Sydney
Marks
Biogeography of Salamanders: Why the Eastern United States is a Hotspot for Salamander Biodiversity
Amphibians class
Fall 2023
The biogeographical patterns of animals often offer a unique window into their complex dynamics of ancestry, evolution, distribution, and adaptation. This is no different for the order Urodela, or the salamanders. Many biologists, herpetologists, and natives of the eastern United States are aware of the biodiversity hotspot for salamanders that is the Appalachian Mountains, but few understand why this is the case. This review paper is seeking to understand where salamanders originated, how they came to occupy the eastern United States, and why the Appalachians have the highest percentage of endemic salamanders in the world (Vieites et al., 2007).
To begin answering these questions, we must look to the past by means of the fossil record. The earliest known fossils of salamander-like, or salamandroid, organisms were found in Asia. In 2012, Gao et al. discovered a fossil from Beiyanerpeton jianpingensis in western Liaoning Province, China that dated back to the Late Jurassic, or roughly 164 million years ago (MYA). At the time, it was the earliest known record of the suborder Salamandroidea (Gao et al., 2012). This finding increased the range of the clade by ~40 million years. Many years later, in 2020, Schoch et al. discovered a fossil of Triassurus sixtelae, in Kyrgyzstan that dates back to the Late Triassic, between 250 to 200 MYA (Schoch et al., 2020; Vieites et al., 2007).
Regardless of when the first salamandroids evolved, these findings place the origin of salamanders in Asia. But how and when did they arrive in North America? While there have been studies on the evolution and dispersal of salamanders in both Eurasia and the Americas, there is a need to study specifically when, how, and why, salamanders arrived in North America. From fossils, we know salamanders were present in Asia in the Late Triassic, and present in North America by the Late Jurassic, indicating their migration between 200 and 144 MYA (Schoch et al., 2020; Vietites et al., 2007). This does not account for why they migrated between continents and how they did so, although studies focusing on later migration patterns shines some light on this. This is backed up by the finding of Anuran and Caudatan remains in a microfossil bonebed located in southern Montana, dating the presence of salamanders in North America as far back as the Early Cretaceous, around 144 MYA (Oreska et al., 2013).
Now we have followed the salamanders from Eurasia and placed them in North America by the end of the Jurassic, but this is not the end of the salamander migration story. The story is more complex than one would expect for such small creatures. One family of salamanders, the Plethodontids, contains about 380 species; 98% of them are found in the Americas, while the other 2% are in Europe and Korea (Kaplan, 2007). Genetic studies on these salamanders have concluded that in the Late Cretaceous, a Plethodontid species made its way back through Europe and Asia (Vieites et al., 2007; Kaplan, 2007). This migration led to a speciation event which formed Hydromantes and Karsenia in Asia. From there, Karsenia continued to Europe (Vieites et al., 2007; Kaplan, 2007). This migration event explains the distribution of Plethodontidae being concentrated in North America with two lineages in Eurasia.
This revelation leads to the question: where and how did the Plethodontids evolve? This family is unique in that all known members are lungless, providing us with a major trait to follow. Currently, the most accepted theory is that ecological factors present in North America, before the current Appalachian topography formed, favored salamander species with a narrower body plan and shorter snout (Ruben & Boucot, 1989). This in turn reduced the effectiveness of buccal respiration, favoring cutaneous respiration in salamanders.
The topography and climate most likely also played a role in the evolution of lungless Plethodontids. Ruben and Boucot claim the region during the Mesozoic was a flat, featureless plane of low elevation; however, this is debated as there is also evidence that the Appalachian Mountains have been towering over this region for 300 million years (1989; Clark, 2005; Jess et al., 2022). For this theory, we will use evidence that Appalachia was flat during this time, with no peaks allowing for mountainous streams. However, later, as the terrain became more mountainous, cold mountain streams formed, and the climate changed along with it, from tropical to subtropical (Ruben & Boucot, 1989). The proto-plethodontids that were present, took advantage of these habitats, as the cold water held a high amount of dissolved oxygen, and were able to easily adapt and diversify in these new niches (Ruben & Boucot, 1989).
The less accepted theory on Plethodontid evolution states that these salamanders originated in the streams of the Appalachians, (again, whether during the Mesozoic or not is still debated regarding the terrain), rather than the lungless trait occurring initially. In fast moving, mountain streams, having reduced or even absent lungs prevents a small-bodied tetrapod from floating away (Dunn et al., 1926). Due to the high levels of dissolved oxygen in the cold water, Dunn et al. had explained that this environmental trait made it more likely for lunglessness to adapt.
