Title Genetic Consequences of a Severe Population Bottleneck in the Guadalupe Fur Seal (Arctocephalus townsendi)
Background The paper titled “the Genetic Consequences of a Severe Population Bottleneck in the Guadalupe Fur Seal (Arctocephalus townsendi)” describes how genetic diversity is influenced by the sharp decline of the Guadalupe Fur Seal population in the 1700 and 1800s and the slow recovery of its population numbers. In the 1800s the Guadalupe Fur seal declined to an extent to be considered in a population bottleneck; which is an event where a population goes through a restriction point similar to squeezing water through a narrow pipe. This event can occur naturally to different animal populations due to numerous reasons such as disease outbreak or natural disasters. In the case of the Guadalupe Fur Seal however, it was human interest that drove them to the brink of extinction.
The Guadalupe fur seal population was once copious along the Pacific coast of the Americas, however, they faced a grave threat in the late 1700s and early 1800s. Commercial sealers, looking to make money off of seal skins and seal oil, persistently hunted them until they were nearly wiped out. In fact, they were believed to have gone extinct in the early 19th century until an exploration team discovered a small breeding group on Isla de Guadalupe. This resurrection was short lived, as a series of interest groups including private and museum collectors quickly massacred the population. This near complete extinction in population size is what scientists call a bottleneck. Picture, if you would, a library with shelves full of books, each embodying a different genetic trait in a population. Before human interest in the Guadalupe fur seal, they had a hearty genetic library, with many slightly different copies of each book, providing resilience and adaptability to changing conditions. Nonetheless, when the hunters dramatically decreased the Guadalupe fur seal population, the library lost most of its copies of each book. In other words, genes are like different subjects and alleles are like textbooks. So when experiencing dramatic population decline, you can be left with only a ‘Precalculus : mathematics for calculus’ textbook, which would not be adaptable to a geometry class. Hence the seal would die.
Central Question The central purpose of the paper is to discern the impact of this population bottleneck on the seal’s genetic diversity.
Evidence The authors inspected a specific section of the seals’ DNA and estimated the genetic diversity by sequencing and counting at the number of distinct alleles in the population. The scientists compared the genetic diversity from ancient Guadalupe fur seal bones, which records the genetic diversity before the human hunting, to that of present day seals corresponding to the genetic diversity after the population bottleneck. As seen in the figure (below) there were seven distinct modern alleles found (bold), and they were clustered into two to three different groups of the phylogenetic tree. However, it’s obvious from the figure that the diversity of the pre bottleneck seals (unbolded) was much greater than what is seen in today’s seals.
Implication Shockingly, the study also revealed through genetic analysis that before the human period of hunting them, the Guadalupe fur seal population was prosperous, and even expanding during certain periods. This suggests that they were once a robust and healthy population. However, today, the recovery of these seals depends less on their own merit, and more on the luck that their own lack of genetic variation doesn’t lead to their extinction. This could lead to further experimentation, possibly discerning to what extent the drop in genetic diversity affects Guadalupe fur seals’ expected lifespan or something along those lines.
Further reading For further self study, there is a very similar study titled the ‘Impact of population bottlenecks on genetic variation and the importance of life-history; a case study of the northern elephant seal’ which follows a similar narrative history to the Guadalupe fur seal; a case of near extinction due to direct human action (Hoelzel, 1999). This paper is a further exploration of the topics covered in this paper, just viewed through a different lens with a different perspective. Also linked is a youtube video from SeaWorld San Diego which shows the rehabilitated Guadalupe fur seal that is set to be sent back into the wild.
Reference HOELZEL, A.R. (1999), Impact of population bottlenecks on genetic variation and the importance of life-history; a case study of the northern elephant seal. Biological Journal of the Linnean Society, 68: 23-39. https://doi.org/10.1111/j.1095-8312.1999.tb01156.x
Weber DS, Stewart BS, Lehman N. Genetic consequences of a severe population bottleneck in the Guadalupe fur seal (Arctocephalus townsendi). The Journal of heredity. 2004;95(2):144-153. doi:10.1093/jhered/esh018
Recent research sheds new light on this ancient puzzle, revealing intriguing insights into the timing and circumstances of mammoth extinction, especially focusing on the remarkable tale of the Wrangel Island mammoths, an island in the Arctic Ocean near Northern Siberia.
