Evidence For Great Ape Common Ancestry - The Chromosome Fusion

Part 1:

Evidence for evolution using the chromosome fusion found in humans (a.k.a the sciencey stuff)

All members of Hominidae (chimpanzees/bonobos, gorillas, humans, orangutans) have 24 pairs of chromosomes, except humans. Homo sapiens have 23 pairs, or 46 total chromosomes…so a pair of chromosomes are missing.

If an entire pair of chromosomes got lost it would have killed us, so there are only two possibilities. If we share a common ancestor with the great apes, that ancestor either had 48 or 46 chromosomes.  All the great apes have 48 so it is more likely that the common ancestor had the same. So, if it had 48, what must have happened is that one pair of chromosomes fused together.  If evolution is correct, we should be able to look at the genome and find two chromosomes that in the great apes correspond to one chromosome in humans.

So let's simplify the structure of the chromosome:

You have a centromere in the center sandwiched between 2 telomeres that are made up of many small DNA repeats running to the end of the chromosome. The section that lies right before the telomeres is a unique pattern called the pre-telomeric region.

If we type this out short hand:

(TeloPreteloCentroPreteloTelo)

The telomere at the end of DNA functions to protect the ends during replication, but the ends are very vulnerable to mutations or deletions. They protect the ends through long stretches of simple DNA sequences that are repeated many times (TTAAAGGG TTTAAGG TTAGGGG). The telomeres tend to shorten over time and are restored by an enzyme which lengthens the sequence. If the telomere becomes too short, errors in duplication can occur and lead to cancers.

So, hypothetically, if two chromosomes fused at their telomeres …what should we expect to find?

We should find at least…

1. Not one centromere but two centromeres
2. Not a centromere in the center, but two additional telomere sequences together
3. Not two pre-telomeric regions but four pre-telomeric regions  

In summary it should resemble this:

(TeloPreteloCentroPreteloTeloTeloPreteloCentroPreteloTelo)

                   

Do we have any chromosomes that look like this?

Human chromosome 2 to the rescue!

Chromosome 2 is the second largest human chromosome, spanning more than 243 million base pairs (building blocks of DNA, guanine-cytosine and adenine-thymine), it represents almost 8% of the total DNA in cells and contains at least 1,491 genes. The human chromosome 2 is accepted to be a result of an end– to–end fusion of two ancestral chromosomes back in our ape past.

So can we find all of the required parts above?

There are DNA sequences in the human chromosome 2 that are identical to sequences in the chimpanzee, but instead of being located in one chromosome the sequences for the human chromosome 2 are found in two chimpanzee chromosomes. Our chromosome 2 is made up of the chimpanzee chromosome 13 which forms the short arm (2p) and the chimpanzee chromosome 12 which forms the long arm (2q).  That is, most of the genes in the chimpanzee chromosome 13 are found in human 2p, and most of the genes in the chimpanzee chromosome 12 are in human 2q. This is also true for the more distant gorilla and orangutan.

When laid end-to-end, the chimpanzee chromosomes 12 and 13 create identical banding to the human chromosome 2 arms 2p and 2q.  

Normally a chromosome has just one centromere in the center but in humans, chromosome 2 has remnants of a second called a vestigial centromere. The active centromere of the short arm (2p) lines up with the chimp chromosome 13 centromere and the inactive long arm centromere (2q) correspond with the chimp chromosome 12 centromere. So both are found exactly where expected!

Remains of the telomere sequences from chimp chromosomes 13 and 12 are located in the center of the human chromosome 2, where the ancestral chromosomes fused.

We have even located the precise site of chromosome 13 and 12 fusion on the human chromosome 2 at base number 114, 455, 823 (give or take 15)!

The predicted sequence for the fusion is present. The chimpanzee telomere in 13 that fused to the telomere of 12 to create the full human chromosome 2 fused in a way that when we line them all up together to compare, we have to read the inactive sections in the long arm the opposite way. So this means that we not only have all the parts that correspond with the chimpanzee chromosomes 13 and 12, but they are also reversed in the 2nd part of the chromosome!

