شبکه تبارزایی: تفاوت میان نسخه‌ها
محتوای حذف‌شده محتوای افزوده‌شده
Aliesmaili (بحث | مشارکت‌ها) بدون خلاصۀ ویرایش |
Aliesmaili (بحث | مشارکت‌ها) بدون خلاصۀ ویرایش |
||
| خط ۱: | خط ۱: | ||
> |
|||
{{بدون منبع}} |
|||
| ⚫ | [[شبکه]] فیلوژنتیک گرافی است که جهت نشان دادن ارتباط تکاملی بین دنباله [[نوکلئوتید]]ها، [[ژن]]ها، [[کروموزوم]]ها، [[ژنوم]]ها، یا گونه‌ها استفاده می‌شود. شبکه فیلوژنتیک وقتی مورد استفاده قرار می گیرد که شبکه ای از وقایع مانند انتقال عمومی ژن ، جفت گیری، تکثیر ژن و انقراض مورد بحث باشد. شبکه فیلوژنتیک یک مدل شدن کاملا متفاوت با درخت فیلوژنتیک هستند. به این معنی که ندهای هیبرید(ند با دو والد)به جای ندهای درختی (ند با یک والد) اضافه شده اند. |
||
<ref name="char_reticulate">{{cite journal|coauthors=Miguel Arenas, Gabriel Valiente, and David Posada|date=2008-10-15|title=Characterization of Reticulate Networks Based on the Coalescent with Recombination|journal=Mol Biol Evol|volume=25|issue=12|pages=2517–2520|doi=10.1093/molbev/msn219|pmid=18927089|last1=Arenas|first1=M|pmc=2582979}}</ref> |
|||
[[رده:ژنتیک]] |
|||
[[ca:Xarxa filogenètica]] |
[[ca:Xarxa filogenètica]] |
||
[[en:Phylogenetic network]] |
[[en:Phylogenetic network]] |
||
[[fr:Réseau phylogénétique]] |
|||
[[pt:Rede filogenética]] |
|||
| ⚫ | [[شبکه]] فیلوژنتیک گرافی است که جهت نشان دادن ارتباط تکاملی بین دنباله [[نوکلئوتید]]ها، [[ژن]]ها، [[کروموزوم]]ها، [[ژنوم]]ها، یا گونه‌ها استفاده می‌شود. شبکه فیلوژنتیک وقتی مورد استفاده قرار می گیرد که شبکه ای از وقایع مانند انتقال عمومی ژن ، جفت گیری، تکثیر ژن و انقراض مورد بحث باشد. شبکه فیلوژنتیک یک مدل شدن کاملا متفاوت با درخت فیلوژنتیک هستند. به این معنی که ندهای هیبرید(ند با دو والد)به جای ندهای درختی (ند با یک والد) اضافه شده اند. |
||
.<ref name="char_reticulate">{{cite journal|coauthors=Miguel Arenas, Gabriel Valiente, and David Posada|date=2008-10-15|title=Characterization of Reticulate Networks Based on the Coalescent with Recombination|journal=Mol Biol Evol|volume=25|issue=12|pages=2517–2520|doi=10.1093/molbev/msn219|pmid=18927089|last1=Arenas|first1=M|pmc=2582979}}</ref> [[Phylogenetic tree]]s are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with software such as [[SplitsTree]]. A standard format for representing phylogenetic networks is a variant of [[Newick format]] which is extended to support networks as well as trees.<ref name="ext_newick">{{cite journal|coauthors=Gabriel Cardona, Francesc Rosselló, and Gabriel Valiente|date=2008-12-15|title=Extended Newick: it is time for a standard representation of phylogenetic networks|journal=BMC Bioinformatics|volume=9|issue=532|doi=10.1186/1471-2105-9-532 |pmid=19077301|last1=Cardona|first1=G|pages=532|pmc=2621367}}</ref> |
|||
Many kinds and subclasses of phylogenetic networks have been defined based on the biological phenomenon they represent or which data they are built from (hybridization networks, usually built from rooted trees, recombination networks from binary sequences, [[median graph|median networks]] from a set of [[Split (phylogenetics)|split]]s, optimal realizations and reticulograms from a [[distance matrix]]), or restrictions to get computationally tractable problems (galled trees, and their generalizations level-k phylogenetic networks, tree-child or tree-sibling phylogenetic networks). |
|||
==Microevolution== |
|||