In the Late Pleistocene there was rapid, worldwide decline of megafauna, partially due to changes in climate. This caused mammoths to spread off into isolated populations off the coasts of Siberia and Alaska using the Bering land bridge. Rising sea levels trapped mammoths on Wrangel island 6,000 years ago, before eventually the mammoths went extinct 4,000 years ago. The cause of mammoth extinction is still under debate though, some think it might be caused by population bottlenecks, local extinction/recolonization events. Sampling bias could have also played a role in having inaccurate timing of extinction, which makes interpretations of the causes of extinction challenging (Dehasque et al., 2021; Guthrie, 2004; Nystrom et al., 2010).
Main Questions
The paper primarily focused on understanding the extinction dynamics of wooly mammoths in different regions in Northern Siberia, particularly exploring the timing of regional extinctions and the genetic relationships among various mammoth populations. They collected mammoth specimens in each region and collected 720 specimens from all regions. They specifically looked at the timing of extinctions between different regions, the genetic relatedness of different mammoth populations with a focus on the mammoths from Wrangel island.
Evidence
Phylogenetic analysis, which is the study of evolutionary history between a set of species, has provided crucial insights into the evolutionary relationships among mammoth populations. By examining ancient DNA extracted from mammoth remains, researchers have found that the mammoths from Eurasia exhibited a well-supported genetic distinction from the mammoths from North America, with exceptions of a few North American samples grouping within the Eurasian clade (Fig. 2). In contrast, the Holocene Wrangel Island mammoths (indicated by “WRA” in the sample names in Figure 2) formed a monophyletic clade within the Eurasian clade (the top portion of the two major clades). Note that the colors of the terminal taxa correspond to the color coding used in the regions of the sampling map (Figure 1) and the Wrangel Island population is coded the same as the eastern population (red). Surprisingly, the mainland mammoths from the central and western regions showed a closer genetic relationship to the Wrangel Island population compared to those from the geographically closer eastern region or North America. More specifically, the mainland mammoths from New Siberian Islands (the central region) and Taimyr Peninsula (the western region) are most closely related to the Wrangel Island mammoths However, the Wrangel Island mammoths showed poorly resolved mitogenome relationships within the monophyletic clade, suggesting rapid diversification within this isolated population.
In the study, genomic material was collected from mammoth remains using ancient DNA sequencing techniques, allowing scientists to analyze the genetic makeup. They determined the mean substitution rate of the mitogenomes, which is the genetic material found within a mitochondria. The substitution rate was found at 1.57 * 10^-8 site year ^-1, meaning on average, there are approximately 1.57 mutations occurring per site (position in the DNA sequence) per year. These estimates made by the authors are used to calibrate the phylogenetic tree.
Using radiocarbon dating records of the 720 samples from all four geographic regions of Northern Siberia, they estimated the time of appearance and disappearance, regional extinction, of mammoth populations, along with other methods to put together estimations of events that happened in chronological order.
The paper mentioned that the extinction dynamics of mammoths reveal a complex interaction of environmental factors, and genetic processes. The gradual decline of mammoth populations, coupled with shifts in climate and habitat, contributed to their eventual demise. The Wrangel Island mammoths persisted long after mammoths on the mainland had gone extinct. They survived into the late Holocene, making them some of the last surviving mammoths on Earth. Cut off from mainland Siberia by rising sea levels, the mammoths on Wrangel Island became a distinct genetic population with limited gene flow from mainland mammoths.
The study provides a possible insight to the timing of regional mammoth extinctions, showing that the process was not uniform across different geographic regions. By analyzing Bayesian age models,which can be used to estimate the timing of mammoth extinctions and colonization events, the researchers suggest that climate-driven vegetation changes likely played a role in the mammoth’s extinctions. They also go in depth about the temporal gap between the extinction of mammoths in the eastern Russia mainland population and the reappearance on Wrangel island. Through carbon dating, the researchers found that the mammoths vanished from the eastern region almost three thousand years before their presence was detected on Wrangel Island during the early Holocene. The researchers concluded that this is compatible with the phylogenetic analysis where the closest group to the Wrangel Island mammoth was not the geographically close eastern region, suggesting that the mammoth eastern region went extinct first and the mammoth from the central or western regions colonized the island subsequently. This gap suggests a complex migratory pattern of colonization process, again possibly influenced by environmental changes and geographical barriers.