13/short arm 2p------------> <----------- 12/long arm 2q

(TeloPreteloCentroPreteloTelooleToleterPortneColeterPoleT)

What is the point of this fusion?

Having 46 chromosomes is not better than having 48 so there is no obvious reason why a designer would fuse two chromosomes in humans and leave them unfused in apes. The only advantage possible would be if the fusion of the two telomeres caused a new gene or a new activity at the fusion point.

If the fusion did give an advantage, it would come from new genes being created or by a gene’s expression being changed in some way. There are a lot of easier ways to create new genes or to change gene activities, especially for a designer. Currently, there is no evidence for an advantage for the fusing two chromosomes.

The fusion point of the two telomeres in the short arm (2p) and the long arm (2q) as well as the inactive pre-telomeric region and centromere have now built up mutations but this is even more evidence for common ancestry.  Evolution predicts that DNA collects random mutations, and that sometimes they do not do anything at all and get passed on. And even though there has been several million years of deterioration, there are sections that match even up to 90% to their corresponding sequences.

A common designer predicts the DNA mutations have a purpose … but this fusion does not give humans any advantage. This fusion is not the only difference between people and apes, as there are millions of other changes throughout the chromosomes. It is these other changes that we find our differences when we look at the great apes.

The only way this fusion makes sense is through a common ancestry with apes, where our common ancestor had 48 chromosomes and at some point after we split away from the chimpanzee the 13 and 12 chromosomes fused into our chromosome 2. This fusion doesn't “make” us human and it doesn't give us an advantage. The fusion was most likely just another mutation that happened to occur in the highly vulnerable telomere.

If you don’t accept evolution, what then is the purpose of creating a chromosome that only appears to be two ape chromosomes that fused but actually isn't  Or what’s the purpose for creating a chromosome only for humans that actually IS from the fusing of two chromosomes…but that fusion does nothing at all?

Part 2: 

Are we alone out there in the chromosome fusion world?

We had a chromosome fusion in our past, but are we the only ones? Definitely not! Chromosome fusions are absolutely found in other species! So, since we can't look at our 47 chromosome ancestor and ask how they accomplished it all…lets look at some things that are alive and well today.

Indian muntjac

A great (and cute) example are the muntjacs, also known as the Barking Deer. Most people don’t know what these animals are but they are the oldest known deer alive today, with their family dating back to possibly 35 million years. There are different subspecies that inhabit different areas including South Asia, Sri Lanka, southern China, Indonesia, Taiwan, and Japan, and it is because of these separate areas that the muntjacs have become so special.

The muntjacs, particularly the Indian muntjacs, have very interesting chromosome numbers. Remember we were just throwing a fit about a change from 48 to 46 above?…well, the female Indian muntjac is sitting at 6 chromosomes, and the males are not much better at 7 chromosomes. The females and males though have different chromosome numbers, mate and reproduce just fine. This is an example of an extreme reduction in chromosome numbers that has resulted from many fusions in several chromosomes.

Other species with variation in chromosome numbers…

§        Tufted deer – 46 F/M, 47 F/M, and 48 F/M variations - closest living relative
§ South China muntjacs – 46 F/M 

§         Myanmar and Thailand muntjacs – 14 F, 13 M

§         Anhui China muntjacs – 8 F, 9 M

§         Indian muntjacs – 6 F, 7 M

Full list: http://mbe.oxfordjournals.org/content/17/9/1326/T1.expansion.html

Tufted deer

The Indian muntjacs possess the lowest chromosome numbers of any mammal with 6 F and 7 M. The Chinese muntjacs are on the same level as us with 46 chromosomes, but variants of 47 and 48 are found in both sexes. The Indian and Chinese populations though have very different chromosome numbers, can actually produce viable offspring hybrids that will end up having 27 chromosomes total.

