From: Preston Garrison (garrisonp@uthscsa.edu)
Date: Fri Oct 31 2003 - 00:15:49 EST
>I think Wells' critique of molecular phylogenies will be much harder
>to sustain after papers like this (Nature 425, 798 - 804 (23 October
>2003):
>
>Genome-scale approaches to resolving incongruence in molecular phylogenies
Phylogenies can also be resolved by using complex mutations such as
transposon insertions in particular locations. The paper below, which
appeared this week, is a nice example using Alu elements in the
primate lineage. They analyzed 133 Alu insertions and all but one
were consistent with only one tree. The one exception, which put
gorilla and human together with chimps branching earlier, instead of
gorilla being more distant than chimps, is attributable to random
fixation of an element that was polymorphic in the population at the
time of branching off of gorillas.
----------
Alu elements and hominid phylogenetics
PNAS October 28, 2003 vol. 100 no. 22 p. 12791
Abdel-Halim Salem*Ýý, David A. Ray*ý, Jinchuan Xing*, Pauline A.
Callinan*, Jeremy S. Myers*, Dale J. Hedges*, Randall K. Garber*,
David J. Witherspoon§, Lynn B. Jorde§, and Mark A. Batzer*¶
Alu elements have inserted in primate genomes throughout the
evolution of the order. One particular Alu lineage (Ye) began
amplifying relatively early in hominid evolution and continued
propagating at a low level as many of its members are found in a
variety of hominid genomes. This study represents the first
conclusive application of short interspersed elements, which are
considered nearly homoplasy-free, to elucidate the phylogeny of
hominids. Phylogenetic analysis of Alu Ye5 elements and elements from
several other subfamilies reveals high levels of support for
monophyly of Hominidae, tribe Hominini and subtribe Hominina. Here we
present the strongest evidence reported to date for a sister
relationship between humans and chimpanzees while clearly
distinguishing the chimpanzee and human lineages.
------------
The fact that the same type of transposon is inserted at exactly the
same location in different species is itself powerful evidence for
common descent, and this kind of pattern, where the transposon is
present in a species pattern that is exactly what is expected based
on a phylogenetic tree determined by other means - I can't think of
any hypothesis from a special creation viewpoint that accounts for
it, other than "God just did it that way."
The same sort of evidence comes up in another recent paper. Francis
Collins used data from this paper in his paper in the Sept. issue of
PSCF (the ASA journal):
--------------
Comparative analyses of multi-species sequences from targeted genomic regions
NATURE VOL 424, 14 AUGUST 2003, p. 788
The systematic comparison of genomic sequences from different
organisms represents a central focus of contemporary genome analysis.
Comparative analyses of vertebrate sequences can identify coding and
conserved non-coding regions, including regulatory elements, and
provide insight into the forces that have rendered modern-day
genomes. As a complement to whole-genome sequencing efforts we are
sequencing and comparing targeted genomic regions in multiple,
evolutionarily diverse vertebrates. Here we report the generation and
analysis of over 12 megabases (Mb) of sequence from 12 species, all
derived from the genomic region orthologous to a segment of about 1.8
Mb on human chromosome 7 containing ten genes, including the gene
mutated in cystic fibrosis. These sequences show conservation
reflecting both functional constraints and the neutral mutational
events that shaped this genomic region. In particular, we identify
substantial numbers of conserved non-coding segments beyond those
previously identified experimentally, most of which are not
detectable by pair-wise sequence comparisons alone. Analysis of
transposable element insertions highlights the variation in genome
dynamics among these species and confirms the placement of rodents as
a sister group to the primates.
Preston G.
Preston Garrison, Ph.D.
Instructor
UTHSCSA
Biochem. Dept. MSC 7760 Insert the usual disclaimers here.
7703 Floyd Curl Dr.
San Antonio, TX 78229-3900
garrisonp@uthscsa.edu
210-567-3702
http://biochem.uthscsa.edu/~barnes
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