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Water frog information -- Newsletter December 1998
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Website: http://waterfrogs.scs.fsu.edu/waterfrogs.html
Distribution: Peter Beerli (beerli@scs.fsu.edu)
Address Questions/Remarks about items in this newsletter to
frog@genetics.washington.edu or to the respective authors of
chapters/columns.
Address organizational questions to beerli@scs.fsu.edu
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Dear researchers,
Shortly before Christmas and New Years Eve, we send you the latest news
about water frog research. We thank all contributors for their time and
effort in supporting us with relevant and interesting news concerning water
frogs. Because there is lots of news, we'll keep this editorial brief.
Have a nice Christmas time and all the best for the upcoming year.
Dirk Schmeller (dirk@falco.Biologie.uni-mainz.de),
Peter Beerli (beerli@scs.fsu.edu)
Thomas Uzzell (uzzell@acnatsci.org)
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Contents
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- Water frog labs: coalescence and maximum likelihood in Seattle
- New literature
- European Science Foundation Network - ESF network
- Announcement: III. International Symposium on
"Genetics, Systematics and Ecology of
western Palearctic Waterfrogs (J. Ploetner)
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Water frog labs: coalescence and maximum likelihood in Seattle
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Perhaps you will ask yourselves why I (Peter Beerli) am contributing from
Seattle to this newsletter. The water frog pages are not my main work, as
many of you know, but more of a hobby. I work in Joseph Felsenstein's lab
at the University of Washington. Our general subject is completely
theoretical; we develop methods for the analyses of phylogenetic
relationships between species [program package PHYLIP (*1)] and for
estimation of population parameters (such as effective population size,
recombination rate, and migration rates) from genetic data (electrophoretic
markers, microsatellites, DNA sequences, SNPs). [program package LAMARC
(*2)].
I am writing methods and programs for the estimation of population sizes
and migration rates. These methods are based on coalescence theory(*3) and
maximum likelihood. It is possible to estimate all population parameters
jointly; for example, in a data set with four subpopulations one can
estimate all subpopulation sizes and all migration rates (a total of 16
parameters). This is a marked improvement over older available methods
(based on Sewall Wright's FST and its newer derivatives), with which one
estimates either one overall 4Nm or four 4Nm_i using pairs of populations.
If you are interested in these kind of analyses for your water frog data,
then you should visit our website
(http://waterfrogs.scs.fsu.edu/lamarc.html). You should also
have a look at the website of our competitors
(http://www.maths.monash.edu.au/~mbahlo/mpg/gtree.html). Publications on
these programs have been accepted, but are not yet in print, although a
comparison between FST-based methods and my program MIGRATE is available.
Literature of interest:
Beerli, P. (1998) Estimation of migration rates and
population sizes in geographically structured populations. In Advances in
molecular ecology (Ed. G. Carvalho). NATO-ASI workshop series. ISO,
Amsterdam. Pp. 39-53.
Kuhner M. K., J. Yamato, and J. Felsenstein. (1995) Estimating effective
population size and mutation rate from sequence data using
Metropolis-Hastings sampling. Genetics 140: 1421-1430.
Kuhner, M. K., J. Yamato, and J. Felsenstein. (1998) Maximum likelihood
estimation of population growth rates basedon the coalescent. Genetics 149:
429-434.
Schnabel, A., P. Beerli, A. Estoup, D. Hillis.
(1998) A guide to software packages for data analysis on molecular ecology.
In Advances in molecular ecology (Ed. G. Carvalho). NATO-ASI workshop
series. ISO, Amsterdam. Pp. 291-303.
(*1) PHYLIP - Phylogenetic Inference Package, a software package to
analyse phylogenetic relationsships (distance, compatiblity, parsimony,
and likleihood methods). Website:
http://waterfrogs.scs.fsu.edu/phylip.html.
(*2) LAMARC - Likelihood Analyses with Markov chain Monte Carlo using
Random Coalescences, a package to estimate population parameters from
genetic data. Website: http://waterfrogs.scs.fsu.edu/lamarc.html
(*3) coalescence theory: Consider a simple population model, in which a
constant number, n, of individuals live exactly one generation, and
contribute a huge number gametes to the next generation of which two are
randomly drawn to form each individual, up to the effective population size
of n individuals. If we try to follow genes from generation 0 forward to
generation m, we are soon lost in the huge number of possible paths through
this genealogy from the beginning to today. In 1982, J. F. C. Kingman
published two articles showing how we can gain information from a sample of
individuals today if we trace back through possible genealogies.
In contrast to the forward-looking methods, if we look back, we have fewer
and fewer relationships; eventually some of the lineages coalesce because
these lineages share the same parent. Additional (and more enlightening)
information can be found in R. R. Hudson's (1990) Gene genealogies and the
coalescent process, published in Oxford Surveys in Evolutionary Biology 7:
1-44.
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NEW LITERATURE
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Limits of the morphometric method for taxonomic field identification of
water frogs. Alytes (1998) 16: 3-4). Alain Pagano & Pierre Joly
ESA CNRS 5023 Ecologie des eaux douces et des grands fleuves,
Universite C. Bernard Lyon 1, 69622 Villeurbanne Cedex, France
e-mail: Pagano@univ-lyon1.fr, Joly@biomserv.univ-lyon1.fr
Taxonomic identification of the water frogs has evolved since
hybridogenesis has been revealed within the Rana esculenta complex.
Although the study of protein polymorphism has proved robust in taxonomic
information, morphometric measurements are currently used despite of some
limits. By comparing results obtained with these two techniques, this study
shows that morphometry is does not always provide a decisive taxonomic
information for field identification. In the three populations studied, in
the mid-Rh=D9ne floodplain, the morphs of Rana ridibunda and the hybrid R.
kl. esculenta greatly overlap in morphometrical characters.
