Rat Species Has No Y Chromosome!

Amami Spiny Rat

A team of researchers at Hokkaido University in Japan has figured out how a species of rat is able to survive and reproduce despite not having a Y chromosome. The rat species they studied was the Amami spiny rat (Tokudaia osimensis), a rodent native to the island of Amami Ōshima in southern Japan. The species, also called the Ryukyu spiny rat, is unique in that males do not have a Y chromosome and females only have one X chromosome as well. Previous attempts to study the rat have not been able to reveal how males are able to develop within the population with no Y chromosome. Typically in mammals, a gene on the Y chromosome called SRY tells the organism's body to express male genes like the SOX9 gene for testes. Not having the Y chromosome scientists were stumped at how males could develop. Lead researcher, Asato Kuroiwa, and her colleagues at Hokkaido have now discovered the answer! The secret was looking at the autosomes, non-sex chromosomes, in the rat. On chromosome 3 they found that one copy had a duplicated region next to the SOX9 gene. The duplication increases the activity of the SOX9 gene and it is able to code for testes. This duplicated region effectively replaces the SRY gene on the Y chromosome and explains how males of this species are formed. If a rat has the duplication region it acts as a proto-Y and the rat will be a male, and if the duplication region is absent, it acts as a proto-X and the rat will be a female. Further work to explore this is limited as the rat is an endangered species but the research so far has shown an amazing trait inherited by this rat population. The researchers predict the trait appeared about 2 million years ago when the Amami spiny rats diverged from their ancestors with a Y chromosome. Kuroiwa believes that a mixed population existed initially on the island but then a natural disaster like flooding or rising seas left mostly rats without the Y chromosome and over time the rats reproduced and evolved into a new species with this trait. 

Personally, this was my favorite article to read so far about genetics. I find it incredible that a species can exist without a Y chromosome and that another chromosome was able to replace its function to make males. This is a really interesting example of population evolution, genetic drift, and speciation. I hope that these rats can be studied more to learn about this unique and interesting trait. 

Does a Flies' Y Chromosome Contribute to a Shorter Life Span?

 

    In a study recently done by Doris Bachtrog, it was confirmed that the male Y chromosome in flies contributes to a shorter life span. She and her team compared the amount of heterochromatin in young and old male and female flies, and discovered that in males, the amount of heterochromatin (densely packed DNA), was far less than it was in females. The amount of heterochromatin was especially lower in the male's Y chromosome. To further test their hypothesis, they looked at the amount of heterochromatin in XXY females, XYY males, and XO males. They discovered that in the females with a Y chromosome and the males with an extra Y chromosome, the amount of heterochromatin was less, and consequently, life span was reduced. To further confirm the hypothesis that heterochromatin loss shortens life span, the XO males in the experiment lived longer than XY males. After reading this article, it makes sense that a loss of heterochromatin would contribute to aging and early death because a change or loss of heterochromatin is ultimately damaging DNA. A question I would ask would be, does this also take place in humans? Does the loss of heterochromatin, especially in the Y chromosome, shorten the lifespan of human males, like it does in male Drosophila? Women do tend to live longer than men... is this because of the men's Y chromosome? Overall, I thought the article was very informative and I especially appreciated how Bachtrog and her team did multiple studies to test their hypothesis, especially on flies with abnormal numbers of Y chromosomes. 

https://www.the-scientist.com/the-literature/male-flies-y-chromosome-may-contribute-to-earlier-deaths-67683

https://www.nature.com/articles/s12276-020-00497-4

https://www.sciencedirect.com/topics/neuroscience/heterochromatin

Medieval Crusaders Were Very Diverse Based on Recent DNA Analysis

A 13th century sea castle built by Crusaders in Sidon, Lebanon.

In a mass grave around the ruins of the Castle of St. Louis, just outside the city of Sidon, south Lebanon, the burnt skeletons of roughly 25 soldiers were found. The castle was a stronghold for the Crusaders from the 12th to 13th centuries. Based on the evidence that many suffered violent deaths and the origin of artifacts that were found – an Italian coin minted in 1245 and European belt buckles, it was concluded that these were Crusader soldiers.


During those late medieval centuries, soldiers and civilians from Europe were pouring into the Levant, a region in West Asia that borders the Mediterranean Sea. They had arrived seeking to control holy sites that were sacred among all the Abrahamic religions (Christianity, Judaism, and Islam). With their arrival, however, came the murder and displacement of native populations, most of which who were Muslim. This was the time of a series of religious wars, known collectively as the Crusades, that would span 200 years. The date on the Italian coin, the location, and radiocarbon dating of the material from the mass grave points to idea that these men were presumably soldiers of the Seventh Crusade who had died in a failed battle at Sidon in 1253. This war was led by the French king Louis IX.


