California Mountain Lions

        Puma concolor, or the mountain lion goes by many names. Puma, cougar, catamount and panther are just a few. While the mountain lion goes by many names, it's genetic code remains relatively the same. Although the mountain are not in direct danger of extinction, their population is decreasing at a high rate. The mountain lion itself is what is known as a indicator species. This means that the speices can be used as a great reference on how an environemnt is doing, and how well the environement has remained connected. The large cat also acts as an umbrella species. These "umbrella species" are extremely important biologically and ecologically. Umbrella species are usually greatly monitored and protected beceause in protecting them, many other species become protected indirectly. Due to this, conservation techniques have been put in place in many areas where the puma exist. However in a recent study to observe how geography changes genes, researchers stumbled upon something rather interesting.
      431 mountain lions from various location were used in a study to collect data about the levels of genetic diversity among the species. In order to accomplish this 12 microsatellites loci were analyzed in each cat. After looking closely at the data gathered, it was found that each cat had distinct genetic  subdivisions that were specific to the region they were from. It was found that cats from coastal regions displayed more heterozygosity than the cats sampled from inland areas. Heterozygosity is important in population genetics, as the heterozygote advantage plays a large role in species survival. Scientists came to the conclusion that geographic barriers like the Los Angeles Basin, the San Fransisco Bay and the Central Valley turned out to be enormous barriers to natural gene flow of the species. The disruption of gene flow can result in many things particularly different allele frequencies among the species. Metapopulations in Southern California have exhibited normal gene flow but recently human development has increased how hard it is for populations to travel, which in turn decreased gene flow. With this, human development has displaced many of these large cats leading them to environments their ancestors did not inhabit before, or into urban areas. These new environments present challenges for the species, one which they may not actually be able to survive.
    In essence this study provided conservationists with a ton of new data to analyze, think about and act upon in the coming years. Most importantly, it displayed an important concept. Conservation genetics, and genetic preservation. This study indicates that not every case can be treated the same way. Each population of these cougars has different genetic subdivisions, and faces different enviroenmtal cahllenges. From this work, scientists hope to come up with movement corridors in unpopulated regions, to help the pumas travel from area to area, and increase biological diversity.  Landscape-level conservation is not only crucial to the survival of this species, but crucial in helping the species become more heterozygotic.
      This study was awesome because it really shows the connectedness of species between each other. In protecting the mountain lion, you protect the big horn sheep, which in turns help stabilize plant growth, and the list goes on and on about the connectedness of the mountain lion to almost everything it interacts with. Population genetics are studied extensively with animal populations, and I hope to work with wildlife one day, so reading these articles get me excited for the future. Hopefully measures can be put in place so that these animals can travel more freely and give themselves a fighting chance against their ever-changing environment.


https://link.springer.com/article/10.1023/A:1024069014911

https://www.sciencedaily.com/releases/2018/12/181221142514.htm

https://www.scientificamerican.com/article/highways-fragment-southern-california-mountain-lion-gene-pool/
       

Cats Domesticated Humans

        The house cat is the most popular pet in the world. Today's house cat is only domesticated species in the family Felidae. This carnivorous mammal comes in 60+ recognized breeds from designer breeds, like the Toyger, to regular mixed breeds like the domestic short-hair. At one point, these animals were bred for milk, fur, labor, or meat. However, it has been long believed by scholars that around 3,600 years ago Egyptians started to keep them as pets. However, new research in the last 10 years has given us a more knowledge on our relationship with cats, and how they evolved with humans.
        Researchers examined 1,000 wild and domestic cats to help determine which subspecies of wildcat gave rise to today's domestic cat. Wildcats are very territorial and typically defend their homes for life. This lead researchers to believe that although the genetic composition of the cats would vary from region to region, in each particular region the genetic composition would be fairly stable over time.  In analyzing their collected data, they were able to determine that the DNA clustered into 5 groups, Middle Eastern Wildcat, Central Asian Wildcat, South African wildcat, European wildcat, Chinese Mountain cat, and Sand Wildcat.  They noticed that wildcats from each of these groups can all have their ancestry traced back to the same region, today's Middle East, and that all are descendants from the wildcat F.s. lybica. In comparing the mitochondrial DNA, and DNA microsatelites of the domestic cat to the wildcat data, it became clear the domestication occurred again in the Middle East. Leading researchers to now believe that domestication actually occurred in the Fertile Crescent and not Egypt.
                                                          (Scottish wildcat)

