Evolution - Resource Thread

[neo-x]

Parallel evolution of genome structure and transcriptional landscape in the Epsilonproteobacteria: A case Study

Abstract:
Background
Gene reshuffling, point mutations and horizontal gene transfer contribute to bacterial genome variation, but require the genome to rewire its transcriptional circuitry to ensure that inserted, mutated or reshuffled genes are transcribed at appropriate levels. The genomes of Epsilonproteobacteria display very low synteny, due to high levels of reshuffling and reorganisation of gene order, but still share a significant number of gene orthologs allowing comparison. Here we present the primary transcriptome of the pathogenic Epsilonproteobacterium Campylobacter jejuni, and have used this for comparative and predictive transcriptomics in the Epsilonproteobacteria.

Results
Differential RNA-sequencing using 454 sequencing technology was used to determine the primary transcriptome of C. jejuni NCTC 11168, which consists of 992 transcription start sites (TSS), which included 29 putative non-coding and stable RNAs, 266 intragenic (internal) TSS, and 206 antisense TSS. Several previously unknown features were identified in the C. jejuni transcriptional landscape, like leaderless mRNAs and potential leader peptides upstream of amino acid biosynthesis genes. A cross-species comparison of the primary transcriptomes of C. jejuni and the related Epsilonproteobacterium Helicobacter pylori highlighted a lack of conservation of operon organisation, position of intragenic and antisense promoters or leaderless mRNAs. Predictive comparisons using 40 other Epsilonproteobacterial genomes suggests that this lack of conservation of transcriptional features is common to all Epsilonproteobacterial genomes, and is associated with the absence of genome synteny in this subdivision of the Proteobacteria.

Conclusions
Both the genomes and transcriptomes of Epsilonproteobacteria are highly variable, both at the genome level by combining and division of multicistronic operons, but also on the gene level by generation or deletion of promoter sequences and 5′ untranslated regions. Regulatory features may have evolved after these species split from a common ancestor, with transcriptome rewiring compensating for changes introduced by genomic reshuffling and horizontal gene transfer.

[neo-x]

Modern speech gene in Neanderthals

Article published in Nature.

[neo-x]

Fastest Evolving Creature is 'Living Dinosaur'

Excerpt: The tuatara, Sphendon punctatus, resembles a lizard and is found only in New Zealand. It is the only surviving member of a reptilian order Sphehodontia that lived alongside early dinosaurs and separated from other reptiles 200 million years ago in the Upper Triassic period.


Tuataras are equally related to lizards and snakes. The name Tuatara derives from the Maori language and means peaks on the back.
Credit: Reb/Dreamstime

[neo-x]

On the evolution of the eye.

[neo-x]

Two From One: Evolution Of Genders From Hermaphroditic Ancestors Mapped Out

Excerpt:

Tia-Lynn Ashman, a plant evolutionary ecologist in the Department of Biological Sciences in Pitt's School of Arts and Sciences, documented early separate-sex evolution in a wild strawberry species still transitioning from hermaphroditism. These findings also apply to animals (via the unified theory) and provide the first evidence in support of the theory that the establishment of separate sexes stemmed from a genetic mutation in hermaphroditic genes that led to male and female sex chromosomes. With the ability to breed but spared the inbred defects of hermaphrodites, the separate sexes flourished.

And for those of you who are technical minded here is the full published paper from Nature.

[neo-x]

Mycobacterium Tuberculosis: Our African Follower for Over 70,000 Years


Multidrug resistant Mycobacterium Tuberculosis


Intro: Tuberculosis (TB) remains one of deadliest infectious diseases of humans, killing 50% of individuals when left untreated. Even today, TB causes 1-2 million deaths every year mainly in developing countries. Multidrug-resistance is a growing threat in the fight against the disease.

An international group of researchers led by Sebastien Gagneux from the Swiss Tropical and Public Health Institute (Swiss TPH) has now identified the origin in time and space of the disease. Using whole-genome sequencing of 259 Mycobacterium tuberculosis strains collected from different parts of the world, they determined the genetic pedigree of the deadly bugs. This genome comparison to be published September 1st in the journal Nature Genetics indicates that TB mycobacteria originated at least 70,000 years ago in Africa.

