Too distant outgroups

Chris CSIMON at UCONNVM.bitnet
Fri Jun 4 09:50:13 EST 1993


        IN REPLY TO THE FOLLOWING MESSAGE:  (see below)


        >From: harley at uctvax.uct.ac.za
        >Subject: The outgroup problem
        >Date: 4 Jun 93 09:03:36 GMT
        >Reply-To: harley at chempath.uct.ac.za
        >
        >I have a topic which might engender some constructive debate, and
        >can be put as the proposal *the outgroup is not appropriate as  a
        >way of rooting molecular phylogenies*. This is, of course, a  bit
        >extreme,  but  I am coming to the conclusion from  looking  at  a
        >number of sequence data sets that one is caught between the devil
        >and  the deep blue sea: if the outgroup is too close it  may  not
        >really  be a valid outgroup, if too far then the number of  sites
        >genuinly identifying the plesiomorphic state may be too few,  and
        >mixed with so many homoplasies (back & parallel mutations, esp if
        >there  is  a high transition bias) as to be worse  than  useless.
        >Put another way, is there a statistical method which will  define
        >a  window   (  of distance ? of shared sites ?)  within  which  a
        >particular  taxon can be used as a valid outgroup. What  is  good
        >for morphologists may not be so good for gene jocks.


        REPLY:

        We are working on that very problem (how distant is a too distant
        outgroup).   We  are using species groups with  well  established
        phylogenies and sequencing mitochondrial 12S, 16S, CO2, and  CytB
        genes.   These  groups  include a hierarchical set  of  taxa  for
        rodents starting with several Peromyscus species and ending  with
        Rattus  and Mus; Drosophila, starting with D. melanogaster  group
        and  ending with D. virilis (in collaboration with L.  Nigro,  U.
        Padova);  we  are also studying various other groups  of  insects
        whose  phylogenies are less well known.  We are finding that  the
        distance  of  the appropriate outgroup varies  depending  on  the
        genes studied.  Ribosomal genes are particularly troublesome.  We
        will be presenting some of our results at the Evolution  meetings
        in  Snowbird Utah in June and in Montpelier (by L. Nigro  and  F.
        Frati) in August.  We are currenlty writing the first of a series
        of papers on the subject.

        Chris Simon
        Jack Sullivan

CHRIS SIMON                      PHONE: 203-486-4640
ECOL. EVOL. BIOLOGY U-43           FAX: 203-486-6364
UNIVERSITY OF CONNECTICUT       BITNET: CSIMON at UCONNVM
STORRS, CT  06269             INTERNET: CSIMON at UCONNVM.UCONN.EDU



More information about the Mol-evol mailing list