Landscape drivers of genomic diversity and divergence in woodland Eucalyptus

The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird

10.1101/561399 ◽

2019 ◽

Cited By ~ 3

Author(s):

Lewis G. Spurgin ◽

Mirte Bosse ◽

Frank Adriaensen ◽

Tamer Albayrak ◽

Christos Barboutis ◽

...

Keyword(s):

Positive Selection ◽

Recombination Rate ◽

Demographic History ◽

Great Tit ◽

Genomic Variation ◽

Genomic Diversity ◽

Hapmap Project ◽

Widespread Species ◽

Continental Scale ◽

Genome Wide

AbstractA major aim of evolutionary biology is to understand why patterns of genomic diversity vary among populations and species. Large-scale genomic studies of widespread species are useful for studying how the environment and demographic history shape patterns of genomic divergence, and with the continually decreasing cost of sequencing and genotyping, such studies are now becoming feasible. Here, we carry out one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning almost the entire geographic range of the European great tit subspecies. We found that genome-wide variation was consistent with a recent colonisation across Europe from a single refugium in South-East Europe, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear “islands of differentiation” even among populations with very low levels of genome-wide differentiation. Low local recombination rate in the genome was a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination is a key driver of highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, most likely as a result of recent directional selection at the range edges of this species. Haplotype-based measures of selection were also related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. These regions under positive selection contained candidate genes associated with morphology, thermal adaptation and colouration, providing promising avenues for future investigation. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into evolution.

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

10.7287/peerj.preprints.27517v1 ◽

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.

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

10.1101/864298 ◽

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.

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

10.1101/2021.09.28.462151 ◽

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.

Broad-scale puma connectivity could restore genomic diversity to fine-scale coastal populations

10.1101/2021.10.08.463677 ◽

2021 ◽

Author(s):

Kyle D Gustafson ◽

Roderick B Gagne ◽

Michael R Buchalski ◽

T Winston Vickers ◽

Seth PD Riley ◽

...

Keyword(s):

Genetic Diversity ◽

Linkage Disequilibrium ◽

Puma Concolor ◽

Genomic Diversity ◽

Strong Linkage Disequilibrium ◽

Fine Scale ◽

High Genetic Diversity ◽

Population Genomic ◽

Genome Wide ◽

Genetic Clusters

Urbanization is decreasing wildlife habitat and connectivity worldwide, including for apex predators, such as the puma (Puma concolor). Puma populations along California's central and southern coastal habitats have experienced rapid fragmentation from development, leading to calls for demographic and genetic management. To address urgent conservation genomic concerns, we used double-digest restriction-site associated DNA (ddRAD) sequencing to analyze 16,285 genome-wide single-nucleotide polymorphisms (SNPs) from 401 broadly sampled pumas. Our analyses indicated support for 4–10 geographically nested, broad- to fine-scale genetic clusters. At the broadest scale, the 4 genetic clusters had high genetic diversity and exhibited low linkage disequilibrium, indicating pumas have retained statewide genomic diversity. However, multiple lines of evidence indicated substructure, including 10 fine-scale genetic clusters, some of which exhibited allelic fixation and linkage disequilibrium. Fragmented populations along the Southern Coast and Central Coast had particularly low genetic diversity and strong linkage disequilibrium, indicating genetic drift and close inbreeding. Our results demonstrate that genetically at-risk populations are typically nested within a broader-scale group of interconnected populations that collectively retains high genetic diversity and heterogeneous fixations. Thus, extant variation at the broader scale has potential to restore diversity to local populations if management actions can enhance vital gene flow and recombine locally sequestered genetic diversity. These state- and genome-wide results are critically important for science-based conservation and management practices. Our broad- and fine-scale population genomic analysis highlights the information that can be gained from population genomic studies aiming to provide guidance for fragmented population conservation management.

Genetic structure is stronger across human-impacted habitats than among islands in the coralPorites lobata

10.1101/574665 ◽

2019 ◽

Cited By ~ 1

Author(s):

Kaho H. Tisthammer ◽

Zac H. Forsman ◽

Robert J. Toonen ◽

Robert H. Richmond

Keyword(s):

