{"id":869,"date":"2013-04-18T15:35:53","date_gmt":"2013-04-18T20:35:53","guid":{"rendered":"https:\/\/skepticink.com\/smilodonsretreat\/?p=869"},"modified":"2013-04-18T11:52:48","modified_gmt":"2013-04-18T16:52:48","slug":"coelacanth-genome-and-what-it-means","status":"publish","type":"post","link":"https:\/\/skepticink.com\/smilodonsretreat\/2013\/04\/18\/coelacanth-genome-and-what-it-means\/","title":{"rendered":"Coelacanth Genome and What It Means"},"content":{"rendered":"

Yesterday (April 17th), Nature published the results of the sequencing of the coelacanth genome (this is the open access paper<\/a>).<\/p>\n

\"\"<\/a>
Latimeria chalumnae model in the Oxford University Museum of Natural History
from http:\/\/en.wikipedia.org\/wiki\/File:Coelacanth1.JPG<\/figcaption><\/figure>\n

The above is a coelacanth (I just like saying it, it’s a neat word).\u00a0 The scientific name is Latimeria chalumnae<\/em> named after Marjorie Courtenay-Latimer, the curator of a small natural history museum in South Africa.\u00a0 She discovered the creature in 1938, after picking through the catch from local fisherman.<\/p>\n

At the time, it was though that the coelacanth’s had gone extinct 70 million years prior.<\/p>\n

At this point people start talking about ‘living fossils’ and crap like that.\u00a0 No, no, no.\u00a0 Evolution happens.\u00a0 It’s a fact.\u00a0 While the coelacanth’s of today are morphologically similar, they are as distinct from their ancestors of 70 millions years ago as birds are distinct from dinosaurs.<\/p>\n

The paper confirms that these animals are not exactly the same as the fossil ones.\u00a0 Of course, that being said, it is very interesting that the rate of mutation and genetic change in coelacanth’s seem to be lower than most anything else.\u00a0 The author’s suspect that because they are such deep water fishes (i.e. a very stable environment) and little or no predation or competition, that adaptation is not the massive advantage it would be in terrestrial species (for example).<\/p>\n

Biologists have thought since 1938 that the coelacanth might be the closest living relative of terrestrial species.\u00a0 They are members of Sarcopterygii<\/a>, lobe-finned fishes and all tetrapods (i.e. all vertebrate land animals) along with lungfish<\/a>.<\/p>\n

\"\"<\/a>
Figure 1: A phylogenetic tree of a broad selection of jawed vertebrates shows that lungfish, not coelacanth, is the closest relative of tetrapods.<\/figcaption><\/figure>\n

This cladogram was developed from 251 genes in all species.\u00a0 The results are statistically at 100% (except for the Armadillo\/Elephant positions at 45%). This cladogram is interesting in that the length of the lines represent (effectively) the rate of evolution (in substitutions per site).<\/p>\n

Statistically, it is clear that lungfish are the nearest living relative to terrestrial vertebrates.\u00a0 And that coelacanths are evolving slowly compared to everything else.<\/p>\n

The report describes some really interesting things about coelacanth’s.<\/p>\n

Based on the coelacanth, it is now inferred that of the 50 or so genes that are present in fishes and not present in terrestrial vertebrates, 4 were definitely lost lost in the tetrapod lineage.\u00a0 The coelacanth has them, other fishes have them, but tetrapods don’t.<\/p>\n

This next one is very interesting.\u00a0 There are sixcis-regulatory sequences in tetrapod genes (for example, a mouse) that are involved in digit formation (this is pretty simplified, so work with me).\u00a0 of those six, three are restricted to tetrapods.\u00a0 One of them, called “island 1”, is also present in the coelacanth, but not present in other fishes.<\/p>\n

What’s really interesting is that the coelacanth version was able to promote expression in the mouse.\u00a0 The conclusion is that island 1 was involved in the development of lobe-fins in fishes and then co-opted into a digit (finger) maker in tetrapods.<\/p>\n

Similar research shows how urea (pee) as a method to get rid of nitrogenous waste was a key innovation to moving from water to land.<\/p>\n

Coelacanth’s (at least the modern ones) give birth to live offspring and have large vascularised eggs.\u00a0 It was determined that the same genes from the Hox<\/em> family are in coelacanths, some sharks (but it is a pseudogene), and all tetrapods.\u00a0 Indeed, it is so highly conserved that the gene is 99% the same in all mammals.<\/p>\n

That gene from coelacanths was used in several transgenic experiments and showed high expression just outside of chick embryos.<\/p>\n

Finally, and this one is for you Michael Behe, The coelacanth lacks Immunoglobulin-M (IgM), a class of antibodies that is considered vital for adaptive immunity and is been found in every vertebrate to date.<\/p>\n

The researchers did find two IgW genes, which are also immunoglobulin genes, but only found in lungfish and cartilaginous fishes (sharks and rays).\u00a0 These IgW genes have been lost in ray-finned fishes and tetrapods.<\/p>\n

The question is, how does the coelacanth respond to new pathogens and do the IgW genes (somehow) play the same role as IgM?\u00a0 Obviously the coelacanth survives quite well, surviving a number of major extinction events.\u00a0 So Behe, perhaps you would care to explain how ID, which predicts that this can’t happen, explains how it happened.<\/p>\n

This is some fascinating research.\u00a0 These are very cool fish.\u00a0 But they are not living fossils.\u00a0 They are just as modern as humans are.\u00a0 They are just as different from their ancestors as humans are from our ancestors… except their ancestors living 70 million years ago instead of 7 million years ago.<\/p>\n","protected":false},"excerpt":{"rendered":"

Yesterday (April 17th), Nature published the results of the sequencing of the coelacanth genome (this is the open access paper).…<\/p>\n","protected":false},"author":27,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[7,24,8,28,89,6],"tags":[385,939,938,117,937,386],"class_list":["post-869","post","type-post","status-publish","format-standard","hentry","category-biology","category-creationism","category-evolution","category-genetics","category-research-2","category-science","tag-coelacanth","tag-creationism","tag-evolution","tag-genetics-2","tag-science","tag-tetrapod"],"_links":{"self":[{"href":"https:\/\/skepticink.com\/smilodonsretreat\/wp-json\/wp\/v2\/posts\/869","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/skepticink.com\/smilodonsretreat\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/skepticink.com\/smilodonsretreat\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/skepticink.com\/smilodonsretreat\/wp-json\/wp\/v2\/users\/27"}],"replies":[{"embeddable":true,"href":"https:\/\/skepticink.com\/smilodonsretreat\/wp-json\/wp\/v2\/comments?post=869"}],"version-history":[{"count":0,"href":"https:\/\/skepticink.com\/smilodonsretreat\/wp-json\/wp\/v2\/posts\/869\/revisions"}],"wp:attachment":[{"href":"https:\/\/skepticink.com\/smilodonsretreat\/wp-json\/wp\/v2\/media?parent=869"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/skepticink.com\/smilodonsretreat\/wp-json\/wp\/v2\/categories?post=869"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/skepticink.com\/smilodonsretreat\/wp-json\/wp\/v2\/tags?post=869"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}