Month: May 2024

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

https://youtu.be/phMZ4O4JdoI?si=q_CD9eU5deyG2Rs2

Background

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.