Regardless of how the Plethodontids adapted their lungless trait, it is finally time to answer our final question: why are the Appalachian Mountains in the eastern United States such a hotspot for salamander biodiversity? To fully answer, we must understand the climate, history, and geography of the region. In the past, what is now North America has been subjected to periods of intense cooling and warming. During the cool periods, or ice ages, huge glacial sheets would form and cover much of the northern half of the continent. As these ice sheets advanced, it would force the fauna south (Clark, 2005). Once the sheets retreated, the animals would have no need to return north and therefore colonized the lower half of the continent. This occurred as early as the Pleistocene, 11,000 years ago (Clark, 2005).
There were also periods of global warming which had the opposite effect; as late as the Early Jurassic, a warm temperate climate expanded northward, forcing many taxa to follow their optimum temperature (Vieites et al., 2007). During these periods, the Bering Land Bridge was above sea level, allowing for a safe passage between continents for salamanders (Vieites et al., 2007). This is one of the ways in which it is hypothesized how salamanders reached the Americas as well as how members of Plethodontidae returned to Eurasia. In addition to warmer climates pushing salamanders north, the warm climate also favored diversification (Vieites et al., 2007).
The salamanders may also have been able to greatly adapt and diversify within this region due to its long, yet stable, history. Some studies claim that the Appalachian Mountains are around 480 to 270 million years old, meaning they were “new” when the supercontinent Gondwana was present (Clark, 2005). More recently, their modern topography began taking shape during the Cenozoic, as late as 65 MYA (Ruben & Boucot, 1989). Due to this relatively stable habitat, the salamanders were able to adapt easily and fill available niches, rather than needing to migrate to new areas for safety or food (Marlon et al., 2017). This is confirmed in a study of dispersal events of salamanders between two regions of the Interior Highlands within Arkansas and Missouri. They used genetic data to develop a phylogeny that shows the disperal of various Plethodontid species between 33 and 2 MYA, indicating the climate has been stable for enough time for these salamanders to continue to adapt and disperse across the region (Martin et al., 2016).
Lastly, mountain ranges themselves are known pockets for high biodiversity. The series of peaks and valleys tend to isolate populations while reducing migration, due to both steep slopes as well as temperature fluctuations going up and down the peaks (Milanovich et al., 2010). However, these temperature fluctuations have also proven to be beneficial. During times of rapid climatic change, mountain dwelling organisms can travel shorter distances up and down the peaks to find their optimum temperature, allowing for more time to diversify in a smaller geographical area (Perrigo et al., 2019). Isolated peaks of mountains also act like islands, allowing for greater genetic diversification if populations are isolated (Perrigo et al., 2019). Lastly, mountains are one of the more difficult habitats for humans to alter. Due to the steep slopes, often rugged terrain, and many creeks, it creates a barrier for logging trucks to access much of the mountain range and prevents agriculture from clearing the land (Perrigo et al., 2019). All these factors have played a role in allowing salamanders to greatly diversify in the Appalachians.
Whether it was due to the climate, history, or geography of the region, or all three, the Plethodontids’ first split occurred within the Late Cretaceous, leading to a great amount of speciation and diversification of salamanders within the Appalachian Mountains (Vieites et al., 2007). Over time, these salamanders, as well as species within other families, have become one of the dominant organisms of the eastern United States.
Unit 4 Genetics
Chapter 7 Genes and Traits
Highschool Biology Workbook
Fall 2022
In chapter one, you learned about DNA and how it makes up genes and chromosomes. In this unit, we’ll be going more in depth into the structures that make up our genetic code, how genetic code is passed down, and how genetic variations within populations are created and influenced.
To review, the most basic unit of genetics, or the study of genes and traits, is DNA. DNA, which is found in almost every cell, contains the genetic instructions that control every heritable characteristic of an organism. Heritable means able to be passed down from parents to offspring; without this ability, traits of organisms would be impossible to study and predict. The instructions found in DNA code for obvious traits, like fur color, as well as how the organism develops, functions, grows, and reproduces. Traits seen in one organism are more likely to be seen in their offspring.
