[MORPHMET] Workshop: UWashington.EvolQuantGenetics.Jun5-9
(note: this course will have about one lecture on the analysis of morphometrics on phylogenies) Evolutionary Quantitative Genetics Workshop Friday Harbor Laboratories, University of Washington, 5-9 June 2017 Non-credit workshop. Participants arrive at Friday Harbor Labs on Sunday, June 4, lectures and exercises occur June 5-9, and participants depart on Saturday, June 10, 2017. Application deadline March 1, 2017. Application forms and details here: http://tinyurl.com/EQG2017 Web page: http://depts.washington.edu/fhl/studentSummer2017.html#SumB-genetics Instructors: Dr. Joe Felsenstein Department of Genome Sciences University of Washington, Seattle j...@gs.washington.edu Dr. Stevan J. Arnold Department of Integrative Biology Oregon State University, Corvallis stevan.arn...@oregonstate.edu Previous versions of this 5-day workshop were given at the National Evolutionary Synthesis Center (NESCENT) at Duke University in Durham, North Carolina from 2011-2013, and then at the National Institute for Mathematical and Biological Synthesis (NIMBioS) at the University of Tennessee in Knoxville from 2014-2016. Like past versions, the Friday Harbor version will review the basics of theory in the field of evolutionary quantitative genetics and its connections to evolution observed at various time scales. The aim of the workshop is to build a bridge between the traditionally separate disciplines of quantitative genetics and comparative methods. Quantitative genetic theory for natural populations was developed considerably in the period from 1970 to 1990 and up to the present, and it has been applied to a wide range of phenomena including the evolution of differences between the sexes, sexual preferences, life history traits, plasticity of traits, as well as the evolution of body size and other morphological measurements. Textbooks have not kept pace with these developments, and currently few universities offer courses in this subject aimed at evolutionary biologists. Evolutionary biologists need to understand this field because of the ability to collect large amounts of data by computer, the development of statistical methods for changes of traits on evolutionary trees and for changes in a single species through time, and the realization that quantitative characters will not soon be fully explained by genomics. This workshop aims to fill this need by reviewing basic aspects of theory and illustrating how that theory can be tested with data, both from single species and with multiple-species phylogenies. Participants will use R, an open-source statistical programming language, to build and test evolutionary models. The workshop involves lectures and in-class computer exercises. You can consult the 2016 tutorial website for examples, it will be found at http://www.nimbios.org/tutorials/TT_eqg2016 The intended participants for this tutorial are graduate students, post-docs, and junior faculty members in evolutionary biology. The workshop can accommodate up to 35 participants. Guest instructors will include: * Marguerite Butler, Biology, Univ. Hawai'i, Mānoa * Patrick Carter, Evolutionary Physiology, Washington State University, Pullman * Adam Jones, Biology, Texas A University, College Station * Brian O'Meara, Ecology & Evolutionary Biology, Univ. of Tennessee, Knoxville * Josef Uyeda, Biological Sciences, Virginia Tech, Blacksburg Cost: $1000 to be paid to Friday Harbor Laboratories. This fee will cover housing and meals at FHL and all other workshop expenses, except travel. Participants who have been admitted to attend will make their payment prior to arrival at FHL. Details of payment by credit card or check will be provided once the applicant has been admitted to attend. J.F. ---- Joe Felsenstein j...@gs.washington.edu Department of Genome Sciences and Department of Biology, University of Washington, Box 355065, Seattle, WA 98195-5065 USA -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] Terminology: Morphometry or Morphometrics?
Back in the days when phenetic clustering was new, at one point someone (Sokal, Rohlf, someone like that) suggested that their field be called "taxometrics". Someone else pointed out that the more proper Greek name would be "taximetrics". Someone else then killed off this suggestion by pointing out that that was too easy for that to be mistaken for the study of taxi meters. Joe Joe Felsenstein j...@gs.washington.edu Department of Genome Sciences and Department of Biology, University of Washington, Box 355065, Seattle, WA 98195-5065 USA On Thu, Sep 8, 2016 at 4:19 PM, Emma Sherratt <emma.sherr...@gmail.com> wrote: > Dear Chris, Norm, Alannah, > > Thank you for your comments and discussion on this term! And for engaging > in a fun and different topic for this forum. > > It is indeed the etymology and usage I find most fascinating. I have > noticed through my years of training in morphometrics (as I would call it) > that colleagues in Brazil and Spanish speaking countries say morphometry > usually and I'd not heard this before - at least I don't remember hearing > it said in Britain. I began to wonder why, but had not found the answer. > I'm glad I'm not the only one interested in this - thanks Mauro! > > Have a lovely weekend all! > > Best wishes, > > Em > > On Thursday, 8 September 2016, Chris Klingenberg <c...@manchester.ac.uk> > wrote: > >> Dear Emma >> >> They are synonyms, with the same meaning. Incidentally, that is the same >> as for "biometry" and "biometrics". >> >> I think "morphometry" may be the older of the two (the Oxford English >> Dictiionary has a first occurrence in 1857, although it is not clear >> whether the meaning is the same, versus 1960 for "morphometrics"), and is >> the more traditional-sounding one. >> During much of the 20th century, words ending in "-ics" had the aura of >> coolness about them (perhaps from physics envy) as it now applies to those >> ending in "-omics". >> >> Also, I have a feeling (which may be wrong) that there may be a >> geographic flavour to the two words. In my impression, the word >> "morphometry" is perhaps more widespread in Britain (plus perhaps the >> Commonwealth), whereas folks in North America seems to use "morphometrics" >> pretty much all the time. >> Furthermore, "morphometry" may come more naturally to writers who >> translate from another language (French "morphométrie", German >> "Morphometrie" etc.). >> >> There would be room for linguistic research here >> >> Best wishes, >> Chris >> >> >> On 08/09/2016 06:01, Emma Sherratt wrote: >> >>> Dear Morphmet-hive mind, >>> >>> I've been curious for some time about the terms "morphometry" and >>> "morphometrics" and whether they are in fact interchangeable or quite >>> distinct. Also, is it related to the difference between phylogeny and >>> phylogenetics? >>> >>> Regards, >>> >>> Emma >>> >>> >>> -- >>> MORPHMET may be accessed via its webpage at http://www.morphometrics.org >>> --- >>> You received this message because you are subscribed to the Google >>> Groups "MORPHMET" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to morphmet+unsubscr...