Based on observed numbers in muntjacs, they have a chromosome number change rate of 1.08 - 2.11 per million years! This change is among the fastest in vertebrates! Within the muntjac subfamily, the fastest evolutionary rate is found in the Myanmar and Thailand lineages (14F, 13M) in which diverged from each other in only about 0.5 million years. Much research needs to be done on the driving force for these rapid changes…but nevertheless, it's just…badass.

Also included in the group of organisms that have chromosome number variations is the swamp wallaby (10 F and 11 M), 3 species of cottontail rabbits (38, 42, and 46) and the gibbon (38, 44, 50, and 52). In a recent report on of a species of island mice, their chromosome numbers nearly cut in half in less than 500 years. That’s what a small breeding population and a fast generation time does to you!

In the end, chromosome fusions look dramatic and confusing but animals have been fusing their chromosomes probably since the beginning. We have 2 less chromosomes than the great apes, and the Indian muntjac has up to 42 chromosomes less than the Chinese muntjac (and they can probably interbreed).

Chromosome fusions are so common...is there really a need for a creator?



Sources: 
http://mbe.oxfordjournals.org/content/17/9/1326.full#xref-ref-58-1
http://evolutionarytransitions.blogspot.com/2011/10/chromosome-fun.html
http://www.evolutionpages.com/chromosome_2.htm
http://mbe.oxfordjournals.org/content/17/9/1326/T1.expansion.html

Evidence for Evolution – Development of the Mammal Kidney

Our own kidney development does not successively resemble an adult fish, amphibian, and reptile before developing mammal characteristics, but we show developmental features resembling our young ancestors.

It turns out that in utero, we as mammals develop three separate kidneys in succession, absorbing the first two before we end up with what will eventually become our adult kidney. The first two kidneys reprise embryonic kidneys of ancestral forms in the proper evolutionary order.

The video below (though in French) shows the production and absorption of the first two ancestral kidneys, as well as the development of the third kidney, the mammalian kidney.

Pronephric kidney (0- 12 seconds)

The Pronephric kidney begins to form at about three weeks in human development. It consists of an organ that in primitive, jawless vertebrates like the hagfish filters wastes from the body cavity and excretes them. The Pronephric kidney does not function in mammals because it begins to disappear shortly after the next kidney forms.

Mesonephric kidney (14 – 40 seconds)

The mesonephric kidney, instead of filtering waste from the body cavity, filters waste from the blood and excretes them through a pair tubes called mesonephric ducts. This kidney eventually will develop into the adult kidney of fish and amphibians. This kidney functions within the human embryo for a few weeks, but also disappears during the final kidney development.

Metanephric kidney (42 seconds – end)

The Metanephric kidney begins development within humans about five weeks into gestation, and consists of an organ like the mesonephric kidney that filters waste from the blood, but excretes them through a pair of new tubes, ureters. In the embryo, the wastes are excreted directly into the amniotic fluid. The Metanephric kidney is the final kidney of reptiles, birds, and mammals.

Male development

Female development

The development of three kidneys begs for explanation, and it sure does not make a lot of sense through the creationist view. The exclamation through an evolutionary view is the fact that the first two kidneys resemble, in order, those of primitive aquatic vertebrates (hagfish), and aquatic and semi aquatic vertebrates (fish and amphibians) in evolutionary order. We go through developmental stages that show organs resembling those of our ancestors because we are descended from fish and amphibians.

Macroevolution and "Kinds"

For the listeners to the Dogma Debate, this is the show on 1/2/13 and I discuss macroevolution, "kinds", and how they bridge together using the big cats and related families.

*Currently excuse typos as I typed this today! A more formal form will be coming in the near future!

Macroevolution

To show macroevolution you have to look at several different but similar groups that link together back in time. This can be an ancient reptile evolving into a mammal or an ancient monkey evolving into a human over time..but creationists misunderstand this because they want animals such as the "crocoduck".  Evolution will never produce this because crocodiles are not ancestors of ducks...they share a common ancestor. If we want to show the macroevolution of crocodiles and ducks we must start with crocodiles and move backwards until its last common ancestor with all birds. You will see the macroevolution of crocodiles to simpler reptiles, which can then be traced back forward in time to the birds to the duck. A chimpanzee didn't evolve into a human and a gecko didn't evolve into a horse. They share common ancestors.