The paper suggested that over time Wrangel Island mammoths likely underwent genetic adaptations to cope with their island habitat’s specific challenges. These adaptations could include changes in body size, metabolism, and behavior to optimize survival in the island’s harsh Arctic environment. The limited availability of food resources on Wrangel Island may have influenced the dietary habits and foraging behavior of mammoths. They might have relied on specialized feeding strategies to exploit available vegetation or adapted to subsist on a narrower range of food sources compared to their mainland counterparts. The small population size of Wrangel Island mammoths and the limited genetic diversity resulting from isolation may have made them more vulnerable to environmental changes and genetic drift. Population bottlenecks and inbreeding could have affected their genetic health and viability over time.
Further Topics
Future studies investigating genomic data from Wrangel Island mammoths can shed light on the genetic mechanisms underlying their unique morphological and physiological traits. By examining population dynamics and genetic diversity over time, researchers may uncover the intricate interaction between climate variability and mammoth demographics. Comparative analyses with mainland mammoth populations could further explain the differential impacts of climate change on mammoth populations across diverse geographic regions. Through paleoecological reconstructions, researchers can reconstruct past environments on Wrangel Island, providing valuable insights into ecosystem dynamics and the cascading effects of climate change on biotic communities. This line of questioning could reveal a critical look inside at the resilience of mammoth populations in the face of climatic challenges and shed light on their evolutionary responses to isolated island ecosystems.
Your Questions
It would be interesting to see how the dating methods used in the study compare to other dating techniques. Or what future research directions could further explain the evolutionary history of mammoths and their interactions with changing environments. How does this study contribute to our broader understanding of Pleistocene extinction and the ecological consequences that came with it. I would like to learn more about the specific genetic differences between Wrangel Island mammoths and mainland mammoths and how the extinction dynamics varied across different regions. I would also like to compare the evolution and extinction of the mammoths in this study to mammoths from other places.
References
Dehasque, M., Pečnerová, P., Muller, H., Tikhonov, A., Nikolskiy, P., Tsigankova, V.I., Danilov, G.K., Díez-del-Molino, D., Vartanyan, S., Dalén, L. and Lister, A.M., 2021. Combining Bayesian age models and genetics to investigate population dynamics and extinction of the last mammoths in northern Siberia. Quaternary Science Reviews, 259, p.106913.
Guthrie, R. D. (2013). Frozen fauna of the mammoth steppe: the story of Blue Babe. University of Chicago Press.
Nyström, V., Dalén, L., Vartanyan, S., Lidén, K., Ryman, N., & Angerbjörn, A. (2010). Temporal genetic change in the last remaining population of woolly mammoth. Proceedings of the Royal Society B: Biological Sciences, 277(1692), 2331-2337.
The unassuming fruit fly is to many people merely a nuisance; however, it has led to breakthroughs so significant to human life it has won numerous Nobel prizes (McKie). Drosophila melanogaster is a species of fly that belongs to the genus Drosophila. These flies have a short lifespan, mature very quickly, and have a genetic make-up that is very similar to humans. Because of these traits the fruit fly is known as a model organism, used in empirical studies to help us understand a wide range of biological phenomena. One such study was conducted in 2022 by researchers from Cornell University and the University of Nebraska, and could possibly provide insight into the factors of divergent intrasexual and intersexual selection (Jin et al., 2022).
Sexual selection is an important evolutionary factor because it can produce new genetic variation, and can be just as crucial to an organism’s success as natural selection. It can be further broken down into intrasexual and intersexual selection. The former pertains to competition between individual organisms of the same sex, with the goal of accessing a mate of the other sex. The latter is closely intertwined, and refers to whom members of differing sexes choose to mate with. Together, these selection factors can work together to create a more genetically diverse population.