DNA itself is a long molecule made up of the sugar deoxyribose, a phosphate molecule, and nitrogen base pairs. These three smaller molecules are bonded in such a way that make the DNA “ladder” twist, forming a shape known as a double helix.
A single continuous DNA strand makes up a chromosome. Humans have 46 chromosomes; 23 from their mother, and 23 from their father. All the DNA in an organism, species, or cell is known as a genome. For one person, their 46 chromosomes make up their genome. The 23 chromosomes from mom can be paired with the 23 chromosomes from dad to form 23 pairs of homologous chromosomes. They are homologous, or the same in relation or structure, based on the size of the chromosome and the genes found on the chromosome.
A gene is a segment of DNA that codes for specific proteins and contains instructions for specific functions. Think back to Chapter 1; we learned how proteins are put together based on the sequence of nitrogen bases within a gene and how proteins allow the organism to function. In a pair of homologous chromosomes, both chromosomes hold the same genes that code for the same types of traits. However, each gene may not code for the same version of that trait.
One trait can have many varieties. Take eye color for example. There is only one gene that codes for eye color, but there are multiple varieties of eye color: brown, blue, and green. The different varieties of genes are known as alleles; some traits have many different alleles while others just have one or two. Each homologous chromosome, one from each parent, holds the same gene but may hold different alleles. This is how variation occurs.
In order to determine which allele will be expressed, we look at the dominance of the traits. Traits can be either dominant or recessive. A dominant trait, represented with a capital letter, will have dominance over a recessive trait, represented with a lowercase letter. For eye color, brown eyes are dominant over blue and green eyes. Since there are two alleles coding for eye color, both alleles, one from each parent, must be for blue or green eyes in order for blue or green eyes to be expressed in the individual. There are many other patterns of inheritance, or the passing of genetic information from parents to offspring, which you’ll learn about later.
Because of this, the physical expression of the trait does not always accurately reflect the alleles that lead to that trait. A person with brown eyes may be carrying a blue- or green-eyed trait. This is the difference between phenotype and genotype. The phenotype is the observable characteristics of an individual, while the genotype is made up of the alleles that lead to those observable traits.
The person with brown eyes (which is their phenotype) has the genotype Bb, meaning one dominant allele and one recessive allele. The brown-eyed trait (B) is dominant over the blue-eyed trait (b), giving them brown eyes. We can also say they are heterozygous, where hetero- means different; their two alleles for eye color are different and therefore, must be Bb. A blue-eyed person will be homozygous, specifically homozygous recessive, where homo- means the same. Since blue eyes are recessive, we know their genotype for eye color is bb. Traits can also be homozygous dominant (BB), so just knowing an individual’s genotype for a particular trait is homozygous does not confirm the specific alleles, but rather eliminants heterozygous alleles.
Lion Experiment
Origins of Complex Life class
Spring 2024
As an immortal, eccentric billionaire who is obsessed with lions and evolutionary transitions in individuality, it is only reasonable to wish to evolve whole lion prides into groups with reproductive division of labor. To increase my odds of evolving more than one pride with reproductive division of labor, the experiment will be conducted many times over rather than just once, as will be described below.
I would start by acquiring a pride of female lions (Panthera leo) from the wild and isolating them in a large, secure Hunger Games-style arena. The pride must be composed of at least five females of differing ages, preferably from a naturally larger pride, around 15 individuals. The arena will be a perfect replica of African lions’ natural habitat and include a range of microhabitats from riverbanks to shrubland (Palmer et al., 2023). In true Hunger Games fashion, the arena will be completely under my control including hidden cameras and speakers and have the capability to release large prey animals seemingly out of thin air, as well as be able to safely cage lions and remove them from the environment.
This pride will live together until the natural deaths of all but three females. This will allow them time to acclimate to living within only female prides and help teach the younger lions proper social behaviors as well as how to hunt. During this time, a male lion must be genetically engineered to only release sperm that will develop into female lion cubs. The male will be released near the females and will only be allowed to mate with the fittest, and likely eldest, female. Since female lions are polyestrous and ovulation begins after copulation, timing of this event is not significant (Lion Reproduction and Offspring, 2020). Once mated, the male is safely removed from the environment.