According to the study to be published September 1st in the journal Nature Genetics, TB bacteria migrated out of Africa hand-in-hand with the first anatomically modern humans.

[neo-x]

Human Sperm Gene Is 600 Million Years Old

[neo-x]

Alternative Evolution: Why Change Your Own Genes When You Can Borrow Someone Else's?

Excerpt

Now, in a paper to be published in the journal Science, University of Rochester biologist John Jaenike and colleagues document a clear example of a new mechanism for evolution. In previous well documented cases of evolution, traits that increase an animal's ability to survive and reproduce are conferred by favorable genes, which the animal passes on to its offspring. Jaenike's team has chronicled a striking example of a bacteria infecting an animal, giving the animal a reproductive advantage, and being passed from mother to children. This symbiotic relationship between host animal and bacteria gives the host animal a readymade defense against a hazard in its environment and thus has spread through the population by natural selection, the way a favorable gene would.

Microscope image of drosophila fly with parasitic nematode and its offspring dissected by University of Rochester biologist John Jaenike June 21, 2010. Jaenike finds that nematodes have a more difficult time growing and developing in black flies that are infected with a type of bacteria called Spiroplasma. Being infected with Spiroplasma is advantageous for the black flies if the nematodes reduce the survival or reproduction of the flies, and this, in turn, encourages the natural spread of Spiroplasma.
Photo credit: J. Adam Fenster, University of Rochester'

[neo-x]

ERV's in Chimps and Human DNA

Most of you reading this should know that Human DNA and Chimp DNA are very close. (roughly 98.5%, closer than horses and zebras)

And Along with this, when you match up both of our DNA you see that the ERV's (Endogenous Retro Virus') are in the exact same locations of both species.

Now ERV's are very random. VERY. they insert themselves in about 1% of the genome.

If you watch this youtube video at the top, it makes great points that it is almost impossible to have these ERV's in the same spots without evolution.

[RickD]

neo wrote:
Evolution is a fact, if you bother to read what I have posted.

Again Neo, some of what you're posting are facts. There is no proof for macro-evolution. You are just assuming macro from micro.

And, you wanted this thread to just be a reference thread for you to post links to educate others of what evolution is. Ive briefly looked at a couple of your links, and they have statements disparaging creationism and creationists. You can't even stick to your own rules you wanted for this thread. So, until I have time to go through each link you posted, to be sure they're just informational links explaining evolution, this thread is locked.
Neo, it's starting to look more like you have an agenda here, other than just trying to help people understand evolution better. I will not allow you as a very well respected member of this board, to take advantage and use that to promote an anti-creationist agenda. Don't test my patience and leniency please.

[RickD]

Thread is unlocked.

If anyone would like to discuss a link in this thread, please create a new thread with the corresponding link attached.

Viva la evolución

[neo-x]

Thanks, Rick Appreciated.

[Danieltwotwenty]

Discovering a Ring Species

I hope you don't mind Neo but someone on another thread talked about this subject and I found it very interesting, I don't think you have posted on it yet so I thought I would add it here.

The Salamander is a prime example of evolution at work, we can actually see it's living progression.

http://evolution.berkeley.edu/evolibrar ... /devitt_02

Ensatina's basic story was laid out by Robert Stebbins 30 years before Tom was born in 1977. Based on the ring-like distribution of the different forms, Robert had proposed that the species started off in Northern California and Oregon and then spread south along both sides of the Central Valley, which was too dry and hot for salamanders.
According to Robert's hypothesis, as the pioneering populations moved south, they evolved into several subspecies with new color patterns and adaptations for living in different environments. By the time they met again in Southern California as the subspecies eschscholtzii and klauberi, he argued, they had each evolved so much that they no longer interbred — even though the subspecies blended into one another around the rest of the ring. Since species are often defined by their inability to interbreed with other species, Ensatina seemed to represent the whole process of speciation — all the gradual changes that accumulate in two lineages and that wind up making them incompatible with one another.

[neo-x]

Great find! all helpful additions are welcome. Thank you, Dan.

[neo-x]

Becoming Human.org

Becoming human website is a great resource to understand human evolution over the span of the last 7 million years.