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Understanding connectivity between populations is key to identifying hotspots of diversity, dispersal sinks and sources, and effective management units for natural resources. Multi-species connectivity seeks to overcome species-specific idiosyncrasies to identify shared patterns that are most critical to spatial management. The linear Hawaiian archipelago provides an excellent platform to assess multi-species connectivity patterns, with shared boundaries to gene flow identified across a majority of the 41 coral reef species surveyed to date. Here, we evaluate genome-scale data by comparing consistency and resolution to previous connectivity studies using far fewer loci. We used pool-seq to genotype 22,503–232,730 single nucleotide polymorphisms per species (625,215 SNPs total) from the same individuals published in previous studies of two fishes, two corals, and two lobsters. Additionally, one coral species (Pocillopora meandrina) without previous archipelago-wide population genetic data was included. With greater statistical power, most genetic differences between pairwise comparisons of islands were significant (250 of 308), consistent with the most recent larval dispersal models for the Hawaiian Archipelago. These data reveal significant differentiation at a finer scale than previously reported using single-marker studies, yet did not overturn any of the conclusions or management implications drawn from previous studies. We confirm that population genomic datasets are consistent with previously reported patterns of multispecies connectivity but add a finer layer of population resolution that is pertinent to management.
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Genetic and biophysical modelling evidence of generational connectivity in the intensively exploited, Western North Atlantic red grouper (Epinephelus morio)
Abstract Understanding the connectivity of reef organisms is important to assist in the conservation of biological diversity and to facilitate sustainable fisheries in these ecosystems. Common methods to assess reef connectivity include both population genetics and biophysical modelling. Individually, these techniques can offer insight into population structure; however, the information acquired by any singular analysis is often subject to limitations, underscoring the need for a multi-faceted approach. To assess the connectivity dynamics of the red grouper (Epinephelus morio), an economically important reef fish species found throughout the Gulf of Mexico and USA western Atlantic, we utilized two sets of genetic markers (12 microsatellite loci and 632 single nucleotide polymorphisms) to resolve this species’ population genetic structure, along with biophysical modelling to deliver a spatial forecast of potential larval “sources” and “sinks” across these same regions and spatial scale. Our genetic survey indicates little, if any, evidence of population genetic structure and modelling efforts indicate the potential for ecological connectivity between sampled regions over multiple generations. We offer that using a dual empirical and theoretical approach lessens the error associated with the use of any single method and provides an important step towards the validation of either of these methodologies.
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- Award ID(s):
- 1754437
- PAR ID:
- 10465001
- Editor(s):
- Gomez-Uchida, Daniel
- Date Published:
- Journal Name:
- ICES Journal of Marine Science
- ISSN:
- 1054-3139
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Mesophotic reefs (30‐150 m) have been proposed as potential refugia that facilitate the recovery of degraded shallow reefs following acute disturbances such as coral bleaching and disease. However, because of the technical difficulty of collecting samples, the connectivity of adjacent mesophotic reefs is relatively unknown compared with shallower counterparts. We used genotyping by sequencing to assess fine‐scale genetic structure of Montastraea cavernosa at two sites at Pulley Ridge, a mesophotic coral reef ecosystem in the Gulf of Mexico, and downstream sites along the Florida Reef Tract. We found differentiation between reefs at Pulley Ridge (~68 m) and corals at downstream upper mesophotic depths in the Dry Tortugas (28–36 m) and shallow reefs in the northern Florida Keys (Key Biscayne, ~5 m). The spatial endpoints of our study were distinct, with the Dry Tortugas as a genetic intermediate. Most striking were differences in population structure among northern and southern sites at Pulley Ridge that were separated by just 12km. Unique patterns of clonality and outlier loci allele frequency support these sites as different populations and suggest that the long‐distance horizontal connectivity typical of shallow‐water corals may not be typical for mesophotic systems in Florida and the Gulf of Mexico. We hypothesize that this may be due to the spawning of buoyant gametes, which commits propagules to the surface, resulting in greater dispersal and lower connectivity than typically found between nearby shallow sites. Differences in population structure over small spatial scales suggest that demographic constraints and/or environmental disturbances may be more variable in space and time on mesophotic reefs compared with their shallow‐water counterparts.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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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 Genetic connectivity lies at the heart of evolutionary theory, and landscape genetics has rapidly advanced to understand how gene flow can be impacted by the environment. Isolation by landscape resistance, often inferred through the use of circuit theory, is increasingly identified as being critical for predicting genetic connectivity across complex landscapes. Yet landscape impediments to migration can arise from fundamentally different processes, such as landscape gradients causing directional migration and mortality during migration, which can be challenging to address. Spatial absorbing Markov chains (SAMC) have been introduced to understand and predict these (and other) processes affecting connectivity in ecological settings, but the relationship of this framework to landscape genetics remains unclear. Here, we relate the SAMC to population genetics theory, provide simulations to interpret the extent to which the SAMC can predict genetic metrics and demonstrate how the SAMC can be applied to genomic data using an example with an endangered species, the Panama City crayfish Procambarus econfinae , where directional migration is hypothesized to occur. The use of the SAMC for landscape genetics can be justified based on similar grounds to using circuit theory, as we show how circuit theory is a special case of this framework. The SAMC can extend circuit‐theoretic connectivity modelling by quantifying both directional resistance to migration and acknowledging the difference between migration mortality and resistance to migration. Our empirical example highlights that the SAMC better predicts population structure than circuit theory and least‐cost analysis by acknowledging asymmetric environmental gradients (i.e. slope) and migration mortality in this species. These results provide a foundation for applying the SAMC to landscape genetics. This framework extends isolation‐by‐resistance modelling to account for some common processes that can impact gene flow, which can improve predicting genetic connectivity across complex landscapes.more » « less
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1093/icesjms/fsz201