Since female lions naturally only have around four cubs every year or every two years, as they nurse and care for the cubs, the female should either be genetically altered to have more than four cubs at a time, or many females should mate after the initial dominant female mates (Palmer et al., 2023). This should be chosen on a pride-by-pride basis, depending on the pride dynamics. Prides that do have a single, more-dominant female can have many females mating while those that do not will have a genetically engineered female. Artificially providing the pride with resources during her gestation will prevent premature termination, as well as selecting for genes that help maintain larger litters. In prides where many females are mating, it will be staggered with the same male. Across years, the male will change to increase genetic diversity within the pride.
During the female’s gestation period, she will be safely tranquilized and removed from the environment so that each embryo can be genetically engineered to have a specific set of traits and genes that are specially designed for a specific role within the pride, as well as sterilizing all but the largest embryo. Specific roles within lion prides include hunting cooperatively, defending their kills, defending their territory, and raising the young (Palmer et al., 2023). For example, one will be faster than the others to be a better hunter, another may be larger than the others to better defend their territory, and others may be able to produce more milk to feed the cubs. This, factors that predispose individuals for specific tasks, is one factor that favors division of labor (Rueffler et al., 2012). The female will give birth to around four lion cubs (as natural females do) each genetically modified for a specific task within the pride which also reduces their ability at other tasks (Palmer et al., 2023). Division of labor is only favored when this individual specialization has a benefit to efficiency thus increasing fitness (Bourke, 2011).
Female lions naturally care for each other’s cubs, especially when the cubs are closely related to themselves (Palmer et al., 2023). This shows kin selection since natural prides are made up of mostly closely related female individuals (Krofel & Packer, 2023). Additionally, males within natural lion prides are often ousted from their prides by new incoming males. These new males will kill all the young cubs and evict all adolescents, as they do not carry his genes. This infanticide reduces the relatedness of pride members since most females will stay within their home pride, and increasing the number of males fathering female members will increase genetic variety and decrease relatedness (Palmer et al., 2023). Artificially preventing new males from joining will keep the relatedness of females high, encouraging additional kin selection.
Once the cubs are adolescents, they will be particularly equipped for one or two tasks in the pride, rather than all of them. This will encourage the beginning of a division of labor, as if all the individuals do not work together, the pride will be worse off. Accelerating performance functions is another factor that favors division of labor; as fitness is increased it creates tradeoffs which encourages further cooperation (Rueffler et al., 2012).
Cooperation is not possible without coordination which is not possible without communication (Cooper et al., 2021). Lions communicate through roars; they can be displays of territoriality meant to challenge other prides nearby, used to recruit nearby pride-mates for defense, and even as warning calls to defend against lone males or to pride-mates that may be away from the rest of the group (Palmer et al., 2023). This level of communication is beneficial when attempting to evolve lion prides to have a division of labor.
Any individuals observed to not be altruistic, or cooperating for the benefit of the group, over time will be safely and permanently removed from the experiment, helping to avoid cheaters. While lions naturally form prides to help one another, this is unlikely (Palmer et al., 2023). To encourage the division of labor amongst the adolescents, any behavior pertaining to their specialized task will be rewarded with extra food for the pride. Cooperative interactions between individuals within a group is one of the factors that favors division of labor (Rueffler et al., 2012).
This will be repeated, with the dominant female only allowed to mate, for as many generations as it takes to reach 25 individuals in the pride. Natural prides will at most contain 30 individuals before the pride splits into two as the intra-pride competition (competition within the pride) will be higher than the inter-pride competition (competition between prides) (Palmer et al., 2023).
Once the pride exceeds 25 individuals within a natural savanna habitat, the habitat will need to be artificially altered. The natural habitat will be replicated based on a real savanna, such as rainfall, the movement of prey animals, and the weather conditions. The amount of resources present within a habitat largely determines the size and structure of cooperative groups (Mbizah et al., 2020). If the resources, such as prey animals, water sources, and denning sites, are balanced so that the pride is better off together, they will remain together and cooperative. This means presenting the pride with enough resources near them so they are not pressured to split and leave one another, but not such available resources that they do not need to work together to hunt or defend their territory (Packer & Ruttan, 1988). Researchers have also noticed that lions tend to establish smaller prides when prey is abundant for this same reason (Mbizah et al., 2020).
Artificially replicating roars from nearby “outside prides” will also be an important factor to keeping the pride together as it surpasses 30 individuals (Packer & Ruttan, 1988). This can be done by playing the roars of unknown individuals through the hidden speakers within the artificial landscape. The unique number of roars from the “outside pride” will need to constantly outnumber the number of individuals within the experimental pride, as this will lead these members to think they are being outcompeted with. Prides will attempt to overtake the territory and/or females of another pride if they greatly outnumber that other pride (Palmer et al., 2023). Enforcing this idea of being outnumbered may help the pride remain together in large numbers.
