scholarly journals Shared genomic outliers across two divergent population clusters of a highly threatened seagrass

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6806 ◽  
Author(s):  
Nikki Leanne Phair ◽  
Robert John Toonen ◽  
Ingrid Knapp ◽  
Sophie von der Heyden
Keyword(s):  
Ecosystem Engineer ◽  
Environmental Gradients ◽  
Keystone Species ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Eastern Africa ◽  
Seagrass Habitat ◽  
Temperature And Precipitation ◽  
Outlier Loci ◽  
Isolation By Environment

The seagrass, Zostera capensis, occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled genomic approach was employed to obtain SNP data and examine neutral genomic variation and to identify potential outlier loci to assess differentiation across 12 populations across the ∼9,600 km distribution of Z. capensis. Results indicate high clonality and low genomic diversity within meadows, which combined with poor protection throughout its range, increases the vulnerability of this seagrass to further declines or local extinction. Shared variation at outlier loci potentially indicates local adaptation to temperature and precipitation gradients, with Isolation-by-Environment significantly contributing towards shaping spatial variation in Z. capensis. Our results indicate the presence of two population clusters, broadly corresponding to populations on the west and east coasts, with the two lineages shaped only by frequency differences of outlier loci. Notably, ensemble modelling of suitable seagrass habitat provides evidence that the clusters are linked to historical climate refugia around the Last Glacial Maxi-mum. Our work suggests a complex evolutionary history of Z. capensis in southern and eastern Africa that will require more effective protection in order to safeguard this important ecosystem engineer into the future.

scholarly journals Shared genomic outliers across two divergent population clusters of a highly threatened seagrass

2019 ◽  
Author(s):  
Nikki Leanne Phair ◽  
Robert John Toonen ◽  
Ingrid Knapp ◽  
Sophie von der Heyden
Keyword(s):  
Ecosystem Engineer ◽  
Environmental Gradients ◽  
Keystone Species ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Eastern Africa ◽  
Seagrass Habitat ◽  
Temperature And Precipitation ◽  
Outlier Loci ◽  
Isolation By Environment

The seagrass, Zostera capensis, occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled genomic approach was employed to obtain SNP data and examine neutral genomic variation and to identify potential outlier loci to assess differentiation across 12 populations across the ~9600km distribution of Z. capensis. Results indicate high clonality and low genomic diversity within meadows, which combined with poor protection throughout its range, increases the vulnerability of this seagrass to further declines or local extinction. Shared variation at outlier loci potentially indicates local adaptation to temperature and precipitation gradients, with Isolation-by-Environment significantly contributing towards shaping spatial variation in Z. capensis. Our results indicate the presence of two population clusters, broadly corresponding to populations on the west and east coasts, with the two lineages shaped only by frequency differences of outlier loci. Notably, ensemble modelling of suitable seagrass habitat provides evidence that the clusters are linked to historical climate refugia around the Last Glacial Maxi-mum. Our work suggests a complex evolutionary history of Z. capensis in southern and eastern Africa that will require more effective protection in order to safeguard this important ecosystem engineer into the future.

scholarly journals Shared genomic outliers across two divergent population clusters of a highly threatened seagrass

2019 ◽  
Author(s):  
Nikki Leanne Phair ◽  
Robert John Toonen ◽  
Ingrid Knapp ◽  
Sophie von der Heyden
Keyword(s):  
Ecosystem Engineer ◽  
Environmental Gradients ◽  
Keystone Species ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Eastern Africa ◽  
Seagrass Habitat ◽  
Temperature And Precipitation ◽  
Outlier Loci ◽  
Isolation By Environment

The seagrass, Zostera capensis, occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled genomic approach was employed to obtain SNP data and examine neutral genomic variation and to identify potential outlier loci to assess differentiation across 12 populations across the ~9600km distribution of Z. capensis. Results indicate high clonality and low genomic diversity within meadows, which combined with poor protection throughout its range, increases the vulnerability of this seagrass to further declines or local extinction. Shared variation at outlier loci potentially indicates local adaptation to temperature and precipitation gradients, with Isolation-by-Environment significantly contributing towards shaping spatial variation in Z. capensis. Our results indicate the presence of two population clusters, broadly corresponding to populations on the west and east coasts, with the two lineages shaped only by frequency differences of outlier loci. Notably, ensemble modelling of suitable seagrass habitat provides evidence that the clusters are linked to historical climate refugia around the Last Glacial Maxi-mum. Our work suggests a complex evolutionary history of Z. capensis in southern and eastern Africa that will require more effective protection in order to safeguard this important ecosystem engineer into the future.

