Accepted Manuscript: Marine Population Genomics: Challenges and Opportunities
Title: Marine Population Genomics: Challenges and Opportunities
Population genomics has provided unprecedented opportunities to unravel the mysteries of marine organisms in the oceans' depths. The world's oceans, which make up 70% of our planet, encompass diverse habitats and host numerous unexplored populations and species. Population genomics studies of marine organisms are rapidly emerging and have the potential to transform our understanding of marine populations, species, and ecosystems, providing insights into how these organisms are evolving and how they respond to different stimuli and environments. This knowledge is critical for understanding the fundamental aspects of marine life, how marine organisms will respond to environmental changes, and how we can better protect and preserve marine biodiversity and resources. This book brings together leading experts in the field to address critical aspects of fundamental and applied research in marine species and share their research and insights crucial for understanding marine ecosystem diversity and function. It also discusses the challenges, opportunities and future perspectives of marine population genomics.
Oleksiak, M.F.; Rajora, O.P.
Population Genomics: Marine Organisms
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Adaptation Without Boundaries: Population Genomics in Marine Systems
https://doi.org/https://doi.org/10.1007/13836_2018_32
Oleksiak, M. F. ( January 2020 , Population Genomics)
From the surface, the world's oceans appear vast and boundless. Ocean currents, which can transport marine organisms thousands of kilometers, coupled with species that spend some or all of their life in the pelagic zone, the open sea, highlight the potential for well-mixed, panmictic marine populations. Yet these ocean habitats do harbor boundaries. In this largely three-dimensional marine environment, gradients form boundaries. These gradients include temperature, salinity, and oxygen gradients. Ocean currents also form boundaries between neighboring water masses even as they can break through barriers by transporting organisms huge distances. With the advent of next-generation sequencing approaches, which allow us to easily generate a large number of genomic markers, we are in an unprecedented position to study the effects of these potential oceanic boundaries and can ask how often and when do locally adapted marine populations evolve. This knowledge will inform our understanding of how marine organisms respond to climate change and affect how we protect marine diversity. In this chapter I first discuss the major boundaries present in the marine environment and the implications they have for marine organisms. Next, I discuss the how genomic approaches are impacting our understanding of genetic connectivity, ocean fisheries, and local adaptation,more »including the potential for epigenetic adaptation. I conclude with considerations for marine conservation and management and future prospects.« less
Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems
https://doi.org/10.7554/eLife.78129
Richter, Daniel J ; Watteaux, Romain ; Vannier, Thomas ; Leconte, Jade ; Frémont, Paul ; Reygondeau, Gabriel ; Maillet, Nicolas ; Henry, Nicolas ; Benoit, Gaëtan ; Da Silva, Ophélie ; et al ( August 2022 , eLife)
Oceans are brimming with life invisible to our eyes, a myriad of species of bacteria, viruses and other microscopic organisms essential for the health of the planet. These 'marine plankton' are unable to swim against currents and should therefore be constantly on the move, yet previous studies have suggested that distinct species of plankton may in fact inhabit different oceanic regions. However, proving this theory has been challenging; collecting plankton is logistically difficult, and it is often impossible to distinguish between species simply by examining them under a microscope. However, within the last decade, a research schooner called Tara has travelled the globe to gather thousands of plankton samples. At the same time, advances in genomics have made it possible to identify species based only on fragments of their DNA sequence. To understand the hidden geography of plankton communities in Earth's oceans, Richter et al. pored over DNA from the Tara Oceans expedition. This revealed that, despite being unable to resist the flow of water, various planktonic species which live close to the surface manage to occupy distinct, stable provinces shaped by currents. Different sizes of plankton are distributed in different sized provinces, with the smallest organisms tending to inhabitmore »the smallest areas. Comparing DNA similarities and speeds of currents at the ocean surface revealed how these might stretch and mix plankton communities. Plankton play a critical role in the health of the ocean and the chemical cycles of planet Earth. These results could allow deeper investigation by marine modellers, ecologists, and evolutionary biologists. Meanwhile, work is already underway to investigate how climate change might impact this hidden geography.« less
Placing human gene families into their evolutionary context
Dornburg, Alex ; Mallik, Rittika ; Wang, Zheng ; Bernal, Moisés A. ; Thompson, Brian ; Bruford, Elspeth A. ; Nebert, Daniel W. ; Vasiliou, Vasilis ; Yohe, Laurel R. ; Yoder, Jeffrey A. ; et al ( November 2022 , Human Genomics)
Following the draft sequence of the first human genome over 20 years ago, we have achieved unprecedented insights into the rules governing its evolution, often with direct translational relevance to specific diseases. However, staggering sequence complexity has also challenged the development of a more comprehensive understanding of human genome biology. In this context, interspecific genomic studies between humans and other animals have played a critical role in our efforts to decode human gene families. In this review, we focus on how the rapid surge of genome sequencing of both model and non-model organisms now provides a broader comparative framework poised to empower novel discoveries. We begin with a general overview of how comparative approaches are essential for understanding gene family evolution in the human genome, followed by a discussion of analyses of gene expression. We show how homology can provide insights into the genes and gene families associated with immune response, cancer biology, vision, chemosensation, and metabolism, by revealing similarity in processes among distant species. We then explain methodological tools that provide critical advances and show the limitations of common approaches. We conclude with a discussion of how these investigations position us to gain fundamental insights into the evolution ofmore »gene families among living organisms in general. We hope that our review catalyzes additional excitement and research on the emerging field of comparative genomics, while aiding the placement of the human genome into its existentially evolutionary context.