Phylogenetic trees also have trouble depicting [[microevolution]]ary events, for example the geographical distribution of muskrat or fish populations of a given species among river networks, because there is no [[species]] boundary to prevent gene flow between populations. Therefore, a more general phylogenetic network better depicts these situations.<ref>{{Cite journal | pmid = 12028728 | year = 2002 | month = Apr | author = Legendre, P; Makarenkov, V | title = Reconstruction of biogeographic and evolutionary networks using reticulograms | volume = 51 | issue = 2 | pages = 199–216 | issn = 1063-5157 | doi = 10.1080/10635150252899725 | journal = Systematic biology | postscript = <!--None-->}}</ref> |
|||
==See also== |
|||
*[[Phylogenetics]] |
|||
*[[Median graph]] |
|||
==References== |
|||
<references/> |
|||
*D. H. Huson and D. Bryant, [http://dx.doi.org/10.1093/molbev/msj030 Application of Phylogenetic Networks in Evolutionary Studies], ''Mol. Biol. Evol.'', '''23'''(2):254-267, 2006.| |
|||
*Makarenkov, V., Kevorkov, D. and Legendre, P. (2006),[http://biol10.biol.umontreal.ca/makarenv/MKL_article.pdf Phylogenetic Network Reconstruction Approaches], Applied Mycology and Biotechnology, International Elsevier Series, vol. 6. Bioinformatics, 61-97. |
|||
* D. H. Huson, R. Rupp and C. Scornavacca, [http://www.phylogenetic-networks.org/ Phylogenetic Networks], Cambridge University Press (2011). http://www.phylogenetic-networks.org/ |
|||
* {{note|ArenasEtAl10}}Arenas, M; Patricio, M; Posada, D; Valiente, G (2010) Characterization of phylogenetic networks with NetTest. [http://www.biomedcentral.com/1471-2105/11/268 ''BMC Bioinformatics'' '''11''': 268] |
|||
==Software to compute phylogenetic networks== |
|||
*[http://www.fluxus-engineering.com/sharenet.htm Network], Free Phylogenetic Network Software. Network generates evolutionary trees and networks from genetic, linguistic, and other data. |
|||
*[http://evolution.genetics.washington.edu/phylip/software.html Phylogeny programs], some of which compute phylogenetic networks |
|||
*[http://www.lirmm.fr/~gambette/PhylogeneticNetworks/show.php?keyword=programs List of programs for phylogenetic network reconstruction, evaluation, visualization, etc.] |
|||
*[[SplitsTree]] |
|||
*[[Dendroscope]] |
|||
*[http://www.trex.uqam.ca/index.php?action=hgt&project=trex Network inferring on the T-REX server] |
|||
*[http://darwin.uvigo.es TCS], Phylogenetic networks from DNA sequences or nucleotide distances using statistical parsimony. |
|||
*[http://darwin.uvigo.es NetTest], Characterization of phylogenetic networks.{{ref|ArenasEtAl10}} |
|||
==External links== |
|||
*A [http://www-ab.informatik.uni-tuebingen.de/talks/pdfs/Phylogenetic%20Networks%20-%20ISMB%202007.pdf tutorial] that reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, their definition and interpretation. |
|||
{{phylo}} |
|||
[[Category:Genetics]] |
|||
{{genetics-stub}} |
|||
[[ca:Xarxa filogenètica]] |
|||
[[fa:شبکه فیلوژنتیک]] |
|||
[[fr:Réseau phylogénétique]] |
[[fr:Réseau phylogénétique]] |
||
[[pt:Rede filogenética]] |
[[pt:Rede filogenética]] |
||
نسخهٔ ۴ ژوئن ۲۰۱۱، ساعت ۱۰:۱۴
> شبکه فیلوژنتیک گرافی است که جهت نشان دادن ارتباط تکاملی بین دنباله نوکلئوتید‌ها، ژن‌ها، کروموزوم‌ها، ژنوم‌ها، یا گونه‌ها استفاده می‌شود. شبکه فیلوژنتیک وقتی مورد استفاده قرار می گیرد که شبکه ای از وقایع مانند انتقال عمومی ژن ، جفت گیری، تکثیر ژن و انقراض مورد بحث باشد. شبکه فیلوژنتیک یک مدل شدن کاملا متفاوت با درخت فیلوژنتیک هستند. به این معنی که ندهای هیبرید(ند با دو والد)به جای ندهای درختی (ند با یک والد) اضافه شده اند.
