Biology Reference
In-Depth Information
•
Large-scale sequencing of key genes from unclassified micro-
organisms has led to phylogenetic studies in which sequences are
not attributed to specific species. Rather, a threshold of sequence
identity is used to classify sequences into species before phylo-
genetic reconstruction begins.
23
This approach may lead to rapid
surveys of ecosystems if sequences attibuted to known species are
added to the dataset, or may yield estimates of biodiversity on their
own. For micro-organisms, the major advantage of such techniques
lies in the fact that unculturable species can be included.
24-26
•
Allelic variations have been included in large-scale phylogenetic
studies
(such data are normally used in population studies).
27
6. Phylogenetics Resources
Due to the highly volatile nature of websites and their diversity, it is dif-
ficult to give Internet references here. Joseph Felsenstein's site
(http://evolution.genetics.washington.edu/phylip.html) does, however,
seem to be fairly stable. It is the home of PHYLIP (PHYLogeny
Inference Package), a classic suite of phylogenetic computer programs
provided for free with the C sources. It is also a good portal to many
other theoretical and practical reference sites on phylogenetics, and
maintains a listing of available phylogenetics software.
References
1. Semple C, Steel M. (2003)
Phylogenetics
. Oxford Lecture Series in Mathematics
and Its Applications. New York, NY: Oxford University Press.
2. Swofford DL. (2003)
PAUP*. Phylogenetic Analysis Using Parsimony (*and
other Methods). Version 4.0b10
. Sunderland, MA: Sinauer Associates.
3. Meier R, Ali FB. (2005) Software review. The newest kid on the parsi-
mony block: TNT (Tree analysis using New Technology).
Syst Entomol
30
:
179-82.
4. Kumar S, Tamura K, Nei M. (2004) Mega3: integrated software for molecular
evolutionary genetics analysis and sequence alignment.
Brief Bioinform
5
:
150-63.
5. Bergsten J. (2005) A review of long-branch attraction.
Cladistics
21
:
163-93.
