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, including the potential for epigenetic adaptation. I conclude with considerations for marine conservation and management and future prospects.
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Population Genomics of Marine Zooplankton
The exceptionally large population size and cosmopolitan biogeographic distribution that distinguish many – but not all – marine zooplankton species generate similarly exceptional patterns of population genetic and genomic diversity and structure. The phylogenetic diversity of zooplankton has slowed the application of population genomic approaches, due to lack of genomic resources for closelyrelated species and diversity of genomic architecture, including highly-replicated genomes of many crustaceans. Use of numerous genomic markers, especially single nucleotide polymorphisms (SNPs), is transforming our ability to analyze population genetics and connectivity of marine zooplankton, and providing new understanding and different answers than earlier analyses, which typically used mitochondrial DNA and microsatellite markers. Population genomic approaches have confirmed that, despite high dispersal potential, many zooplankton species exhibit genetic structuring among geographic populations, especially at large ocean-basin scales, and have revealed patterns and pathways of population connectivity that do not always track ocean circulation. Genomic and transcriptomic resources are critically needed to allow further examination of micro-evolution and local adaptation, including identification of genes that show evidence of selection. These new tools will also enable further examination of the significance of small-scale genetic heterogeneity of marine zooplankton, to discriminate genetic “noise” in large and patchy populations from local adaptation to environmental conditions and change.
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- Award ID(s):
- 1643825
- NSF-PAR ID:
- 10073153
- Date Published:
- Journal Name:
- Population Genomics
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Chaetognatha are highly-effective predatory components of the marine planktonic assemblages. Many species exhibit disjunct biogeographical distributions throughout the global ocean, and thus serve as sentinel species for examining climate-driven changes in ocean circulation on zooplankton species, communities, and food webs. Of particular interest are ecological changes in the Arctic, a region being drastically affected by climate change. In this study, a 650 base-pair region of the mitochondrial cytochrome oxidase I (mtCOI) gene was sequenced for 131 individuals for the chaetognath Eukrohnia hamata collected from diverse regions throughout the Arctic. DNA sequence analysis was done to characterize population genetic diversity and structure, phylogeography (i.e., geographic distribution of genetic lineages within species), and connectivity among regional populations. High haplotype diversity (Hd) and significant (p <0.02) negative values for Fu’s and Li’s F statistic imply that E. hamata is undergoing population expansion.. Patterns and pathways of population connectivity examined to test several migration hypotheses revealed that pan-Arctic population connectivity followed the primary ocean currents. The reliance of this ecologically important zooplankton species on Arctic Ocean currents has implications for future warming conditions, which have the potential to modify these currents, resulting in altered biogeographical distributions and population connectivity of Arctic zooplankton.more » « less
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Chaetognatha are highly-effective predatory components of the marine planktonic assemblages. Many species exhibit disjunct biogeographical distributions throughout the global ocean, and thus serve as sentinel species for examining climate-driven changes in ocean circulation on zooplankton species, communities, and food webs. Of particular interest are ecological changes in the Arctic, a region being drastically affected by climate change. In this study, a 650 base-pair region of the mitochondrial cytochrome oxidase I (mtCOI) gene was sequenced for 131 individuals for the chaetognath Eukrohnia hamata collected from diverse regions throughout the Arctic. DNA sequence analysis was done to characterize population genetic diversity and structure, phylogeography (i.e., geographic distribution of genetic lineages within species), and connectivity among regional populations. High haplotype diversity (Hd) and significant (p <0.02) negative values for Fu’s and Li’s F statistic imply that E. hamata is undergoing population expansion.. Patterns and pathways of population connectivity examined to test several migration hypotheses revealed that pan-Arctic population connectivity followed the primary ocean currents. The reliance of this ecologically important zooplankton species on Arctic Ocean currents has implications for future warming conditions, which have the potential to modify these currents, resulting in altered biogeographical distributions and population connectivity of Arctic zooplankton.more » « less
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Abstract Context Processes that shape genomic and ecological divergence can reveal important evolutionary dynamics to inform the conservation of threatened species.
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Fontainea species. Our aim was to compare spatial patterns of genetic variation between the vulnerableFontainea australis (Southern Fontainea) and critically endangeredF. oraria (Coastal Fontainea), endemic to the heterogeneous subtropical region of central, eastern Australia, where large-scale clearing has severely reduced rainforest habitat to a fraction (< 1%) of its pre-European settlement extent.Methods We used a set of 10,000 reduced-representation markers to infer genetic relationships and the drivers of spatial genetic variation across the two species. In addition, we employed a combination of univariate and multivariate genome-environment association analysis using a set of topo-climatic variables to explore potential patterns of local adaptation as a factor impacting genomic divergence.
Results Our study revealed that Coastal Fontainea have a close genetic relationship with Southern Fontainea. We showed that isolation by distance has played a key role in their genetic variation, indicating that vicariance can explain the spatial genetic distribution of the two species. Genotype-environment analyses showed a strong association with temperature and topographic features, suggesting adaptation to localised thermal environments. We used a multivariate redundancy analysis to identify a range of putatively adapted loci associated with local environmental conditions.
Conclusions Divergent selection at the local-habitat scale as a result of dispersal limitations and environmental heterogeneity (including physical barriers) are likely contributors to adaptive divergence between the two
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Abstract Adaptation to environmental change requires that populations harbor the necessary genetic variation to respond to selection. However, dispersal‐limited species with fragmented populations and reduced genetic diversity may lack this variation and are at an increased risk of local extinction. In freshwater fish species, environmental change in the form of increased stream temperatures places many cold‐water species at‐risk. We present a study of rainbow darters (
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1007/13836_2017_9
