:
227-237
L. Rüber, J. L. Van Tassell y R. Zardoya (2003) The influence of
ecological specialization and biogeography on the evolutionary history
of the American seven-spinned gobies (Gobiidae, Gobiosomatini) Evolution
In press
A. Meyer y R. Zardoya (2003) Recent Advances in the molecular Phylogeny
of Vertebrates. Ann. Rev. Ecol. Evol. Syst. 34: In press
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