.[۱] Phylogenetic trees are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with software such as SplitsTree. A standard format for representing phylogenetic networks is a variant of Newick format which is extended to support networks as well as trees.[۲]
Many kinds and subclasses of phylogenetic networks have been defined based on the biological phenomenon they represent or which data they are built from (hybridization networks, usually built from rooted trees, recombination networks from binary sequences, median networks from a set of splits, optimal realizations and reticulograms from a distance matrix), or restrictions to get computationally tractable problems (galled trees, and their generalizations level-k phylogenetic networks, tree-child or tree-sibling phylogenetic networks).
Microevolution
Phylogenetic trees also have trouble depicting microevolutionary events, for example the geographical distribution of muskrat or fish populations of a given species among river networks, because there is no species boundary to prevent gene flow between populations. Therefore, a more general phylogenetic network better depicts these situations.[۳]
See also
References
- ↑ Arenas, M (2008-10-15). "Characterization of Reticulate Networks Based on the Coalescent with Recombination". Mol Biol Evol. 25 (12): 2517–2520. doi:10.1093/molbev/msn219. PMC 2582979. PMID 18927089.
{{cite journal}}: Unknown parameter|coauthors=ignored (|author=suggested) (help) - ↑ Cardona, G (2008-12-15). "Extended Newick: it is time for a standard representation of phylogenetic networks". BMC Bioinformatics. 9 (532): 532. doi:10.1186/1471-2105-9-532. PMC 2621367. PMID 19077301.
{{cite journal}}: Unknown parameter|coauthors=ignored (|author=suggested) (help) - ↑ Legendre, P; Makarenkov, V (2002). "Reconstruction of biogeographic and evolutionary networks using reticulograms". Systematic biology. 51 (2): 199–216. doi:10.1080/10635150252899725. ISSN 1063-5157. PMID 12028728.
{{cite journal}}: Unknown parameter|month=ignored (help)نگهداری یادکرد:نام‌های متعدد:فهرست نویسندگان (link)
- D. H. Huson and D. Bryant, Application of Phylogenetic Networks in Evolutionary Studies, Mol. Biol. Evol., 23(2):254-267, 2006.|
- Makarenkov, V., Kevorkov, D. and Legendre, P. (2006),Phylogenetic Network Reconstruction Approaches, Applied Mycology and Biotechnology, International Elsevier Series, vol. 6. Bioinformatics, 61-97.
- D. H. Huson, R. Rupp and C. Scornavacca, Phylogenetic Networks, Cambridge University Press (2011). http://www.phylogenetic-networks.org/
- ^ Arenas, M; Patricio, M; Posada, D; Valiente, G (2010) Characterization of phylogenetic networks with NetTest. BMC Bioinformatics 11: 268
Software to compute phylogenetic networks
- Network, Free Phylogenetic Network Software. Network generates evolutionary trees and networks from genetic, linguistic, and other data.
- Phylogeny programs, some of which compute phylogenetic networks
- List of programs for phylogenetic network reconstruction, evaluation, visualization, etc.
- SplitsTree
- Dendroscope
- Network inferring on the T-REX server
- TCS, Phylogenetic networks from DNA sequences or nucleotide distances using statistical parsimony.
- NetTest, Characterization of phylogenetic networks.[۱]
External links
- A tutorial that reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, their definition and interpretation.