Dear colleagues - the most exciting news certainly is that Joerg Ploetner is organizing the third Waterfrog symposium in Berlin in this Fall, 20 years after the first waterfrog symposium at the same place.Peter Beerli
Coalescence and maximum likelihood in Seattle
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 LAMARC website . You should also have a look at the website of our competition (here). 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.
Pagano, Alain, and Pierre Joly (1998) Limits of the morphometric method for taxonomic field identification of water frogs. Alytes 16:3-4.
Abstract: 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-Rhone floodplain, the morphs of Rana ridibunda and the hybrid R. kl. esculenta greatly overlap in morphometrical characters.
Plenet, S. and P. Joly, and A. Pagano (1998) Is habitat requirement by an oxygen-dependent frog (Rana ridibunda) governed by its larval stage? Arch. Hydrobiol. (1998) 143/1: 107-119.
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.
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:
We will start 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 (firstname.lastname@example.org).
III. International Symposium on
- 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 October 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: email@example.com
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
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) or 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).