Going further, when a population becomes separated, whether it is by physical separation (geographic isolation), different times of reproduction (temporal isolation), or different behaviors (behavioral isolation) it can become reproductively isolated. This isolation can happen relatively quickly, due to sexual selection creating expeditious changes in mating preferences. But what changes are being made, and why do they matter? These are the questions being pursued with fruit flies (Jin et al. 2022).
What’s more important? Behavior or Chemical Traits?
The researchers in this study attempted to determine what traits were under divergent selection by using strains of fruit flies that modeled larger populations that had asymmetrical reproductive isolation. Reproductive isolation is the process of preventing matings between individuals from different populations. This can be achieved by a number of different mechanisms such as geographic isolation, behavioral isolation, or physiological differences. You may ask, how can reproductive isolation be asymmetrical? This occurs when one strain mates without preference, while the other strain has preference for partners of the same strain only. Examining asymmetrical isolation can help researchers pinpoint which traits, whether it is chemical or behavioral, makes the difference in preference.
In this case, Drosophila melanogaster populations from around the world are reproductively isolated by differing behavioral and chemical traits. This is a result of divergent selection, which occurred when two strains of fruit flies were separated geographically. Because of this separation they began to develop different diverse behaviors and chemical signals. Knowing this, the goal of the research was to determine “which specific male traits are females selecting, and are these traits under divergent sexual selection?” (Jin et al., 2022).
Evidence
The two strains that were used in this research study were denoted as M-type and Z-type, and were from different territories. The Z-type stayed in the ancestral territory of southern Africa. The M-type strains were those that had left Africa 10,000 to 15,000 years ago to locations in Europe and North America. With a physical separation of this nature the two strains became geographically isolated. Courtship traits and cuticular hydrocarbons (CHCs) have been under divergent selection during this separation, creating diversity in both Z-type and M-type strains. Geographic isolation over a time period this large for a species with a relatively quick lifespan resulted in an incompatibility to mate between strains (Jin et al., 2022). The reproductive isolation between these strains was asymmetric, meaning that M-type females would mate with both M- and Z-type males, while Z-type females preferred to mate with only Z-type males.
To examine whether divergent selection is currently ongoing, researchers examined cuticular hydrocarbons, for differences in compound abundance. Cuticles are present in many insects and are a main component of the exoskeleton. CHCs are thought to have waterproofing functions, but to also act as a type of communication signal (Menzel et al., 2017). By determining the abundance of different compounds found on the CHCs of different strains, researchers can narrow in on commonalities and differences. These differences could play a role in why one strain may have successful copulation amongst members of the same strain, and unsuccessful encounters with a different strain.
They also sorted mating behaviors they put into the categories of “separate, engaging, singing, singing-2, scissoring, circling, attempted copulation, and copulating” (Jin et al., 2022). It was established that courtship initiation would be recorded after non “separate” behaviors occurred. In other words, if the fly’s were interacting in any capacity it was considered a courtship behavior.
Once data was compiled, it was statistically analyzed to examine courtship behavior and plasticity. They concluded that courtship of Z-type and M-type males is significantly different, and that geographic strains are reproductively isolated. In addition, they found that male courtship behavior and cuticular hydrocarbons are plastic. A plastic trait is one that has the ability to change when presented with different conditions in the environment. In other words, the CHCs and courtship behavior changed in different settings. One example of behavior that Z-type strains used and was not found in M-type flies was scissoring, which is quick opening and closing of the wings. They also observed Z-type males spending less time singing on average (Jin et al., 2022). CHC compound amounts varied when males were presented with different strains of females, displaying that they are plastic and could play a role in courtship.
The conclusion of reproductive isolation arose from M-type males and Z-type females producing larvae much less than crosses between Z-type males and Z-type females (Jin et al., 2022). This exhibits that if two individuals cannot produce viable offspring with one another they have become reproductively isolated.
Now What?
While the results of the study did show divergent selection and asymmetrical reproductive isolation, more experiments need to be conducted to determine the role of traits under selection. For example, it was unclear whether African male behaviors (Z-type) had developed different behaviors. It was also expressed several times that sample sizes were too low, resulting in an inability to determine if some male strains were significantly different from one another (Jin et al., 2022). It may be beneficial to revisit these crosses with a larger sample size to increase the confidence of any significant results.