@morphometrics.org >> morphmet+unsubscr...@morphometrics.org>. >>> >> >> -- >> *** >> Christian Peter Klingenberg >> School of Biological Sciences >> University of Manchester >> Michael Smith Building >> Oxford Road >> Manchester M13 9PT >> United Kingdom >> >> Web site: http://www.flywings.org.uk >> E-mail: c...@manchester.ac.uk >> Phone: +44 161 2753899 >> Skype: chris_klingenberg >> *** >> >> -- >> MORPHMET may be accessed via its webpage at http://www.morphometrics.org >> --- You received this message because you are subscribed to the Google >> Groups "MORPHMET" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to morphmet+unsubscr...@morphometrics.org. >> >> > > -- > > ~~~ > > Emma Sherratt, PhD. > > > Postdoctoral Researcher in the Keogh Lab > <http://biology-assets.anu.edu.au/hosted_sites/Scott/> > Division of Evolution, Ecology &
Re: [MORPHMET] allometry and phylogeny
Damienet al. -- > Thanks a lot for the answer Joe! > However, I think you need to have species average for using methods like > independent contrasts and PGLS right? How would you do it for a trajectory > or series of specimens per species? > I not quite sure about the trajectory issue. However for samples from each species, when one does not have precise population means, one has to ask how phylogenetic comparative methods cope with that. The relevant papers are by Ives, Midford and Garland (Evolution, 2007) and of course best of all my own 2008 paper in American Naturalist. Alas, it is not just a matter of getting contrasts and then treating those as independent. I have options in my PHYLIP program Contrast that can do this case. "Trajectory", I'm less sure. Joe Joe Felsenstein j...@gs.washington.edu Department of Genome Sciences and Department of Biology, University of Washington, Box 355065, Seattle, WA 98195-5065 USA -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] allometry and phylogeny
Damien Esquerre Gheur <damien.esque...@anu.edu.au> wrote: > Dear morphometricians, > > > I have a pretty big dataset of specimens for most species of pythons > encompassing most of the size range for every species. I have been > projecting the allometric trajectories and doing pairwise slope comparisons > and things like that in Geomorph. However, it seems very obvious that the > is a very strong phylogenetic signal in the data, as species within the > same clade tend to have parallel trajectories. > ... > Would there be a way, for example, to extract a value for the slope and do > an ancestral state reconstruction on that? Also, is there a way to > incorporate phylogeny in slope comparison models? > I don't know which package of morphometric programs you should use for that, but in phylogenetic comparative methods, you can use your tree of N species and obtain N-1 phylogenetic contrasts from your data. Those can then be treated as independent data points, each of which has your full set of coordinates. You could obtain a Generalized Procrustes superposition of your forms, without resizing the specimens, then feed the resulting coordinates for each species into one of the phylogenetic comparative methods packages. Joe Joe Felsenstein j...@gs.washington.edu Department of Genome Sciences and Department of Biology, University of Washington, Box 355065, Seattle, WA 98195-5065 USA -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] using regression residuals for other analyses
These complicated issues aside, there is a simpler reason not to use a residual from a regression as the basis for further analyses. If two characters are under natural selection based on some combination -- such as selection on a ratio between them -- then the current value of character Y is a response, not to the current value of character X, but to its value in the past. Response to selection is not instant, so we'd really want to regress Y on past values of X. How far in the past depends on information on the strength of selection. We don't yet know that, and we don't have values of X in the past. Far better to make a joint analysis of selection on both of them. Once one takes the residual one has built in the assumption that the response of one character to another is instantaneous, in effect that the selection involved is infinitely strong and the heritabilities complete. I believe that Hansen and Bartoszek have warned about this in a paper in Systematic Biology in 2012. Joe Joe Felsenstein j...@gs.washington.edu Department of Genome Sciences and Department of Biology, University of Washington, Box 355065, Seattle, WA 98195-5065 USA -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [R-sig-phylo] [MORPHMET] Re: Stability of p-values (physignal and testing for morphological integration)
Tsung Fei Khang -- If the expectation of the empirical estimator for mean p-value is a function of the number iterations that becomes asymptotically unbiased, then this would explain the simulation results (attachment in the original posting), since for small number of iterations, some bias would remain, and only disappear (hence the stabilization feeling) when number of iterations is large. Thanks again for all for clarifying the issue. The issue didn't get clarified if that's the conclusion. In a permutation test each replicate is independent and equivalent to a coin toss. Thus the estimate of P is unbiased, not asymptotically unbiased. Joe Joe Felsenstein j...@gs.washington.edu Department of Genome Sciences and Department of Biology, University of Washington, Box 355065, Seattle, WA 98195-5065 USA -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
