tag:blogger.com,1999:blog-8386055846297828307.post3856500632191574986..comments2024-03-28T07:34:49.133+01:00Comments on The Genealogical World of Phylogenetic Networks: How do we interpret a rooted haplotype network?Unknownnoreply@blogger.comBlogger7125tag:blogger.com,1999:blog-8386055846297828307.post-47718351905161249612021-03-26T04:57:13.071+01:002021-03-26T04:57:13.071+01:00Hello, How can I interpret my haplotype network us...Hello, How can I interpret my haplotype network using haplogroup,shapeayodeleoguntuasehttps://www.blogger.com/profile/04185775037325613419noreply@blogger.comtag:blogger.com,1999:blog-8386055846297828307.post-65487363507046483862019-10-29T16:08:22.776+01:002019-10-29T16:08:22.776+01:00Hi Dechung,
This seems to be a semantic question....Hi Dechung,<br /><br />This seems to be a semantic question. <br /><br />No matter whether we use a single or several combined genes, we would call it a haplotype network. When showing several networks based on different genes (let's say <i>trnL-trnF</i> and <i>matK</i>, two classic plant barcodes) and they are different, I'd call them by a combined name such as "trnLF haplotype" "matK haplotype".<br /><br />The only tricky thing are multi-copy nuclear genes, because here you may have more than one variant per haplome. For ITS, people have hence started to use 'ribotype' as a replacement (which is not a good pick, but more and more widespread).<br /><br />But the network doesn't inform the haplotypes. You can establish haplotypes without any inference (tree or network) by just grouping the sequence variants by similarity, the most strict cut-off would be: all sequences that are identical form one haplotype.<br /><br />After we grouped our haplotypes, we use the network to establish (evolutionary) links between them. It's the other way round: <br />the haplotypes inform the network.<br /><br />Hope this answers your question, <br />Cheers GuidoDas Grimmhttps://www.blogger.com/profile/13213125622809796109noreply@blogger.comtag:blogger.com,1999:blog-8386055846297828307.post-20218525751186829112019-10-29T16:01:23.116+01:002019-10-29T16:01:23.116+01:00This comment has been removed by the author.Das Grimmhttps://www.blogger.com/profile/13213125622809796109noreply@blogger.comtag:blogger.com,1999:blog-8386055846297828307.post-19643986979332328632019-10-29T08:25:26.167+01:002019-10-29T08:25:26.167+01:00Hello, David. Can we say we can construct haplotyp...Hello, David. Can we say we can construct haplotype network of specific gene to inform the haplotypes of the gene??<br /><br />Dechung LimAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-8386055846297828307.post-52757536668689538702014-11-14T03:30:02.637+01:002014-11-14T03:30:02.637+01:00Thank you for your answer.
I think that the use o...Thank you for your answer. <br />I think that the use of rooted networks can become a very important tool. <br />In rooted networks, I have found several situations in which a sequence of haplotypes with a relationship of ancestrality occurs in a direction north / south, or west / east. It is suggestive that this pattern could indicates a route of colonization. I think that the alternative explanations are more unlikely. <br />It is intuitive to me that a spatial sequence is also a time sequence, because the plants take time to colonize new areas. However, I can not prove this and, surely, colonization of different areas may occur almost simultaneously.<br />Unhappily, I have found very few examples of this approach in the literature, and I dont found any experimental confirmation.<br /><br />João Paulo Fonseca<br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-8386055846297828307.post-43576721857166764142014-09-12T14:20:25.505+02:002014-09-12T14:20:25.505+02:00Dear João, I presume that by "gradient of anc...Dear João, I presume that by "gradient of ancestry" you are referring to a lineage of hypothesized ancestors in the graph matching a geographical gradient. If, so then one possible explanation for the pattern would be that the geographic gradient represents a time sequence, in which case the root might be inferable. However, this form of inference relies on substituting space for time (ie. a spatial sequence represents a time sequence), and it does not always lead to the correct conclusion (ie. there might be other explanations). /DavidDavid Morrisonhttps://www.blogger.com/profile/05469392205239443608noreply@blogger.comtag:blogger.com,1999:blog-8386055846297828307.post-42421989973207781842014-09-12T02:50:06.549+02:002014-09-12T02:50:06.549+02:00Thanks for your text.I would like to ask a questio...Thanks for your text.I would like to ask a question: <br />If a gradient of ancestry corresponds to a geographic direction, can we infer the origin of a lineage?<br /><br />João Paulo Fonseca (Portugal). Phd. ISPA-IU (jfonseca@ispa.pt)Anonymousnoreply@blogger.com