To find macroevolution with modern animals you must find the animals that are closely related and then move backwards through the next closest families. This is what we will be doing! We will be linking the big cats to animals such as civets, which are considered different "kinds" and even showing the similarities to other groups such as mongooses, dogs, and bears.

Since we are using animals alive today...they didn't evolve into each other but instead share characteristics. As the groups become less and less related, their shared characteristics also become less...and eventually they look completely different.

Every animal we look at shared a common ancestor and have evolved into different species since that since. What we can see with modern animals is the animals that have maintained more of the common ancestors features will actually be representing the ancient populations. The older the family the less they have in common with whatever animal you are looking at.

Macroevolution does not happen genetically as a cat cannot be born from a civet, but macroevolution is represented in the shared characteristics in modern animals. In this blog we will be linking the cats all the way down the line to civets and further. 

Creationist "kind" classification

According to Answers in Genesis and Creationwiki, if animals can interbreed they are the same created "kind". They state that even non-breeding can be the same "kind", admitting that there might be blurring lines. They also state that the scientific classification of Family is very similar to a "kind", but they believe there is some intermixing of these groups (really whenever they feel like it, no structure involved) so what they consider a "kind" is very confusing.

Answers Research Journal 4 (2011): 195-201.

www.answersingenesis.org/articles/arj/v4/n1/Ark-kinds-Flood-baraminology-cognitum

Creation scientists believe that Noah fit all the animals in the Ark by bringing in original pairs of one "kind", in which can then mutate and speciate into all of the species today.  (Yes, according to AiG they accept that animals can mutate and speciate from natural selection) This means that an original "cat kind" left the ark and became all of the species we know today...interbreeding or not. It is at the point above "kind" that they believe no transitional animals exist.

They state " It is impossible to identify in such specimens many of the important features that have historically defined mammals, as soft tissue is nearly always absent. Even the skeletal remains can be fragmentary, making their placement difficult and severely limiting our understanding of how they appeared in life" (http://www.answersingenesis.org/articles/arj/v5/n1/mammalian-ark-kinds)  so I will avoid using them but fossils are EXTREMELY important in understanding how families link together. The fossils are really just too difficult for them so they ignore them completely.

Answersingensis.org quote: “The concept of kind is important for understanding how Noah fit all the animals on the Ark. If kind is at the level of family/order, there would have been plenty of room on the Ark to take two of every kind and seven of some. For example, even though many different dinosaurs have been identified, creation scientists think there are only about 50 “kinds” of dinosaurs.”

Note: Creationists may recognize the Family classification but they completely ignore the next step up, the Suborder. It is completely left out of their websites...and this category happens to be THE category that bridges the Families together! Convenient.

Offical answers in genesis list of mammalian ark kinds: http://www.answersingenesis.org/articles/arj/v5/n1/mammalian-ark-kinds

Examples of species forming a "kind" from Answers in Genesis

Able to interbreed:

• Lion + Tiger = Same "cat kind"
• Horse + Donkey = Same "horse kind"

Unable to interbreed:

• Wolf + Fox or Coyote + African wild dog = Still same "dog kind"

To keep things simple we will stick with 3 accepted "kinds", though a few others will be shown for comparison. These 3 groups are considered original ancestors and can never be linked together.

Answers in Genesis accepted "kinds" we will bridge together

Family - Felidae (fee-leh-day) - Everything they consider a cat.

• Family - Viverridae (veh-vair-eh-day) - Everything they consider a civet.

• Family - Nandiniidae (nan-din-eh-day) - The strange accepted "kind" involving only one type of civet.

These 3 kinds can not only be linked together but can also then be linked to...