        With new genetic evidence pointing to the Fertile Crescent as the sight of domestication, another break-through discovery was made in cat domestication. In 2004, on the island Cyprus, archeologist uncovered human remains buried next to a cat. After dating the evidence, it was determined to be 9,500 years old, roughly 6,000 years before the Egyptian domestication theory. This finding is extremely crucial in dating the domestication of house cats because wildcats are not native to the island Cyprus, meaning the only way a feline could have gotten there is if it was transported there by boat.  This suggests again, that people of the Middle East had been keeping cats long before Egyptians, and were even transporting them on boats.
       The newest theory of cat domestication revolves around the Middle East and the Fertile Crescent. It is believed that maybe humans did not originally intend to domesticate cats at all, and the felines were exploiting our newly found agriculture to survive. Wildcats are strictly carnivourous animals, so crops do not appeal to them, however, the new rodents that came along with farming did. Wildcats could take advantage of the field new mice and rodents that came along with humans newest agriculture trend. When thinking about the domestication of the house cat, it's quite comical that essentially cats have not served much purpose to humans. They do not listen to commands. Do not carry out specific tasks for humans unless it benefits them. And rarely do they want to be held captive inside a house. Even the house cats of today still display these qualities.
        All of this evidence comes down to one new theory. Humans never domesticated cats. Cats just chose to live near us because we provided them food. In today's day we still provide them with food but also with shelter, and in typical cat fashion, they even have us picking up their feces and throwing it out for them. It seems like cats really have domesticated us in a way that their wildcat ancestors could only dream.
       I love cats, and thought this article was great because it gave insight into a thought that is commonly misinterpreted. Humans never really domesticated cats with a particular purpose.  It is remarkable to think that we now take care of our house cats because their ancestors decided to feed on the rodents from ancient crops. When thinking of dogs, horses, chickens, or most domesticated species the animal typically serves a purpose. However, without the mice for cats to eat in the Fertile Crescent, cats would probably not be house pets today, and most definitely not the most popular one.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5790555/
https://science.sciencemag.org/content/317/5837/519
https://books.google.com/books?hl=en&lr=&id=GgUwg6gU7n4C&oi=fnd&pg=PA179&dq=cat+domestication&ots=V07J3Eg67f&sig=MeFR_gQpnNMzWgwk9Ggbmk16uTo#v=onepage&q=cat%20domestication&f=false

Adaptations of the Rock Pocket Mouse

         Throughout the the southwest United States and Mexico, a tiny rodent, called the Rock Pocket Mouse, lives in the rocky deserts. Light brown sand covers most of the desert, and has for quite some time. About 1.7 million years ago, volcanic eruptions spewed lava into the desert causing portions of the land to be fractured with dark black colors. For the pocket mice, this was a huge ecological change, which in turn resulted in a rather fascinating genetic phenomenon.
         Currently, two forms of pocket mice exist. One dark colored, and one light colored. From an biological standpoint it might be rather easy to see why the two coat colors exist. Mammalian and avian predators have perfectly modeled out what is known as natural selection. Natural selection is a process in which organisms most fit for their environment survive and produce offspring. Having this knowledge, it makes sense that the mice living in the brown sand environment have a brown coat, and the mice living in the dark lava colored sand have a dark black coat. Their coat colors clearly emphasize the importance of a tactic animals use crypsis, which is essentially camouflage. Natural selection has driven these animals to evolve based on their environment being more brown, or more black. Now, these mice have different phenotypes for coat color, but the story becomes more interesting when we start to analyze the genetic information about the mice coat colors.
       Researchers have worked diligently in recent years to try to find correlation between ecological and environmental changes, and changes in animal genetics. However, in order to do this, the biologist working on the project must have a solid understanding of genetic information of the animal they are working on, AND then compare it to how the environment has newly changed that genetic information. Luckily for the researchers in the rock pocket mice, many studies have been done on the pigmentation of laboratory mice, which lended a hand in the study done on the rock pocket mice. Due to the pocket mice wild nature, they are hard to breed in captivity. This made crossing them with each other almost impossible. Instead, researchers studied the current mice comparing them with lab mice and came up with some interesting results.
     In the lava dwelling mice, four mutations were found in the MC1R gene. The MC1R plays a crucial role in normal pigmentation. From the information gathered, it was concluded that the dark colored coat was more dominant that the light colored coat, which is consistent with the observations seen on laboratory mice. All mice with that were homozygous dominant, or heterozygous dominant showed a dark coat. The change of just 4 nucleotides seem to have caused the drastic shift from a light brown, to a dark almost black coat color. These studies leave scientist to even more questions. In the dark colored sand, approximately 9% of mice are born with a light coat, and 89% are born with a dark coat. Since selection is driving these phenotypic changes, this makes perfect sense. But does this mean that all the mice in light-colored sand area have only recessive genotypes? In the future, researches hope to answer two questions that have arisen: 1.) Has the color change in mice been driven by a single nucleotide, and the other 3  have just come along for the ride? *or perhaps* 2.) It takes multiple nucleotide variants to produce the colored phenotype of the rock pocket mouse?
     This was an awesome article to read up on because it really shows how LITERALLY one nucleotide could potentially change the whole future of a species. If what the study suggests is true, imagine if the mutation of the MC1R never occurred, and all the mice stayed light colored. The species would probably not even be able to continue on because the light colored mice would be eaten by prey. It's amazing to think that one nucleotide changed the whole course of the rock pocket mouse's future.