Geneticist Marc Haber and his colleagues from the Wellcome Sanger Institute obtained DNA sequences from nine of the skeletons. The results of their genetic analysis were astounding. The Crusader armies were much more ethnically diverse than historians had previously believed. In fact, when they compared the DNA of the soldiers to reference databases of modern people’s DNA, they found that three were probably European (two Spaniards and one Sardinian), four were probably Lebanese, and the final two were intermediate between European and Near Eastern.


The last two individuals are evidently of mixed ancestry. When the researchers then analyzed the Y chromosome and Mitochondrial DNA sequences, they discovered that the three European and the two mixed ethnicity soldiers all belonged to Y chromosome haplogroups typical of Europe. However, the latter two had Mitochondrial DNA broadly found across both Europe and the Near East. This suggests that these men were most likely the children of European men who intermarried with local Near Eastern women, or that they were the children of parents who were of mixed ancestries themselves.


This research truly illustrates how long the Crusades lasted. For two hundred years, men from many cultures converged in one place to live, fight, and die together, united by the same religious goal. During their lives, these groups of people forged lasting connections with one another despite coming from different places. This multicultural brotherhood is evident in the genetic legacy they passed on to subsequent generations of Crusaders, born of intermarriages.

Sex Differentiation in Amami Spiny Rats

In mammals, the presence of the Y chromosome during embryonic development decides whether its offspring will be male or female. Although that is usually the case in mammals, The Amami spiny rat is something extraordinary for they lack Y chromosomes and Sry genes. The Sry gene—Sex-determining Region Y—is located on the short branch of the Y chromosome which initiates the embryonic development of males. In male Amami spiny rats, they only have one X chromosome, while females have both XX.

           

            To understand the gene expression differences in female and male, Cheryl Rosenfeld collaborated with Asato Kuroiwa from Hokkaido University Takamichi Jogahara of the Frontier Science Research Center in Japan, and Scott Givan, associate director of the MU Informatics Research Core Facility to experiment on brain activity of Amami spiny rats. They collected brain samples were collected and RNA was sequenced to compare. Male encoded for various zinc finger protein genes which could be what balanced the loss of SRY genes. The gonad then progressed as testes as a way to help program the brain to be a male. The absence of zinc finger protein led to the development of female. By turning on all the zinc finger proteins this stimulates the differentiation in the sexes.

            Animals that are not mammals have different sex-determination than humans. I think people are so focused and interested in learning about the SRY genes that people tend to overlook that there are other contributing factors in the determination of sexes. By researching more on unexplained sexes with the absences of the Y chromosome, we can fully go in depth on how gonadal and brain sexual differentiation works for different animals.

Male Sensitivity Written in the Genes

In a study, it was found that the gene responsible for activating male development is surprisingly unstable, leaving inconsistencies in the pathway to male sexuality. Normally, in human development certain genes act as master switches that ensure we are born with similar attributes such as one hand, two lungs and 10 fingers. These genes tend to highly reliable and resistant against environmental factors. However, the SRY gene on the Y chromosome has the job to set off the growth of male sex organs in human embryos but if this gene is unstable and fails to fire, it can leave a genetically male embryo to develop as a sterile female. Researchers found that the SRY is highly vulnerable, allowing any interruption to alter male sexual development, which would ultimately lead to a variety of testosterone related male attributes.

I liked this article because I’ve heard of these cases in the past where the female inherits male attributes as an embryo. To realize that it’s the SRY gene that causes this defect is interesting especially because they say it’s very sensitive to environmental factors. It would be nice to see if they would research what exactly these factors are to help prevent this defect from reoccurring in the future.

Study Reveals Results Based on Neanderthal Y Chromosome

Research at the Stanford University School of Medicine was the first ever to study a Neanderthal Y chromosome. Most investigations pertaining to our ancient relatives have aimed to show that modern human DNA is 2.5 to 4 percent Neanderthal DNA, from when modern humans and Neanderthals bred 50,000 years ago. The scientists discovered that the Neanderthal Y chromosome was not passed to humans at this period. Previously, most research from mitochondrial DNA indicates that Neanderthals and modern humans diverged anywhere from 400,000 to 800,000 years ago, but based on the Y chromosome in this study, scientists have been able to get a more specific estimate, which is around 550,000 years ago.

The team who worked on this study is not sure yet as to why there is no traces of the Neanderthal Y chromosome left in the human genome. Some theories are that the genes could have just drifted out of the gene pool by chance or that there Y chromosome is incompatible with homo sapiens genes.

I think that this particular study can be very beneficial for us to find out our ancestor's relationship with Neanderthals and how we lived, communicated, and bred with each other. Maybe it can also shed light on the how's and why's Neanderthals came to be extinct.