• Family - Herpestidae (herp-est-eh-day) - Mongoose

• Family - Hyaenidae (hi-aye-ee-neh-day) - Hyenas

• Family - Canidae (cane-eh-day) - Dogs, wolves, and foxes

• Family - Ursidae (urse-eh-day)- Bears

• and many more we dont have time for today

Each is labeled with its common name but nothing else. This is because you aren't supposed to know where each animal fits in each "kind" until the end...Keep in mind that even if something is called a "brown civet", it doesn't always mean creationists consider it in the "civet kind"...it could be placed in the "cat kind" and even outside the original 3 "kinds". All extra information about classifications and "kinds" are at the end.

Most creationists cant even recognize where the "kinds" are even though creationists claim the lines between them are absolute and noticeable.

All you must do now is look at these animals and ask yourself is it a "cat kind", a "civet kind", an "african palm civet kind", or even if it belongs to other groups including the "mongoose kind". "bear kind" or "dog/fox kind"...so watch out for random foxes, bears, dogs, and raccoons!

By the way: These animals are not always in order of relatedness but each animal IS related to another in the group. There are also many more animals in between these showing the gradual shared characteristics, but we will only look at 8 today.



Let's start!

1.) Lion

2.) Leopard

3.) Clouded leopard

4.) Margay

5.) Spotted Linsang and Banded Linsang

6.) Spotted Gennet

7.) Indian civet 
(Remember this doesnt automatically place it in the "civet kind")

8.) Asian palm civet 
(Remember this doesnt automatically place it in the "civet kind")

9.) African palm civet 
(Remember this doesnt automatically place it in the "civet kind")

These next animals I will not name and are for the people who followed along in this blog. So what are these animals "kinds"? Are these cats? dogs/foxes? mongooses? bears? raccoons? weasels? something else?

1.)

2.)

3.)

4.)

5.)

6.)

 

Answers - Scientific classifications and creationist "kinds"

1.) Lion
Scientific Classification
Family - Felidae
Suborder- Feliformia
Order - Carnivora
Answersingensis.org & Creationwiki.org
Considered to be the "cat kind", or Felidae by most creationists.
(http://creationwiki.org/Felidae)

Comments
The lion can interbreed with the other big cats (jaguar, tiger, leopard) with varying degrees of success from infertile but living offspring to stillborn. This animal is part of the "cat kind", or the Family Felidae and is part of the cat-like Feliformia.

2.) Leopard
Scientific Classification

Family - Felidae

Suborder- Feliformia
Order - Carnivora
Answersingenesis.org & Creationwiki.org

Considered to be the "cat kind", or Felidae by most creationists.
(http://creationwiki.org/Felidae)

Comments
Can interbreed with the other big cats (jaguar, tiger, leopard) with varying degrees of success from infertile but living offspring to stillborn.  This animal is part of the "cat kind", or the Family Felidae and is part of the cat-like Feliformia.

3.) Clouded leopard
Scientific Classification

Family - Felidae

Suborder- Feliformia
Order - Carnivora
Answersingenesis.org & Creationwiki.org

Considered to be the "cat kind", or Felidae by most creationists.
(http://creationwiki.org/Felidae)

Comments
Unable to interbreed with the 4 big cats but still very cat-like. This animal is part of the "cat kind", or the Family Felidae and is part of the cat-like Feliformia.

4.) Margay
Scientific Classification

Family - Felidae

Suborder- Feliformia
Order - Carnivora
Answersingenesis.org & Creationwiki.org
Considered to be the "cat kind", or Felidae by most creationists.
(http://creationwiki.org/Felidae)

Comments
Belongs with the group including cheetahs and ocelots. Group can interbreed with varying degrees of success from infertile but living offspring to stillborn.  Group as a whole unable to reproduce with any of the big cats. This makes sense as they have been separated from the big cats for longer.  This animal is part of the "cat kind", or the Family Felidae and is part of the cat-like Feliformia.