Environment and phenology shape local adaptation in thermal performance
https://doi.org/10.1098/rspb.2021.0741
Villeneuve, Andrew R. ; Komoroske, Lisa M. ; Cheng, Brian S. ( July 2021 , Proceedings of the Royal Society B: Biological Sciences)
Populations within species often exhibit variation in traits that reflect local adaptation and further shape existing adaptive potential for species to respond to climate change. However, our mechanistic understanding of how the environment shapes trait variation remains poor. Here, we used common garden experiments to quantify thermal performance in eight populations of the marine snail Urosalpinx cinerea across thermal gradients on the Atlantic and the Pacific coasts of North America. We then evaluated the relationship between thermal performance and environmental metrics derived from time-series data. Our results reveal a novel pattern of 'mixed' trait performance adaptation, where thermal optima were positively correlated with spawning temperature (cogradient variation), while maximum trait performance was negatively correlated with season length (countergradient variation). This counterintuitive pattern probably arises because of phenological shifts in the spawning season, whereby 'cold' populations delay spawning until later in the year when temperatures are warmer compared to 'warm' populations that spawn earlier in the year when temperatures are cooler. Our results show that variation in thermal performance can be shaped by multiple facets of the environment and are linked to organismal phenology and natural history. Understanding the impacts of climate change on organisms, therefore, requires the knowledge of howmore »climate change will alter different aspects of the thermal environment.« less
Differentiated Evolutionary Strategies of Genetic Diversification in Atlantic and Pacific Thaumarchaeal Populations
https://doi.org/10.1128/msystems.01477-21
Hwang, Yunha ; Girguis, Peter R. ( June 2022 , mSystems)
Bowman, Jeff (Ed.)
ABSTRACT Some marine microbes are seemingly "ubiquitous," thriving across a wide range of environmental conditions. While the increased depth in metagenomic sequencing has led to a growing body of research on within-population heterogeneity in environmental microbial populations, there have been fewer systematic comparisons and characterizations of population-level genetic diversity over broader expanses of time and space. Here, we investigated the factors that govern the diversification of ubiquitous microbial taxa found within and between ocean basins. Specifically, we use mapped metagenomic paired reads to examine the genetic diversity of ammonia-oxidizing archaeal (" Candidatus Nitrosopelagicus brevis") populations in the Pacific (Hawaii Ocean Time-series [HOT]) and Atlantic (Bermuda Atlantic Time Series [BATS]) Oceans sampled over 2 years. We observed higher nucleotide diversity in " Ca. N. brevis" at HOT, driven by a higher rate of homologous recombination. In contrast, " Ca. N. brevis" at BATS featured a more open pangenome with a larger set of genes that were specific to BATS, suggesting a history of dynamic gene gain and loss events. Furthermore, we identified highly differentiated genes that were regulatory in function, some of which exhibited evidence of recent selective sweeps. These findings indicate that different modes of genetic diversification likely incur specificmore »adaptive advantages depending on the selective pressures that they are under. Within-population diversity generated by the environment-specific strategies of genetic diversification is likely key to the ecological success of " Ca. N. brevis." IMPORTANCE Ammonia-oxidizing archaea (AOA) are one of the most abundant chemolithoautotrophic microbes in the marine water column and are major contributors to global carbon and nitrogen cycling. Despite their ecological importance and geographical pervasiveness, there have been limited systematic comparisons and characterizations of their population-level genetic diversity over time and space. Here, we use metagenomic time series from two ocean observatories to address the fundamental questions of how abiotic and biotic factors shape the population-level genetic diversity and how natural microbial populations adapt across diverse habitats. We show that the marine AOA " Candidatus Nitrosopelagicus brevis" in different ocean basins exhibits distinct modes of genetic diversification in response to their selective regimes shaped by nutrient availability and patterns of environmental fluctuations. Our findings specific to " Ca. N. brevis" have broader implications, particularly in understanding the population-level responses to the changing climate and predicting its impact on biogeochemical cycles.« less
https://doi.org/10.1007/13836_2019_70
Oleksiak, M.F., and Rajora, O.P.. Marine Population Genomics: Challenges and Opportunities. Retrieved from https://par.nsf.gov/biblio/10147602. Population Genomics: Marine Organisms . Web. doi:10.1007/13836_2019_70.
Oleksiak, M.F., & Rajora, O.P.. Marine Population Genomics: Challenges and Opportunities. Population Genomics: Marine Organisms, (). Retrieved from https://par.nsf.gov/biblio/10147602. https://doi.org/10.1007/13836_2019_70
Oleksiak, M.F., and Rajora, O.P.. "Marine Population Genomics: Challenges and Opportunities". Population Genomics: Marine Organisms (). Country unknown/Code not available. https://doi.org/10.1007/13836_2019_70. https://par.nsf.gov/biblio/10147602.
place = {Country unknown/Code not available}, title = {Marine Population Genomics: Challenges and Opportunities}, url = {https://par.nsf.gov/biblio/10147602}, DOI = {10.1007/13836_2019_70}, abstractNote = {Population genomics has provided unprecedented opportunities to unravel the mysteries of marine organisms in the oceans' depths. The world's oceans, which make up 70% of our planet, encompass diverse habitats and host numerous unexplored populations and species. Population genomics studies of marine organisms are rapidly emerging and have the potential to transform our understanding of marine populations, species, and ecosystems, providing insights into how these organisms are evolving and how they respond to different stimuli and environments. This knowledge is critical for understanding the fundamental aspects of marine life, how marine organisms will respond to environmental changes, and how we can better protect and preserve marine biodiversity and resources. This book brings together leading experts in the field to address critical aspects of fundamental and applied research in marine species and share their research and insights crucial for understanding marine ecosystem diversity and function. It also discusses the challenges, opportunities and future perspectives of marine population genomics.}, journal = {Population Genomics: Marine Organisms}, author = {Oleksiak, M.F. and Rajora, O.P.}, }