https://www.pnas.org/content/100/9/5268
https://www.ncbi.nlm.nih.gov/pubmed/12704245
https://learn.genetics.utah.edu/content/selection/comparative
https://www.biointeractive.org/classroom-resources/making-fittest-natural-selection-and-adaptation

Hibernating Bears and their Gene Expression

                The average black bear hibernates for 5-7 months, depending on their location. During this period, many physiological changes occur within the animal's body. Their body temperatures lower, they stop producing waste, metabolic rates severely decline and they even stop eating for these long periods. In order to prepare for this hibernation period, bears will eat upwards of 20,000 calories a day in the summer months, adding around 4-5 inches of fat for insulation under their coat. By the time the hibernation period is over, they will have lost almost 20% of their body fat, and again be ravenously hungry. While it is still being studied whether or not these changes come from environmental factors, like scarcity of food, or if they come from different hormones being released, it is evident that bears express different genes during winter hibernation, and the summer active periods.

              In a recent study of the America Black Bear, 245 genes in the heart, and 319 genes in the liver identified to be expressed differently during the summer and winter months. Of these a select 24 genes had significantly elevated expression. It was found that these genes mainly were involved in the lipid catabolism, and protein synthesis. During hibernation, these processes are linked to important things like keeping muscles from experiencing atrophy, and keeping the heart strong as the animals slows down its metabolic processes. A bear in hibernation will severely slow down it's heart rate. These different gene expressions can help keep the bear's heart strong, and at the same time allow the bear to walk when it is time to come out of the den. After all, wouldn't it be hard to stand up after taking a nap for 6 months? The expression of these genes help contribute to the muscle preservation of the bear. 

          As the bear sleeps through the winter, another phenomena occurs, thanks to genes being expressed differently. At the mRNA and protein level, a slow shift from glucose catabolism to glucose synthesis occurs in the liver. This allows the bear to have energy, which will be used to power the brain and other tissue that is being starved.  While the bears hibernate and slowly stop breaking down glucose for cellular respiration, they are able to reduce their metabolic rate by nearly 50%. 

          

        I have always love animals, but bears are truly incredible, and have always interested me. It is a wonder that they can accomplish the feat of going months and months on end without eating or defecating. I first started looking into this topic about a year ago, and have been interested ever since. There are a few researchers who say that bears never actually enter a true "hibernation" but rather a state of torpor. To myself, it doesn't matter how they classify the bear's winter nap. It is interesting to see what the expression of genes can do to keep a bear alive through the winter. When reading this article, I felt like I was reading science fiction. The bear had the ability to make it's heart slow down, keep itself from losing muscle, and even make itself stop producing waste.

https://www.sciencedirect.com/science/article/abs/pii/S1043276009001568
https://bear.org/do-black-bears-hibernate/
https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-171