5.) Spotted and Banded linsang
Scientific Classification
Family - Prionodontidae
Suborder - Feliformia
Order - Carnivora
Answersingenesis.org & Creationwiki.org
Not mentioned by Answers in Genesis or Creationwiki.  Not even listed on the list of families of Carnivora. (http://creationwiki.org/Carnivora). In short, completely ignored.

Comments
The linsangs represent the closest group to the Felidae. The linsangs are quite cat-like and are often mistaken to be felines. This is because they still belong to the Suborder Feliformia, meaning they are related to the cats, and have cat-like features instead of dog-like features. Is it a coincidence that the closest living relative to cats linking to the civets is not mentioned...?

6.) Spotted Genet
Scientific Classification
Family - Viverridae
Suborder - Feliformia
Order - Carnivora
Answersingenesis.org & Creationwiki.org
Considered to be the"civet kind", or Viverridae by creationists. (http://creationwiki.org/Viverridae)

Comments
Cat-like carnivore thats also placed in the suborder Feliformia with the cats and linsangs. This animal is not considered a cat anymore and creationists don't recognize the similarities linking them to the felines.

7.) Indian civet
Scientific Classification
Family - Viverridae
Suborder - Feliformia
Order - Carnivora
Answersingensis.org & Creationwiki.org
Considered to be the"civet kind", or Viverridae by creationists. (http://creationwiki.org/Viverridae)

Comments
Cat-like carnivore thats also placed in the suborder Feliformia with the cats and linsangs. This animal is not considered a cat anymore and creationists dont recognize the similarities linking them to the felines.

8.) Asian palm civet
Scientific Classification
Family - Viverridae
Suborder - Feliformia
Order - Carnivora
Answersingensis.org & Creationwiki.org
Considered to be the"civet kind", or Viverridae by creationists. (http://creationwiki.org/Viverridae)

Comments
Cat-like carnivore that's also placed in the suborder Feliformia with the cats and linsangs. This animal is not considered a cat anymore and creationists don't recognize the similarities linking them to the felines.

9.) African palm civet
Scientific Classification

Family - Nandiniidae

Suborder - Feliformia
Order - Carnivora
Answersingensis.org & Creationwiki.org
Considered seperate family "African palm civet kind", or Nandiniidae, outside of civets and cats.
(http://www.answersingenesis.org/articles/arj/v5/n1/mammalian-ark-kinds)
Link broken on creationwiki.org (http://creationwiki.org/Carnivora)

Comments
Cat-like carnivore that's also placed in the suborder Feliformia with the cats and linsangs. This animal is not considered a cat anymore and creationists don't recognize the similarities linking them to the felines.

Summarized relations:
African palm civet split away from line earliest and maintains the primitive civet look
Genet, Indian civet, and Asian palm civet ancestor split away next and then split becoming the civets
Spotted linsang broke off the line right before the main Felidae cats and is similar to the previous african palm civet
Clouded leopard broke off after the Spotted linsang and can only sometimes breed with other older cats like Ocelot and Margay.
Lions, Leopards, Jaguars, and Tigers broke off after clouded leopards and can still sometimes breed within the group

Hyenas developed from civet-like ancestors so their ancestor broke off before the Felidae and has developed into its dog-like form since.

To see how each is related to each other in detail, wikipedia is actually great!  Just look up Carnivora, Feliformia, Viverridae, Nandiniidae, and Pronodontidae.


Extra pictures
1.) Banded mongoose - Creationists ="Mongoose kind" / Science = Feliformia (cat-like carnivore)
2.) Yellow mongoose - Creationists ="Mongoose kind" / Science = Feliformia (cat-like carnivore)
3.) Fennec fox - Creationists ="Dog kind" / Science = Caniformia (dog-like carnivore)
4.) Raccoon dog - Creationists ="Dog kind" / Science = Caniformia (dog-like carnivore)
5.) Red panda - Creationists ="Red panda kind" / Science = Caniformia (dog-like carnivore)
6.) Brown hyena - Creationists ="Hyena kind"/ Science = Feliformia (cat-like carnivore)