Genetic Structure ◽

Isolation By Distance ◽

Geographic Distance ◽

High Stress ◽

Disruptive Selection ◽

Single Location ◽

Isolation By Environment ◽

Genetic Patterns ◽

Significant Genetic Structure ◽

Contrasting Habitats

ABSTRACTWe examined genetic structure in the lobe coralPorites lobataamong pairs of highly variable and high-stress nearshore sites and adjacent less variable and less impacted offshore sites on the islands of Oʻahu and Maui, Hawai‘i. Using an analysis of molecular variance framework, we tested whether populations were more structured by geographic distance or environmental extremes. The genetic patterns we observed followed isolation by environment, where nearshore and adjacent offshore populations showed significant genetic structure at both locations (AMOVAFST= 0.04 ∼ 0.19,P< 0.001), but no significant isolation by distance between islands. In contrast, a third site with a less impacted nearshore site showed no significant structure. Strikingly, corals from the two impacted nearshore sites on different islands over 100km apart with similar environmentally stressful conditions were genetically closer (FST∼ 0, P = 0.733) than those within a single location less than 2 km apart (FST= 0.041∼0.079, P < 0.01). Our results suggest that ecological boundaries appear to play a strong role in forming genetic structure in the coastal environment, and that genetic divergence in the absence of geographical barriers to gene flow may be explained by disruptive selection across contrasting habitats.

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

PeerJ ◽

10.7717/peerj.6806 ◽

2019 ◽

Vol 7 ◽

pp. e6806 ◽

Cited By ~ 8

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.

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

10.7287/peerj.preprints.27517 ◽

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.

Panmixia across elevation in thermally sensitive Andean dung beetles

10.1101/783233 ◽

2019 ◽

Author(s):

Ethan Linck ◽

Jorge E. Celi ◽

Kimberly S. Sheldon

Keyword(s):

Thermal Tolerance ◽

Climatic Variability ◽

Geographic Distance ◽

Dung Beetles ◽

Range Limits ◽

Realized Niche ◽

Physiological Constraints ◽

Snp Data ◽

Genome Wide ◽

Isolation By Environment

AbstractJanzen’s seasonality hypothesis predicts that organisms inhabiting environments with limited climatic variability will evolve a reduced thermal tolerance breadth compared with organisms experiencing greater climatic variability. In turn, narrow tolerance breadth may select against dispersal across strong temperature gradients, such as those found across elevation. This can result in narrow elevational ranges and generate a pattern of isolation-by-environment, or neutral genetic differentiation correlated with environmental variables that is independent of geographic distance. We tested for signatures of isolation-by-environment across elevation using genome-wide SNP data from five species of Andean dung beetles (subfamily Scarabaeinae) with well-characterized, narrow thermal physiologies and narrow elevational distributions. Contrary to our expectations, we found no evidence of population genetic structure associated with elevation and little signal of isolation- by-environment. Further, elevational ranges for four of five species appear to be at equilibrium and show no evidence of demographic constraints at range limits. Taken together, these results suggest physiological constraints on dispersal may primarily operate outside of a stable realized niche.Abstract Figure

First genome-wide analysis of an endangered lichen reveals isolation by distance and strong population structure

10.1101/237164 ◽

2017 ◽

Cited By ~ 2

Author(s):

Jessica L. Allen ◽

Sean K. McKenzie ◽

Robin S. Sleith ◽

S. Elizabeth Alter

Keyword(s):

Genetic Diversity ◽

Population Genomics ◽

Isolation By Distance ◽

Geographic Distance ◽

Distribution Models ◽

Extrinsic Factors ◽

Biogeographic Patterns ◽

Ecological Requirements ◽

Genome Wide ◽

Isolation By Environment

AbstractLichenized fungi are evolutionarily diverse and ecologically important, but little is known about the processes driving diversification and genetic differentiation in these lineages. Though few studies have examined population genetic patterns in lichens, their geographic distributions are often assumed to be wholly shaped by ecological requirements rather than dispersal limitations. Furthermore, while their reproductive structures are observable, the lack of information about recombination mechanisms and rates can make inferences about reproductive strategies difficult. Here we investigate the population genomics ofCetradonia linearis, an endangered lichen narrowly endemic to the southern Appalachians of eastern North America, to test the relative contributions of environmental factors and geographic distance in shaping genetic structure, and to gain insights into the demography and reproductive biology of range restricted fungi. Analysis of genome-wide SNP data indicated strong evidence for both low rates of recombination and for strong isolation by distance, but did not support isolation by environment. Hindcast species distribution models and the spatial distribution of genetic diversity also suggested thatC. linearishad a larger range during the last glacial maximum, especially in the southern portion of its current extent, consistent with previous findings in other southern Appalachian taxa. These results contribute to our understanding of intrinsic and extrinsic factors shaping genetic diversity and biogeographic patterns inC. linearis, and more broadly, in rare and endangered fungi.