There are some constraints to lions living in large groups, notably competition and disease transmission. With artificially controlling the number of large prey animals, intra-pride competition will be less than inter-pride competition, making the benefits outweigh the costs when it comes to staying with the pride. As for disease transmission, all individuals can be vaccinated to prevent detrimental effects of living in close quarters with many other individuals. While the environment is completely artificial, microorganisms and parasites are still required to have a fully functioning ecosystem but should not prevent the purpose of the experiment.
As the pride continues to grow, the cubs should naturally begin to evolve and grow better suited for their specific task. If not, the genes from previous individuals can be edited into their genomes to artificially make this happen. As the generations progress, the individuals should naturally adapt to this new division of labor as the social strategies of lions have been observed to be highly plastic and capable of adapting to maximize fitness and survivability (Palmer et al., 2023). This will be important as the requirement of cooperation for survival allows division of labor to function.
In the beginning, this experimental protocol satisfies the B, bottleneck, criterion by starting off with only a few wild lions, initially reducing the amount of genetic material (Godfrey-Smith, 2012). Additionally, for a female lion to start her own pride after the division of reproductive labor has been established, she will either need to wait for the dominant, reproductive female to die or leave to start her own pride, as the dominant individual(s) will not allow her to reproduce otherwise. Based on this, the experimental pride has an intermediate level of bottlenecking (Figure 1).
The initial single reproductive female within a pride satisfies the G, germ line, criterion, but eventually many females will be needed as female lions do not naturally have litters more than once a year or once every two years (Godfrey-Smith, 2012; Palmer et al., 2023). Regardless, only the dominant, and eldest, female(s) will be allowed to mate. Based on this, there is a high level of germ line distinction (Figure 1).
L
Experimental Lion Pride (.5, 1, 1)
astly, each member having their own specialized task within the pride satisfies the I, integration, criterion (Godfrey-Smith, 2012). The labor of maintaining a pride is divided between all individuals, who all depend on one another for survival. Those outside of this cooperative are not part of the collection and thus do not receive the benefits those part of the group receive. Based on this, there is a high level of integration within the pride (Figure 1).
Figure 1: Collective reproduction graph for the experimental lion pride showing where they fall with the B, G, and I criteria as explained by Peter Godfrey-Smith in Darwinian Individuals (Godfrey-Smith, 2012). Bottleneck is intermediate because new lion prides begin with one individual lion, rather than one individual cell. Germ line is high because there is a sharp distinction established early in life as to who will become a reproductive individual. Integration is high because each member of the pride has their own specialized role creating dependency on the other members of the pride.
In this way, all individuals will show the golden rule of altruism by only providing benefits to those who will benefit others (Goodman, 2014). Additionally, this methodology encourages kin selection within the pride. While kin selection lowers an individual’s chance of reproducing and passing on their genes, it increases the chance of their kin to do so, which is beneficial for the individual since they share genes with one another (Hughes et al., 2008).
In other words, the individual’s fitness is included within the fitness of their kin. While an individual is capable of reproducing on her own, few of her offspring will survive long enough to reproduce. If this same individual uses her energy to help raise her kins’ offspring, through any of the main tasks within a pride, those offspring will have a better chance of survival and reproduction, passing on more genes in the end than she would be able to do while alone. While these methods show aspects of cheater avoidance and group selection, kin selection is the primary selection scenario.
In the end, division of labor will pay off in this scheme because the large pride is better off together than within small prides or alone. For lions, the environmental reasoning is paramount; within African savanna biomes, resources are patchy and spread unevenly over the environment. This is the leading theory as to why lions, out of all the large felids, formed social groups when others did not (Mbizah et al., 2020). Since resources are spread out, individuals will be better off working with others to acquire food and defend territory, making cooperation essential. Generally, the larger the group, the more access to resources as more members can defend a larger territory (Mbizah et al., 2020).
As for the genetics, the altruist alleles benefit because without the group, genes would be passed on less than they would be within a group. The cooperative group allows for more offspring to be produced and raised, leading to higher relatedness, increased kin selection, and better coordination (Liu et al., 2021).