It was determined that four out of the five examined CHC compounds had differences among strains, but the role of these differences was not explained. Furthermore, without knowing what job the traits or compounds in the CHCs do, further exploration into the significance of different CHC compounds is needed to figure out their role in the courtship puzzle. This experiment could be easily replicated with greater sample sizes, and further emphasis on cuticular hydrocarbon analysis, to corroborate the results of Jin et al,. 2022 and increase the importance Drosophila melanogaster has in modern evolutionary biology.
Further Reading
Dean M Castillo, Daniel A Barbash, Moving Speciation Genetics Forward: Modern Techniques Build on Foundational Studies in Drosophila, Genetics, Volume 207, Issue 3, 1 November 2017, Pages 825–842, https://doi.org/10.1534/genetics.116.187120
This journal article from 2017 provides a larger perspective on the discoveries that can be achieved with the genus drosophila. It was compiled by two of the authors from this research article; Dean Castillo and Daniel Barbash.
Mirzoyan Z, Sollazzo M, Allocca M, Valenza AM, Grifoni D and Bellosta P (2019) Drosophila melanogaster: A Model Organism to Study Cancer. Front. Genet. 10:51. doi: 10.3389/fgene.2019.00051
This review article provides a comprehensive list of the cancer research that Drosophila melanogaster has played a part in. Similar development of cancer in flies and humans are described. The relevance of fruit flies in scientific research for human disease is dramatic.
References
Jin, B., Barbash, D. A., & Castillo, D. M. (2022). Divergent selection on behavioural and chemical traits between reproductively isolated populations of Drosophila melanogaster. Journal of Evolutionary Biology, 35, 693 – 707. https://doi.org/10.1111/jeb.14007
Leslie, M. (2020, April 2). Proteins that sense light also sense taste, at least in fruit flies. Science. Retrieved March 4, 2023, from http://dx.doi.org/10.1126/science.abc0403
Markow, T. A. (2015, June 4). The natural history of model organisms: The secret lives of drosophila flies. eLife. Retrieved March 23, 2023, from http://dx.doi.org/10.7554/eLife.06793
Menzel Florian, Blaimer Bonnie B., & Schmitt Thomas (2017). How do cuticular hydrocarbons evolve? Physiological constraints and climatic and biotic selection pressures act on a complex functional traitProc. R. Soc. B.284: 20161727. 20161727. Retrieved April 14th, 2023, from http://doi.org/10.1098/rspb.2016.1727
This article covers the 2020 study by Ulaski, Finkle and Westley on the direction and magnitude of natural selection of body size among age-classes of seaward-migrating sockeye salmon.
“Bigger Isn’t Always Better”
The idea that “bigger is better” is a prevalent one in biology. Body size has a significant impact on fitness, the ability of organisms to survive and reproduce, across all branches of life. In wolves, a larger body size gives them greater success in grappling and subduing large prey like moose or elk (MacNulty et al., 2009). In dall sheep, a larger body size gives males a reproductive advantage when they compete for the right to mate, and since adult sheep may lose up to 16% of their body mass during winter, those with a higher body mass are more likely to survive (U.S. National Park Service, 2020). However, “bigger” is not always a “better” lifestyle method for some animals, and can be actively harmful to their chances of survival.
Insects and arthropods are limited in their body size because they breathe by soaking in oxygen like a sponge. If they are too large, they cannot absorb sufficient oxygen and die of hypoxia. It was only during the Paleozoic, when oxygen concentrations reached as high as 35% during the Carboniferous period, that insects were capable of gigantism, with some dragonflies as large as seagulls (Harrison et al., 2010). Furthermore, it is costly to support a large body mass: the larger the body, the greater the energy requirements and the more food is required to sustain the animal. There are also factors of predation, where a larger body size may reduce agility, increase detection by predators, or increase costs to reproduction (Blanckenhorn, 2000). In essence, how natural selection acts on size is complex. Understanding how size correlates with survival is important, particularly when we are examining the salmon populations of Alaska.
You’ve most likely had an infection that required treatment with antibiotics. At the time that you were prescribed antibiotics, you probably heard that familiar spiel about needing to take the entire course of antibiotics even if you feel better before finishing them. You might be wondering, why does it matter? Hopefully after reading this post you will be able to answer that question for yourself.
