Thursday, November 4, 2010

We Are All Mutants: Measurement Of Mutation Rate In Humans By Direct Sequencing

ScienceDaily (Sep. 1, 2009) - An international team of 16 scientists today reports the first direct measurement of the general rate of genetic mutation at individual DNA letters in humans. The team sequenced the same piece of DNA - 10,000,000 or so letters or 'nucleotides' from the Y chromosome - from two men separated by 13 generations, and counted the number of differences. Among all these nucleotides, they found only four mutations.

Remarkably, the new research, recently published in Current Biology, shows that these early estimates were spot on - in total, we all carry 100-200 new mutations in our DNA. This is equivalent to one mutation in each 15 to 30 million nucleotides. Fortunately, most of these are harmless and have no apparent effect on our health or appearance.

"The amount of data we generated would have been unimaginable just a few years ago," says Dr Yali Xue from the Wellcome Trust Sanger Institute and one of the project's leaders. "But finding this tiny number of mutations was more difficult than finding an ant's egg in the emperor's rice store."

Team member Qiuju Wang recruited a family from China who had lived in the same village for centuries. The team studied two distant male-line relatives - separated by thirteen generations - whose common ancestor lived two hundred years ago.

To establish the rate of mutation, the team examined an area of the Y chromosome. The Y chromosome is unique in that, apart from rare mutations, it is passed unchanged from father to son; so mutations accumulate slowly over the generations.

Despite many generations of separation, researchers found only 12 differences among all the DNA letters examined. The two Y chromosomes were still identical at 10,149,073 of the 10,149,085 letters examined. Of the 12 differences, eight had arisen in the cell lines used for the work. Only four were true mutations that had occurred naturally through the generations. ...

Understanding mutation rates is key to many aspects of human evolution and medical research: mutation is the ultimate source of all our genetic variation and provides a molecular clock for measuring evolutionary timescales. ...

via We Are All Mutants: Measurement Of Mutation Rate In Humans By Direct Sequencing.

We do change over time, and the rate of change of our species is now roughly known, thanks to genetic analysis.  You have between 100 and 200 mutations, sequences of DNA that match neither your mother nor  your father.  This is like one tick of the evolutionary clock.  If the average human lives 30 years per generation, then the genus Homo appeared 83,000 generations ago and Homo sapiens appeared 5,300 generations ago. So, one might figure it takes only 11.6 million random mutations when combined with environmental selection pressures to get from "Homo antecessor" ( an extinct human species or subspecies ) to ourselves, Homo sapiens.

I can hear them now saying, "These ancestors were still human looking, this is not Macro evolution."

If you follow the fossil record back, not just 1.2 million years, but 65 million years, we grow tails.  Due to random genetic mutations which drive evolution, tails still appear from time to time in modern humans, just to remind us that the genes are still there.

Anyway, keep going back in time and we get smaller.  Slowly, slowly, we reach the point where the first primates appeared... 60 million years ago.

drawing of Smilodectes as it may have appearedThe genus Altiatlasius (left), whose bones are found at that time period, looked a bit like a lemur.

The first primates evolved from other mammals. About 200 million years ago we have one of the oldest mammals, Morganucodon watsoni, (right) a one inch long weasel-like creature.

The transition from reptile to mammal is well documented in the fossil record:
"The following fossils are just a sampling. ... Reptiles have one bone in the middle ear and several bones in the lower jaw. Mammals have three bones in the middle ear and only one bone in the lower jaw. These species show transitional jaw-ear arrangements (Hunt 1997; White 2002b). The sequence shows transitional stages in other features, too, such as skull, vertebrae, ribs, and toes.

  1. Sphenacodon (late Pennsylvanian to early Permian, about 270 million years ago (Mya)). Lower jaw is made of multiple bones; the jaw hinge is fully reptilian. No eardrum.

  2. Biarmosuchia (late Permian). One of the earliest therapsids. Jaw hinge is more mammalian. Upper jaw is fixed. Hindlimbs are more upright.

  3. Procynosuchus (latest Permian). A primitive cynodont, a group of mammal-like therapsids. Most of the lower jaw bones are grouped in a small complex near the jaw hinge.

  4. Thrinaxodon (early Triassic). A more advanced cynodont. An eardrum has developed in the lower jaw, allowing it to hear airborne sound. Its quadrate and articular jaw bones could vibrate freely, allowing them to function for sound transmission while still functioning as jaw bones. All four legs are fully upright.

  5. Probainognathus (mid-Triassic, about 235 Mya). It has two jaw joints: mammalian and reptilian (White 2002a).

  6. Diarthrognathus (early Jurassic, 209 Mya). An advanced cynodont. It still has a double jaw joint, but the reptilian joint functions almost entirely for hearing.

  7. Morganucodon (early Jurassic, about 220 Mya). It still has a remnant of the reptilian jaw joint (Kermack et al. 1981).

  8. Hadrocodium (early Jurassic). Its middle ear bones have moved from the jaw to the cranium (Luo et al. 2001; White 2002b).

via TalkOrigins

By about 350 million years ago the land had had plants and insects for about 50 million years available to any brave fish that could jump out of the water for a bit.

Tetrapods evolved from lobe-finned fishes between 380 and 365 million years ago.  The Tiktaalik, for example, lived about 375 million years ago it is a transition between fish and early tetrapods.

Currently the first verified land animal was a one-centimeter myriapod dated at 428 million years ago.

Fish themselves first show up about 510 million years ago. It took about 135 million years of mutations before they adapted to spending time on land to find food and safety from predator fish.

There is so much evidence. Despite the frequent small upsets and shifts in the exact timings, despite the fact that most dead animals do not leave fossils, we currently have a remarkably consistent picture of the evolution of life on earth from many different sources around the world.

Does it matter if you believe in evolution or creation? Usually not. I'm still trying to figure out how this great knowledge of evolution can be put to practical day to day use.

I'm glad I know it... but I don't see how knowing this makes me better or worse off than someone who believes we were created from nothing by a magical bearded light being.


Cheng said...

You're probably worse off Xeno.
Creationists KNOW that they have eternal happiness to look forward to in the afterlife with the "magical bearded light being", where as evolutionists KNOW there is only death.

It may give the evolutionists amongst us a greater zest for life though!

Xeno said...

I'm thinking a world full of people who believe death is the end will work a little harder on regenerative medicine and the ability to upload my entire mind to an equivalent and upgradable device that lasts thousands of years.

Cheng said...

Sadly, the majority of the world's population is still banking on the former option of eternal afterlife. I read somewhere that 98% of americans (a statistic that probably applies pretty much anywhere) believe in some sort of god.
The other 2% will be working their socks off to create the technology you envisage....or die trying :(