scholarly journals Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species

2020 ◽  
Author(s):  
Erica Nielsen ◽  
Romina Henriques ◽  
Maria Beger ◽  
Robert Toonen ◽  
Sophie von der Heyden
Keyword(s):  
Global Change ◽  
Outlier Detection ◽  
Genomic Variation ◽  
Sea Surface ◽  
Environmental Drivers ◽  
Comparative Approach ◽  
Evolutionary Potential ◽  
Environmental Selection ◽  
Outlier Loci ◽  
Isolation By Environment

Abstract Background: As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species’ potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare putative environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin (Parechinus angulosus), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis). Results: Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus. Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus, but not for C. punctatus. Conclusion: The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses may be better predictors of evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.

scholarly journals Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species

2020 ◽  
Author(s):  
Erica Nielsen ◽  
Romina Henriques ◽  
Maria Beger ◽  
Robert Toonen ◽  
Sophie von der Heyden
Keyword(s):  
Global Change ◽  
Outlier Detection ◽  
Genomic Variation ◽  
Sea Surface ◽  
Environmental Drivers ◽  
Comparative Approach ◽  
Evolutionary Potential ◽  
Environmental Selection ◽  
Outlier Loci ◽  
Isolation By Environment

Abstract Background: As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species’ potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare the dominant environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin ( Parechinus angulosus ), Common shore crab ( Cyclograpsus punctatu s), and Granular limpet ( Scutellastra granularis ). Results: Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus . Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus , but not for C. punctatus . Conclusion: The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses better predict evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.

scholarly journals Landscape drivers of genomic diversity and divergence in woodland Eucalyptus

2019 ◽  
Author(s):  
Kevin Murray ◽  
Jasmine Janes ◽  
Helen Bothwell ◽  
Ashley Jones ◽  
Rose Andrew ◽  
...  
Keyword(s):  
Geographic Distance ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
High Genetic Diversity ◽  
Genome Wide ◽  
Isolation By Environment ◽  
Genetic Patterns ◽  
Discrete Population ◽  
Eucalyptus Albens ◽  
Eucalyptus Sideroxylon

AbstractSpatial genetic patterns are influenced by numerous factors, and they can vary even among coexisting, closely related species due to differences in dispersal and selection. Eucalyptus (L’Héritier 1789; the “eucalypts”) are foundation tree species that provide essential habitat and modulate ecosystem services throughout Australia. Here we present a study of landscape genomic variation in two woodland eucalypt species, using whole genome sequencing of 388 individuals of Eucalyptus albens and Eucalyptus sideroxylon. We found exceptionally high genetic diversity (π ≈ 0.05) and low genome-wide, inter-specific differentiation (FST = 0.15). We found no support for strong, discrete population structure, but found substantial support for isolation by geographic distance (IBD) in both species. Using generalised dissimilarity modelling, we identified additional isolation by environment (IBE). Eucalyptus albens showed moderate IBD, and environmental variables have a small but significant amount of additional predictive power (i.e., IBE). Eucalyptus sideroxylon showed much stronger IBD, and moderate IBE. These results highlight the vast adaptive potential of these species, and set the stage for testing evolutionary hypotheses of interspecific adaptive differentiation across environments.

scholarly journals Spatial, climate, and ploidy factors drive genomic diversity and resilience in the widespread grass Themeda triandra

2019 ◽  
Author(s):  
CW Ahrens ◽  
EA James ◽  
AD Miller ◽  
NC Aitken ◽  
JO Borevitz ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Isolation By Distance ◽  
Management Strategies ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
List Type ◽  
Themeda Triandra ◽  
Reduced Representation ◽  
Isolation By Environment ◽  
Susceptible Populations

SummaryFragmented grassland ecosystems, and the species that shape them, are under immense pressure. Restoration and management strategies should include genetic diversity and adaptive capacity to improve success but these data are generally unavailable. Therefore, we use the foundational grass, Themeda triandra, to test how spatial, environmental, and ploidy factors shape patterns of genetic variation.We used reduced-representation genome sequencing on 487 samples from 52 locations to answer fundamental questions about how the distribution of genomic diversity and ploidy polymorphism supports adaptation to harsher climates. We explicitly quantified isolation-by-distance (IBD), isolation-by-environment (IBE), and predicted population genomic vulnerability in 2070.We found that a majority (54%) of the genomic variation could be attributed to IBD, while 22% of the genomic variation could be explained by four climate variables showing IBE. Results indicate that heterogeneous patterns of vulnerability across populations are due to genetic variation, multiple climate factors, and ploidy polymorphism, which lessened genomic vulnerability in the most susceptible populations.These results indicate that restoration and management of T. triandra should incorporate knowledge of genomic diversity and ploidy polymorphisms to increase the likelihood of population persistence and restoration success in areas that will become hotter and more arid.

scholarly journals Fine scale population structure and extensive gene flow within an Eastern Nearctic snake complex (Pituophis melanoleucus)