As you might imagine, bacteria developing the ability to survive antibiotic treatment is bad news for us. This means that over time, our commonly used antibiotics are becoming less effective at killing bacteria. As bacteria evolves more antibiotic resistance, we may no longer be able to treat common infections unless we come up with another alternative treatment. It is important that we try to delay the evolution of antibiotic resistance as much as we can to buy time to develop other effective treatments. So what are the driving forces of bacterial evolution and what can we do about it?
Stress, the sort that persists and comes from sources beyond our control, can be detrimental to our health, and even more so to the young (Luna R. et al. 2015). When outside sources of stress are present from a young age, normal development and the adult stress response is impacted in a way that makes healthy coping with stress more difficult throughout life (McEwen et al. 2011) (Eliand L. et al. 2013). Environmental stressors can not only cause developmental changes and impact overall health but can also cause changes to a person’s microbiome or the sum of microbes that coexist with an individual. Which could in-turn alter the sort of metabolites a person secretes (Verbeke K et al. 2015).
Mental health diseases like depression and anxiety have plagued humans presumably since we achieved sentience, and lately it seems like the mental health crisis in America is getting worse and worse. Everyone blames this rise on something different; social media, the pandemic, tumultuous politics, or just the dramatics of younger generations. No matter where the blame is placed, statistics show that the rise in the number of diagnoses is real. Almost all mental health diseases show growth, but anxiety and depression have skyrocketed (ADAA). Even before the COVID 19 pandemic, anxiety was at an all time high, as shown in the figure below.
Fig. 1: These graphs show the number of people diagnosed with anxiety in 1990 (left) and 2017 (right). The United States shows a drastic increase. Darker areas indicate higher numbers of anxiety diagnoses. Image sourced from Our World in Data. Continue reading “Mental to Dental Connection”
People may be familiar with products that claim to impact gut health via probiotics and prebiotics, like kombucha and supplements. Prebiotics are plant fibers that encourage growth of beneficial gut bacteria, while probiotics are usually live bacteria that are associated with good gut health (Mayo Clinic Staff, 2021). Diversity comes up often in discussions about gut microbes. Diversity refers to the amount of different species present in a sample, and more diverse samples contain a wider range of microbes. We know that a less diverse community of gut microbes is associated with inflammatory bowel diseases (Cénit et al., 2014) and obesity (Turnbaugh et al., 2008). However, relatively little is known about how the performance of endurance exercise might impact the microbes living within the gut.
International travel is part of modern life, your life. Whether that is visiting family in Europe, business trips to Asia, or a dream vacation to the tropics, these all have something in common. The microbes and germs in these places are different and not what your body is used to at home.
Your body is covered, inside and out, with little microbes that influence your health both mentally and physically (Beaumont et al. 2018. Hathaway et al. 2021). These symbionts (organisms that coexist and interact closely with another organism) are not the same for every person, especially at a global scale. Recent advancements in global sampling of microorganisms has shown that novel and unknown microbes are not only common in the cities of the world but often differ based on the climate, country, and various other environmental factors. Consequently, when a person travels to a new part of the globe, they are exposed to microbes that their bodies may never have seen before and contact with microbes like these can lead to some uncomfortable conditions (Danko et al. 2021).
Colorectal Cancer (CRC) makes up a large proportion of cancer in the United States. CRC occurs in two locations, the colon and rectum. It is the 3rd most diagnosed type of cancer in the U.S., and in 2021 it is estimated there will be just over 100,000 cases of colon cancer and around 45,000 cases of rectal cancer leading to more than 50,000 deaths (American Cancer Society, 2021).
Colorectal cancer causes the third most cancer-related deaths among men and women separately, and if you combine into one population it causes the second most. The actual death rate of CRC has decreased in the last couple of decades due to increase in effectiveness and quantity of screenings (e.g. colonoscopy) which look for signs of CRC, including polyps (small clump of cells that can be cancerous) located in the rectum/colon (Stewart and Carter-Templeton, 2017). Even with the ability to screen and look for physical changes in the colon/rectum, many people still die from CRC and it is a major problem facing the field of oncology and medicine in general.