Fathered by the Mailman? It's Mostly an Urban Legend

There is a show on television that plays fives times a week called “Paternity Court”. It brings couples onto the show over paternity disputes. Many people find this is a source of entertainment, which however, dates back hundreds of years to Shakespeare’s time where he would write about cuckolds, often depicted wearing horns. Cuckold is defined as the husband to an adulteress. Despite all the cases shown on television and common belief, cuckolded fathers are completely blown out of proportion. Maarten H.D. Larmuseau is a geneticist leading new research on the topic at the University of Leuven in Belgium and believes it is absurd that people believe that mistaken paternity is so common. Up until fairly recently, paternity cases have been very hard to solve. There have been many legal cases pertaining to paternity that have taken place with controversial outcomes. It was discovered in the 1900’s that blood types are a distinct and clear way to determine the father of the parents. It wasn’t until the 1990’s that DNA sequencing was accepted in courts as being precise.

Lab tests began to pile up and surprisingly 10 to 30 percent of the men tested were not the biological fathers of their children. However, the problem with this is that it was not a random sampling. All of the tests came from people who already had reasonable doubt of paternity. Dr. Larmuseau and his colleagues had developed a new study in which they could get an unbiased look on paternity. Fathers pass down a nearly identical Y chromosome to their sons. Dr. Larmuseau went back and sequenced random families and their living ancestors. The result they found is that cuckoldry had a rate of less than 1 percent. Some of the countries that were tested were Spain, Italy, and Germany. There are some tribes in South America that have high cuckoldry rates. These people also have beliefs that more than one man can contribute to a child being born. These small populations are exceptions to the rule.

I have always thought that paternity disputes were a common controversy due to all of the television showing cases. Looking more closely at this topic, I now believe that most of these shows do this strictly for entertainment. Humans surprisingly have low sperm quality where there can be many defects. Half of the sperm can be duds or there can be many defects with the sperm itself such as having two heads. So a lot needs to go right in order to have a child. This would show that cuckoldry is not as common as believed. I do think that paternity tests are effective and should continue to be used in legal cases. I also believe that more research needs to be conducted on this topic to help further prove that cuckoldry is not as common as believed.

Links:

http://www.nytimes.com/2016/04/12/science/extra-marital-paternity-less-common-than-assumed-scientists-find.html?rref=collection%2Fsectioncollection%2Fscience&action=click&contentCollection=science&region=rank&module=package&version=highlights&contentPlacement=1&pgtype=sectionfront&_r=0

http://family.findlaw.com/paternity/paternity-tests-blood-tests-and-dna.html

Lack of Neanderthal Y Chromosome Genes in Humans

Figure 1. Neanderthal woman (left) and modern human (right)

It is not widely known, but modern humans carry up to 4% of Neanderthal DNA. This occurred because of interbreeding between the two species about 50,000 years ago when Homo sapiens were expanding to Eurasia. Of this 4% of DNA, there is none coming from the Neanderthal Y chromosome. Some scientists believe this merely due to chance that it was lost in the human gene pool, but new research presents a more likely option. Several of the Y chromosome genes of Neanderthals are a part of the immune system, so a woman's immune system would attack these genes because they see it as a threat because of the incompatibility. This would have also led to miscarriages between the two species. So far this is only a hypothesis, but the mother's immune system has been known to perform similar acts.

Before reading this article, I had no knowledge that a part of our DNA was that of the Neanderthal's. Though it is insignificant it is still fascinating to see that it is even present. It makes one wonder if there is other Homo DNA in our genomes. I also believe that the 4% will surely disappear completely within a few hundred years. If their hypothesis is correct, then mother immune systems will continue to eradicate any remaining Neanderthal Y chromosomes due to its incompatibilities.

Where Did Your Pet Dog Originate From?

Originally, scientists had evidence of the household dog being traced back to ancestors of the gray wolf in Europe, Siberia, the Near East, and South China.  However, recently, scientists Laura M. Shannon and Adam R. Boyko from Cornell University, as well as other international scientists, did a large study on dogs all over the world, including purebreds and village/street dogs.  They took three different types of DNA, to account for such a large and diverse population of 4,500 dogs of 161 breeds and 549 village dogs from 38 countries.  This assortment allowed "the researchers to determine which geographic groups of modern dogs were closest to ancestral populations genetically" (NY Times).  Their findings: that dogs originated and were primarily domesticated in Central Asia.  Their techniques for these findings were very similar to the techniques used in order to find out that humans originated in East Africa.    "The team analyzed DNA from all the chromosomes in the cell nucleus, from the Y chromosome specifically, found only in males, and from mitochondria, cellular energy machines outside the nucleus that are inherited from the mother" (NY Times).  Originally, they had expected their results to be "messy," however, instead all of the DNA seemed to follow the same pattern.  In their analysis, they explain the location of the origination, and also explain that the time of origination cannot be precisely dated; however, there is evidence of at least 15,000 years of the domesticated dog's existence.

I found this article very interesting, not only because I have a dog of my own, whom we've always questioned her mix of breeds, but also because within the first week of class we discussed the different domestication of animals and where they originated from.  This discussion included the domestication of dogs and we spoke about how they originated in Europe, and now, just within a few weeks to a month, our whole perspective is changed.