2021 ◽  
Author(s):  
Zachary L Nikolakis ◽  
Richard Orton ◽  
Brian I Crother
Keyword(s):  
Gene Flow ◽  
Isolation By Distance ◽  
Genomic Structure ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Evolutionary Relationships ◽  
Population Genomic ◽  
Isolation By Environment ◽  
Pituophis Melanoleucus ◽  
Lineage Divergence

Understanding the processes and mechanisms that promote lineage divergence is a central goal in evolutionary biology. For instance, studies investigating the spatial distribution of genomic variation often highlight biogeographic barriers underpinning geographic isolation, as well as patterns of isolation by environment and isolation by distance that can also lead to lineage divergence. However, the patterns and processes that shape genomic variation and drive lineage divergence may be taxa-specific, even across closely related taxa co-occurring within the same biogeographic region. Here, we use molecular data in the form of ultra-conserved elements (UCEs) to infer the evolutionary relationships and population genomic structure of the Eastern Pinesnake complex (Pituophis melanoleucus) – a polytypic wide-ranging species that occupies much of the Eastern Nearctic. In addition to inferring evolutionary relationships, population genomic structure, and gene flow, we also test relationships between genomic diversity and putative barriers to dispersal, environmental variation, and geographic distance. We present results that reveal shallow population genomic structure and ongoing gene flow, despite an extensive geographic range that transcends geographic features found to reduce gene flow among many taxa, including other squamate reptiles within the Eastern Nearctic. Further, our results indicate that the observed genomic diversity is spatially distributed as a pattern of isolation by distance and suggest that the current subspecific taxonomy do not adhere to independent lineages, but rather, show a significant amount of admixture across the entire P. melanoleucus range.

scholarly journals Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Erica S. Nielsen ◽  
Romina Henriques ◽  
Maria Beger ◽  
Robert J. Toonen ◽  
Sophie von der Heyden
Keyword(s):  
Global Change ◽  
Outlier Detection ◽  
Genomic Variation ◽  
Sea Surface ◽  
Environmental Drivers ◽  
Comparative Approach ◽  
Evolutionary Potential ◽  
Environmental Selection ◽  
Outlier Loci ◽  
Isolation By Environment

Abstract Background As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species’ potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare putative environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin (Parechinus angulosus), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis). Results Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus. Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus, but not for C. punctatus. Conclusion The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses may be better predictors of evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.

scholarly journals Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species

2020 ◽  
Author(s):  
Erica Nielsen ◽  
Romina Henriques ◽  
Maria Beger ◽  
Robert Toonen ◽  
Sophie von der Heyden
Keyword(s):  
Global Change ◽  
Outlier Detection ◽  
Genomic Variation ◽  
Sea Surface ◽  
Environmental Drivers ◽  
Comparative Approach ◽  
Evolutionary Potential ◽  
Environmental Selection ◽  
Outlier Loci ◽  
Isolation By Environment

Abstract Background: As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species’ potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare putative environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin (Parechinus angulosus ), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis ). Results: Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus. Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus, but not for C. punctatus . Conclusion: The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses may be better predictors of evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.

scholarly journals Applying genomic data to seagrass conservation

2020 ◽  
Author(s):  
Nikki L Phair ◽  
Erica S Nielsen ◽  
Sophie von der Heyden
Keyword(s):  
South African ◽  
Habitat Type ◽  
Keystone Species ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Anthropogenic Pressure ◽  
Evolutionary Potential ◽  
Snp Data ◽  
High Degree ◽  
Conservation Prioritisation

AbstractAlthough genomic diversity is increasingly recognised as a key component of biodiversity, it is seldom used to inform conservation planning. Estuaries and keystone species such as the southern African seagrass, Zostera capensis, are under severe anthropogenic pressure and are often poorly protected. In this study we integrated SNP data generated from populations of Z. capensis across the South African coastline into the spatial prioritisation tool Marxan. We included different measures of genomic variation to account for genomic diversity, distinctness and evolutionary potential to explore spatial planning scenarios. We investigated how conservation priority areas identified by targeting only habitat type, differed from those identified by also including genomic measures; further we assessed how different genetic diversity metrics change prioritisation outcomes. All scenarios targeting genomic variation identified unique conservation prioritisation areas compared to scenarios only targeting habitat type. As such, omitting these estuaries from regional MPA networks risks the loss of evolutionarily important populations, threatening resilience and persistence of associated estuarine communities and their ecosystem services. We also observed a high degree of overlap between prioritisation outcomes across targeted measures of genomic variation. As such, by including even single measures of genomic variation, it may be possible to sufficiently represent the evolutionary processes behind the patterns of variation, while simplifying the conservation prioritisation procedure.

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