---------------------------------------------------
Is habitat requirement by an oxygen-dependent frog (Rana ridibunda)
governed by its larval stage? Arch. Hydrobiol. (1998) 143/1: 107-119. S.
PLENET, P. JOLY & A. PAGANO
Ecologie fonctionnelle, E.S.A. CNRS 5023 : Ecologie des Eaux Douces et
des Grands Fleuves, Univ. Lyon I, 43 Bd du 11 Nov. 1918, 69622 VILLEURBANNE
cedex, FRANCE E-mail: plenet@univ-lyon1.fr
According to the literature and to our own experience, R. ridibunda is
absent from ponds with occasionally low oxygen concentrations. We tested
the effects of stochastically fluctuating oxygen concentration on tadpole
survival and growth under laboratory conditions. Two experimental
treatments (constant and fluctuating oxygen regimes) were arranged in a
factorial design with three populations of R. ridibunda.
Stochastic oxygen fluctuation with drops from normoxia to hypoxia did not
clearly influence long-term survival (which remained high in all blocks) or
growth and development. Only in one population did survival differ between
oxygen treatments, and survival was greater under the fluctuating than
under the stable oxygen conditions. One population differed from the others
in exhibiting slight variations in morphology between treatments. But in no
case did these laboratory experiments provide evidence that oxygen regime
can affect development of R. ridibunda tadpoles and explain
oxygen-dependent habitat use by this species.
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European Science Foundation Network - ESF network
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Principles and characteristics of ESF Networks
ESF networks are primarily
oriented towards coordinating activities in order to stimulate and
consolidate the European scientific community in specific topics, to
promote mobility of scientists within the community, and to increase mutual
awareness in the relevant scientific community. In common with all ESF
activities, the fields include the natural and physical sciences, the
medical and life sciences, economics and the social sciences, and the
humanities, reflecting the full disciplinary spread of ESF Standing
Committees. Interdisciplinarity within and between scientific areas is
encouraged. Activities may include organization of workshops in specific
fields, international meetings, and exchanges. In certain instances, ESF
networks may also lead to the establishment and implementation of larger
ESF or other collaborative research activities.
Underlying the ESF Network concept are the following characteristics:
- It should bring together people working in the same field in Europe in
order to strengthen that area of science or to further develop an area of
science that is already strong;
- It should aim to increase the mobility of scientists in Europe;
- It should be self-managed. The scientists themselves should undertake its
initiation, organization and scientific direction;
- The ESF provides funding towards the costs of management and
collaboration. The relevant scientific community should seek other
appropriate support structures and financial means from national or
international sources;
- It should be a flexible mechanism and may adopt a wide variety of forms
of cooperation and communication. It is not exclusive in nature and other
scientists may be added to the Network, as appropriate, during its lifetime;
- It should encourage an interdisciplinary approach, where possible;
- It may be concerned not only with integrating European scientists but
also with creating links to scientists elsewhere, especially the USA and
Japan.
(Dirk Schmeller)
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Morphology/Development/Gametogenesis (edited by Maria Ogielska)
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We will start soon a new column on the topics mentioned in the title.
Any recent
literature/thoughts /ideas etc. that you want to share are welcome. Send
them directly to Maria Ogielska (ogielska@biol.uni.wroc.pl).
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III. International Symposium on "Genetics, Systematics and Ecology of
western Palearctic Waterfrogs (J. Ploetner)
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- First Circular -
Berlin, 11.-15. October 1999
Four years ago, the II. International Symposium on Ecology and Genetics of
European water frogs took place in Wroclaw, Poland. The participants of
this meeting agreed to organize water frog symposia at regular intervals to
update researchers on accumulated knowledge, to exchange information, and
to reactivate cooperation in the field of water frog research. Because of
the rapid development of new genetic methods, with new results on all
aspects of the genetics, evolution, systematics, ecology, and behavior of
western Palearctic water frogs, we propose to organize a third symposium in
September 1999. We hope that many people will be interested in this meeting
and invite you to Berlin to the Museum of Natural History (Museum fuer
Naturkunde). We would be grateful to receive your preregistration by the
30th of January. Please send it, together with the title of your
contribution, to the following address:
Dr. Joerg Ploetner
Museum fuer Naturkunde
Institut fuer Systematische Zoologie
Invalidenstr. 43
10115 Berlin
Phone: 4930 2093 8508
Fax: 4930 2093 9528
e-mail: joerg.ploetner@rz.hu-berlin.de
Below you will find brief information about the meeting. After
preregistration, we will send you a definitive registration form and more
detailed information.
Needless to say, we look forward to seeing many of you again, meeting some
of you for the first time, and working with all of you in making this
symposium a truly successful and memorable event.
About the meeting
Scientific topics:
1. Systematics and Evolution
2. Population biology and genetics
3. Gametogenesis and development
4. Ecology and Behavior
Communications:
Papers will be given in single sessions (no parallel sessions), with 1-2
invited speakers per topic and 8-10 contributed papers (25- 30 minutes, 15
minutes discussion) per day
Official language: English
Posters: one poster session will be organized
Registration fees: 50 US$ (full fee)
30 US$ (students)
Financial support:
For colleagues who are not able to raise the costs for travel and
participation we will try to take over the expenses. Applications can be
made to the organizer not later then the 31st of January.
Payments: Registration fee must be paid when definitive registration is made.
Accommodation:
Accommodation is available at the guesthouse of the Humboldt-Universitat zu
Berlin (55-67 DM per day for a single room, 110 DM for a double room) or at
several hotels in the vicinity of the museum (the current prices per day
will be given with the second circular).
